diff --git a/.yamlfmt b/.yamlfmt new file mode 100644 index 0000000000..93c7038f90 --- /dev/null +++ b/.yamlfmt @@ -0,0 +1,4 @@ +formatter: + type: basic + include_document_start: true + max_line_length: 0 diff --git a/Makefile b/Makefile index fe8e28f8a9..f4361e0b46 100644 --- a/Makefile +++ b/Makefile @@ -149,6 +149,40 @@ examples/output: src/mixs/schema/mixs.yaml --output-directory $@ \ --schema $< > $@/README.md +.PHONY: standardize-schema + +# |\ + # yamlfmt -in -conf .yamlfmt > + +standardize-schema: + $(RUN) python src/scripts/describe_enums_by_slots_using.py \ + --schema_file src/mixs/schema/mixs.yaml \ + --output_file src/mixs/schema/mixs_with_enum_descriptions.yaml + $(RUN) gen-linkml \ + --format yaml \ + --no-mergeimports \ + --no-materialize-attributes \ + --materialize-patterns src/mixs/schema/mixs_with_enum_descriptions.yaml |\ + yq eval '(.. | select(has("from_schema")) | .from_schema) style="" | del(.. | select(has("from_schema")).from_schema)' |\ + yq eval '.classes[] |= select(has("annotations")).annotations |= map_values(.value)' |\ + yq eval '.prefixes |= map_values(.prefix_reference)' |\ + yq eval '.settings |= map_values(.setting_value)' |\ + yq eval '.slots[] |= select(has("annotations")).annotations |= map_values(.value)' |\ + yq eval 'del(.classes.[].name)' |\ + yq eval 'del(.classes.[].slot_usage.[].name)' |\ + yq eval 'del(.enums.[].name)' |\ + yq eval 'del(.enums.[].permissible_values.[].text)' |\ + yq eval 'del(.slots.[].domain)' |\ + yq eval 'del(.slots.[].name)' |\ + yq eval 'del(.source_file)' |\ + yq eval 'del(.subsets.[].name)' | cat > src/mixs/schema/mixs_standardized.yaml + mv src/mixs/schema/mixs_standardized.yaml src/mixs/schema/mixs.yaml + rm -rf src/mixs/schema/mixs_standardized.yaml src/mixs/schema/mixs_with_enum_descriptions.yaml + +test1: + echo $$PATH + yamlfmt -conf .yamlfmt src/mixs/schema/mixs.yaml > src/mixs/schema/mixs_standardized.yam + # Test documentation locally serve: mkd-serve diff --git a/mixs.yaml b/mixs.yaml new file mode 100644 index 0000000000..0bd121fd05 --- /dev/null +++ b/mixs.yaml @@ -0,0 +1,20305 @@ +--- +name: mixs +description: 'This file contains a YAML-formatted specification of the Minimum Information about any (x) Sequence (MIxS) standard, generated using LinkML (https://linkml.io/linkml/). This file is released by the Genomic Standards Consortium (GSC; https://www.gensc.org/) for use by anyone handling data or information about biological sequences. This file is also used as an authoritative ''source of truth'' to generate downstream GSC artifacts, available here: https://github.com/GenomicsStandardsConsortium/mixs/tree/main/project' +comments: + - 'slot titles that are associated with more than one slot name/SCN: host sex' +source: https://github.com/GenomicsStandardsConsortium/mixs/raw/issue-610-temp-mixs-xlsx-home/mixs/excel/mixs_v6.xlsx +id: https://w3id.org/mixs +version: v6.2.0 +imports: + - linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + MIXS: https://w3id.org/mixs/ + xsd: http://www.w3.org/2001/XMLSchema# + shex: http://www.w3.org/ns/shex# + schema: http://schema.org/ +default_prefix: MIXS +default_range: string +subsets: + combination_classes: {} + sequencing: {} + environment: {} + nucleic acid sequence source: {} + investigation: {} +enums: + BiolStatEnum: + description: Permissible values, used by term biol_stat + permissible_values: + breeder's line: {} + clonal selection: {} + hybrid: {} + inbred line: {} + mutant: {} + natural: {} + semi-natural: {} + wild: {} + AssemblyQualEnum: + description: Permissible values, used by term assembly_qual + permissible_values: + Finished genome: {} + High-quality draft genome: {} + Medium-quality draft genome: {} + Low-quality draft genome: {} + Genome fragment(s): {} + AeroStrucEnum: + description: Permissible values, used by term aero_struc + permissible_values: + glider: {} + plane: {} + AnimalBodyCondEnum: + description: Permissible values, used by term animal_body_cond + permissible_values: + normal: {} + over conditioned: {} + under conditioned: {} + AnimalSexEnum: + description: Permissible values, used by term animal_sex + permissible_values: + castrated female: {} + castrated male: {} + intact female: {} + intact male: {} + ArchStrucEnum: + description: Permissible values, used by term arch_struc + permissible_values: + building: {} + home: {} + shed: {} + BinParamEnum: + description: Permissible values, used by term bin_param + permissible_values: + codon usage: {} + combination: {} + coverage: {} + homology search: {} + kmer: {} + BioticRelationshipEnum: + description: Permissible values, used by term biotic_relationship + permissible_values: + commensalism: {} + free living: {} + mutualism: {} + parasitism: {} + symbiotic: {} + BuildingSettingEnum: + description: Permissible values, used by term building_setting + permissible_values: + exurban: {} + rural: {} + suburban: {} + urban: {} + BuildDocsEnum: + description: Permissible values, used by term build_docs + permissible_values: + building information model: {} + commissioning report: {} + complaint logs: {} + contract administration: {} + cost estimate: {} + janitorial schedules or logs: {} + maintenance plans: {} + schedule: {} + sections: {} + shop drawings: {} + submittals: {} + ventilation system: {} + windows: {} + BuildOccupTypeEnum: + description: Permissible values, used by term build_occup_type + permissible_values: + airport: {} + commercial: {} + health care: {} + high rise: {} + low rise: {} + market: {} + office: {} + residence: {} + residential: {} + restaurant: {} + school: {} + sports complex: {} + wood framed: {} + BuiltStrucSetEnum: + description: Permissible values, used by term built_struc_set + permissible_values: + rural: {} + urban: {} + CeilFinishMatEnum: + description: Permissible values, used by term ceil_finish_mat + permissible_values: + PVC: {} + drywall: {} + fiberglass: {} + metal: {} + mineral fibre: {} + mineral wool/calcium silicate: {} + plasterboard: {} + stucco: {} + tiles: {} + wood: {} + CeilStrucEnum: + description: Permissible values, used by term ceil_struc + permissible_values: + concrete: {} + wood frame: {} + CeilTypeEnum: + description: Permissible values, used by term ceil_type + permissible_values: + barrel-shaped: {} + cathedral: {} + coffered: {} + concave: {} + cove: {} + dropped: {} + stretched: {} + ComplApprEnum: + description: Permissible values, used by term compl_appr + permissible_values: + marker gene: {} + other: {} + reference based: {} + ContamScreenInputEnum: + description: Permissible values, used by term contam_screen_input + permissible_values: + contigs: {} + reads: {} + CultResultEnum: + description: Permissible values, used by term cult_result + permissible_values: + absent: {} + active: {} + inactive: {} + negative: {} + 'no': {} + positive: {} + present: {} + 'yes': {} + DeposEnvEnum: + description: Permissible values, used by term depos_env + permissible_values: + Continental - Aeolian: {} + Continental - Alluvial: {} + Continental - Fluvial: {} + Continental - Lacustrine: {} + Marine - Deep: {} + Marine - Reef: {} + Marine - Shallow: {} + Other - Evaporite: {} + Other - Glacial: {} + Other - Volcanic: {} + Transitional - Beach: {} + Transitional - Deltaic: {} + Transitional - Lagoonal: {} + Transitional - Lake: {} + Transitional - Tidal: {} + other: {} + DominantHandEnum: + description: Permissible values, used by term dominant_hand + permissible_values: + ambidextrous: {} + left: {} + right: {} + DoorCompTypeEnum: + description: Permissible values, used by term door_comp_type + permissible_values: + metal covered: {} + revolving: {} + sliding: {} + telescopic: {} + DoorDirectEnum: + description: Permissible values, used by term door_direct + permissible_values: + inward: {} + outward: {} + sideways: {} + DoorMatEnum: + description: Permissible values, used by term door_mat + permissible_values: + aluminum: {} + cellular PVC: {} + engineered plastic: {} + fiberboard: {} + fiberglass: {} + metal: {} + thermoplastic alloy: {} + vinyl: {} + wood: {} + wood/plastic composite: {} + DoorMoveEnum: + description: Permissible values, used by term door_move + permissible_values: + collapsible: {} + folding: {} + revolving: {} + rolling shutter: {} + sliding: {} + swinging: {} + DoorTypeEnum: + description: Permissible values, used by term door_type + permissible_values: + composite: {} + metal: {} + wooden: {} + DoorTypeMetalEnum: + description: Permissible values, used by term door_type_metal + permissible_values: + collapsible: {} + corrugated steel: {} + hollow: {} + rolling shutters: {} + steel plate: {} + DrainageClassEnum: + description: Permissible values, used by term drainage_class + permissible_values: + excessively drained: {} + moderately well: {} + poorly: {} + somewhat poorly: {} + very poorly: {} + well: {} + DrawingsEnum: + description: Permissible values, used by term drawings + permissible_values: + as built: {} + bid: {} + building navigation map: {} + construction: {} + design: {} + diagram: {} + operation: {} + sketch: {} + ExtrWeatherEventEnum: + description: Permissible values, used by term extr_weather_event + permissible_values: + drought: {} + dust storm: {} + extreme cold: {} + extreme heat: {} + flood: {} + frost: {} + hail: {} + high precipitation: {} + high winds: {} + FacilityTypeEnum: + description: Permissible values, used by term facility_type + permissible_values: + ambient storage: {} + caterer-catering point: {} + distribution: {} + frozen storage: {} + importer-broker: {} + interstate conveyance: {} + labeler-relabeler: {} + manufacturing-processing: {} + packaging: {} + refrigerated storage: {} + storage: {} + FaoClassEnum: + description: Permissible values, used by term fao_class + permissible_values: + Acrisols: {} + Alisols: {} + Andosols: {} + Anthrosols: {} + Arenosols: {} + Calcisols: {} + Cambisols: {} + Chernozems: {} + Cryosols: {} + Durisols: {} + Ferralsols: {} + Fluvisols: {} + Gleysols: {} + Greyzems: + deprecated: true, value no longer recognized by FAO, https://github.com/GenomicsStandardsConsortium/mixs/issues/696 + Gypsisols: {} + Histosols: {} + Kastanozems: {} + Lithosols: + deprecated: true, value no longer recognized by FAO, https://github.com/GenomicsStandardsConsortium/mixs/issues/696 + Leptosols: {} + Lixisols: {} + Luvisols: {} + Nitosols: {} + Phaeozems: {} + Planosols: {} + Plinthosols: {} + Podzols: {} + Podzoluvisols: + deprecated: true, value no longer recognized by FAO, https://github.com/GenomicsStandardsConsortium/mixs/issues/696 + Rankers: + deprecated: true, value no longer recognized by FAO, https://github.com/GenomicsStandardsConsortium/mixs/issues/696 + Regosols: + deprecated: true, value no longer recognized by FAO, https://github.com/GenomicsStandardsConsortium/mixs/issues/696 + Rendzinas: + deprecated: true, value no longer recognized by FAO, https://github.com/GenomicsStandardsConsortium/mixs/issues/696 + Solonchaks: {} + Solonetz: {} + Stagnosols: {} + Technosols: {} + Umbrisols: {} + Vertisols: {} + Yermosols: + deprecated: true, value no longer recognized by FAO, https://github.com/GenomicsStandardsConsortium/mixs/issues/696 + FarmWaterSourceEnum: + description: Permissible values, used by term farm_water_source + permissible_values: + brackish: {} + canal: {} + collected rainwater: {} + ditch: {} + estuary: {} + freshwater: {} + lake: {} + manmade: {} + melt pond: {} + municipal: {} + natural: {} + pond: {} + reservior: {} + river: {} + saline: {} + storage tank: {} + stream: {} + well: {} + FilterTypeEnum: + description: Permissible values, used by term filter_type + permissible_values: + HEPA: {} + chemical air filter: {} + electrostatic: {} + gas-phase or ultraviolet air treatments: {} + low-MERV pleated media: {} + particulate air filter: {} + FireplaceTypeEnum: + description: Permissible values, used by term fireplace_type + permissible_values: + gas burning: {} + wood burning: {} + FloorStrucEnum: + description: Permissible values, used by term floor_struc + permissible_values: + balcony: {} + concrete: {} + floating floor: {} + glass floor: {} + raised floor: {} + sprung floor: {} + wood-framed: {} + FloorWaterMoldEnum: + description: Permissible values, used by term floor_water_mold + permissible_values: + bulging walls: {} + ceiling discoloration: {} + condensation: {} + floor discoloration: {} + mold odor: {} + peeling paint or wallpaper: {} + wall discoloration: {} + water stains: {} + wet floor: {} + FoodCleanProcEnum: + description: Permissible values, used by term food_clean_proc + permissible_values: + drum and drain: {} + manual spinner: {} + rinsed with sanitizer solution: {} + rinsed with water: {} + scrubbed with brush: {} + scrubbed with hand: {} + soaking: {} + FoodTraceListEnum: + description: Permissible values, used by term food_trace_list + permissible_values: + cheeses-other than hard cheeses: {} + crustaceans: {} + cucumbers: {} + finfish-including smoked finfish: {} + fruits and vegetables-fresh cut: {} + herbs-fresh: {} + leafy greens-including fresh cut leafy greens: {} + melons: {} + mollusks-bivalves: {} + nut butter: {} + peppers: {} + ready to eat deli salads: {} + shell eggs: {} + sprouts: {} + tomatoes: {} + tropical tree fruits: {} + FreqCleanEnum: + description: Permissible values, used by term freq_clean + permissible_values: + Annually: {} + Daily: {} + Monthly: {} + Quarterly: {} + Weekly: {} + other: {} + FurnitureEnum: + description: Permissible values, used by term furniture + permissible_values: + cabinet: {} + chair: {} + desks: {} + GenderRestroomEnum: + description: Permissible values, used by term gender_restroom + permissible_values: + all gender: {} + female: {} + gender neutral: {} + male: {} + male and female: {} + unisex: {} + GrowthHabitEnum: + description: Permissible values, used by term growth_habit + permissible_values: + erect: {} + prostrate: {} + semi-erect: {} + spreading: {} + HandidnessEnum: + description: Permissible values, used by term handidness + permissible_values: + ambidexterity: {} + left handedness: {} + mixed-handedness: {} + right handedness: {} + HcrEnum: + description: Permissible values, used by term hcr + permissible_values: + Coalbed: {} + Gas Reservoir: {} + Oil Reservoir: {} + Oil Sand: {} + Shale: {} + Tight Gas Reservoir: {} + Tight Oil Reservoir: {} + other: {} + HcProducedEnum: + description: Permissible values, used by term hc_produced + permissible_values: + Bitumen: {} + Coalbed Methane: {} + Gas: {} + Gas-Condensate: {} + Oil: {} + other: {} + HeatCoolTypeEnum: + description: Permissible values, used by term heat_cool_type + permissible_values: + forced air system: {} + heat pump: {} + radiant system: {} + steam forced heat: {} + wood stove: {} + HeatSysDelivMethEnum: + description: Permissible values, used by term heat_sys_deliv_meth + permissible_values: + conductive: {} + radiant: {} + HostCellularLocEnum: + description: Permissible values, used by term host_cellular_loc + permissible_values: + extracellular: {} + intracellular: {} + not determined: {} + HostDependenceEnum: + description: Permissible values, used by term host_dependence + permissible_values: + facultative: {} + obligate: {} + HostPredApprEnum: + description: Permissible values, used by term host_pred_appr + permissible_values: + CRISPR spacer match: {} + co-occurrence: {} + combination: {} + host sequence similarity: {} + kmer similarity: {} + other: {} + provirus: {} + HostSpecificityEnum: + description: Permissible values, used by term host_specificity + permissible_values: + family-specific: {} + generalist: {} + genus-specific: {} + species-specific: {} + IndoorSpaceEnum: + description: Permissible values, used by term indoor_space + permissible_values: + bathroom: {} + bedroom: {} + elevator: {} + foyer: {} + hallway: {} + kitchen: {} + locker room: {} + office: {} + IndoorSurfEnum: + description: Permissible values, used by term indoor_surf + permissible_values: + cabinet: {} + ceiling: {} + counter top: {} + door: {} + shelving: {} + vent cover: {} + wall: {} + window: {} + LibLayoutEnum: + description: Permissible values, used by term lib_layout + permissible_values: + other: {} + paired: {} + single: {} + vector: {} + LightTypeEnum: + description: Permissible values, used by term light_type + permissible_values: + desk lamp: {} + electric light: {} + fluorescent lights: {} + natural light: {} + none: {} + LithologyEnum: + description: Permissible values, used by term lithology + permissible_values: + Basement: {} + Chalk: {} + Chert: {} + Coal: {} + Conglomerate: {} + Diatomite: {} + Dolomite: {} + Limestone: {} + Sandstone: {} + Shale: {} + Siltstone: {} + Volcanic: {} + other: {} + MagCovSoftwareEnum: + description: Permissible values, used by term mag_cov_software + permissible_values: + bbmap: {} + bowtie: {} + bwa: {} + other: {} + MechStrucEnum: + description: Permissible values, used by term mech_struc + permissible_values: + boat: {} + bus: {} + car: {} + carriage: {} + coach: {} + elevator: {} + escalator: {} + subway: {} + train: {} + ModeTransmissionEnum: + description: Permissible values, used by term mode_transmission + permissible_values: + horizontal:castrator: {} + horizontal:directly transmitted: {} + horizontal:micropredator: {} + horizontal:parasitoid: {} + horizontal:trophically transmitted: {} + horizontal:vector transmitted: {} + vertical: {} + NegContTypeEnum: + description: Permissible values, used by term neg_cont_type + permissible_values: + DNA-free PCR mix: {} + distilled water: {} + empty collection device: {} + empty collection tube: {} + phosphate buffer: {} + sterile swab: {} + sterile syringe: {} + OccupDocumentEnum: + description: Permissible values, used by term occup_document + permissible_values: + automated count: {} + estimate: {} + manual count: {} + videos: {} + OxyStatSampEnum: + description: Permissible values, used by term oxy_stat_samp + permissible_values: + aerobic: {} + anaerobic: {} + other: {} + PlantReprodCropEnum: + description: Permissible values, used by term plant_reprod_crop + permissible_values: + plant cutting: {} + pregerminated seed: {} + ratoon: {} + seed: {} + seedling: {} + whole mature plant: {} + PlantSexEnum: + description: Permissible values, used by term plant_sex + permissible_values: + Androdioecious: {} + Androecious: {} + Androgynomonoecious: {} + Androgynous: {} + Andromonoecious: {} + Bisexual: {} + Dichogamous: {} + Diclinous: {} + Dioecious: {} + Gynodioecious: {} + Gynoecious: {} + Gynomonoecious: {} + Hermaphroditic: {} + Imperfect: {} + Monoclinous: {} + Monoecious: {} + Perfect: {} + Polygamodioecious: {} + Polygamomonoecious: {} + Polygamous: {} + Protandrous: {} + Protogynous: {} + Subandroecious: {} + Subdioecious: {} + Subgynoecious: {} + Synoecious: {} + Trimonoecious: {} + Trioecious: {} + Unisexual: {} + PredGenomeStrucEnum: + description: Permissible values, used by term pred_genome_struc + permissible_values: + non-segmented: {} + segmented: {} + undetermined: {} + ProfilePositionEnum: + description: Permissible values, used by term profile_position + permissible_values: + backslope: {} + footslope: {} + shoulder: {} + summit: {} + toeslope: {} + QuadPosEnum: + description: Permissible values, used by term quad_pos + permissible_values: + East side: {} + North side: {} + South side: {} + West side: {} + RelSampLocEnum: + description: Permissible values, used by term rel_samp_loc + permissible_values: + center of car: {} + edge of car: {} + under a seat: {} + RelToOxygenEnum: + description: Permissible values, used by term rel_to_oxygen + permissible_values: + aerobe: {} + anaerobe: {} + facultative: {} + microaerophilic: {} + microanaerobe: {} + obligate aerobe: {} + obligate anaerobe: {} + RoomCondtEnum: + description: Permissible values, used by term room_condt + permissible_values: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible signs of mold/mildew: {} + visible wear: {} + RoomConnectedEnum: + description: Permissible values, used by term room_connected + permissible_values: + attic: {} + bathroom: {} + closet: {} + conference room: {} + elevator: {} + examining room: {} + hallway: {} + kitchen: {} + mail room: {} + office: {} + stairwell: {} + RoomLocEnum: + description: Permissible values, used by term room_loc + permissible_values: + corner room: {} + exterior wall: {} + interior room: {} + RoomSampPosEnum: + description: Permissible values, used by term room_samp_pos + permissible_values: + center: {} + east corner: {} + north corner: {} + northeast corner: {} + northwest corner: {} + south corner: {} + southeast corner: {} + southwest corner: {} + west corner: {} + RouteTransmissionEnum: + description: Permissible values, used by term route_transmission + permissible_values: + environmental:faecal-oral: {} + transplacental: {} + vector-borne:vector penetration: {} + SampCaptStatusEnum: + description: Permissible values, used by term samp_capt_status + permissible_values: + active surveillance in response to an outbreak: {} + active surveillance not initiated by an outbreak: {} + farm sample: {} + market sample: {} + other: {} + SampCollectPointEnum: + description: Permissible values, used by term samp_collect_point + permissible_values: + drilling rig: {} + other: {} + separator: {} + storage tank: {} + test well: {} + well: {} + wellhead: {} + SampDisStageEnum: + description: Permissible values, used by term samp_dis_stage + permissible_values: + dissemination: {} + growth and reproduction: {} + infection: {} + inoculation: {} + other: {} + penetration: {} + SampLocConditionEnum: + description: Permissible values, used by term samp_loc_condition + permissible_values: + damaged: {} + new: {} + rupture: {} + visible signs of mold-mildew: {} + visible weariness repair: {} + SampSubtypeEnum: + description: Permissible values, used by term samp_subtype + permissible_values: + biofilm: {} + not applicable: {} + oil phase: {} + other: {} + water phase: {} + SampSurfMoistureEnum: + description: Permissible values, used by term samp_surf_moisture + permissible_values: + intermittent moisture: {} + not present: {} + submerged: {} + SampTransportContEnum: + description: Permissible values, used by term samp_transport_cont + permissible_values: + bottle: {} + cooler: {} + glass vial: {} + plastic vial: {} + vendor supplied container: {} + SampWeatherEnum: + description: Permissible values, used by term samp_weather + permissible_values: + clear sky: {} + cloudy: {} + foggy: {} + hail: {} + rain: {} + sleet: {} + snow: {} + sunny: {} + windy: {} + ScLysisApproachEnum: + description: Permissible values, used by term sc_lysis_approach + permissible_values: + chemical: {} + combination: {} + enzymatic: {} + physical: {} + SeasonUseEnum: + description: Permissible values, used by term season_use + permissible_values: + Fall: {} + Spring: {} + Summer: {} + Winter: {} + SedimentTypeEnum: + description: Permissible values, used by term sediment_type + permissible_values: + biogenous: {} + cosmogenous: {} + hydrogenous: {} + lithogenous: {} + SeqQualityCheckEnum: + description: Permissible values, used by term seq_quality_check + permissible_values: + manually edited: {} + none: {} + ShadingDeviceLocEnum: + description: Permissible values, used by term shading_device_loc + permissible_values: + exterior: {} + interior: {} + ShadingDeviceTypeEnum: + description: Permissible values, used by term shading_device_type + permissible_values: + bahama shutters: {} + exterior roll blind: {} + gambrel awning: {} + hood awning: {} + porchroller awning: {} + sarasota shutters: {} + slatted aluminum: {} + solid aluminum awning: {} + sun screen: {} + tree: {} + trellis: {} + venetian awning: {} + CompassDirections8Enum: + description: 'Permissible values, used by 6 terms: door_loc, ext_wall_orient, ext_window_orient, heat_deliv_loc, wall_loc, window_loc' + permissible_values: + east: {} + north: {} + northeast: {} + northwest: {} + south: {} + southeast: {} + southwest: {} + west: {} + MoldVisibilityEnum: + description: 'Permissible values, used by 5 terms: ceil_water_mold, door_water_mold, shad_dev_water_mold, wall_water_mold, window_water_mold' + permissible_values: + no presence of mold visible: {} + presence of mold visible: {} + DamagedRupturedEnum: + description: 'Permissible values, used by 3 terms: door_cond, shading_device_cond, window_cond' + permissible_values: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + DamagedEnum: + description: 'Permissible values, used by 3 terms: ceil_cond, floor_cond, int_wall_cond' + permissible_values: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + CeilingWallTextureEnum: + description: 'Permissible values, used by 2 terms: ceil_texture, wall_texture' + permissible_values: + Santa-Fe texture: {} + crows feet: {} + crows-foot stomp: {} + double skip: {} + hawk and trowel: {} + knockdown: {} + orange peel: {} + popcorn: {} + rosebud stomp: {} + skip trowel: {} + smooth: {} + stomp knockdown: {} + swirl: {} + GeolAgeEnum: + description: 'Permissible values, used by 2 terms: hcr_geol_age, sr_geol_age' + permissible_values: + Archean: {} + Cambrian: {} + Carboniferous: {} + Cenozoic: {} + Cretaceous: {} + Devonian: {} + Jurassic: {} + Mesozoic: {} + Neogene: {} + Ordovician: {} + Paleogene: {} + Paleozoic: {} + Permian: {} + Precambrian: {} + Proterozoic: {} + Silurian: {} + Triassic: {} + other: {} + SoilHorizonEnum: + description: Permissible values, used by term soil_horizon + permissible_values: + A horizon: {} + B horizon: {} + C horizon: {} + E horizon: {} + O horizon: {} + Permafrost: {} + R layer: {} + SoilTextureClassEnum: + description: Permissible values, used by term soil_texture_class + permissible_values: + clay: {} + clay loam: {} + loam: {} + loamy sand: {} + sand: {} + sandy clay: {} + sandy clay loam: {} + sandy loam: {} + silt: {} + silt loam: {} + silty clay: {} + silty clay loam: {} + SortTechEnum: + description: Permissible values, used by term sort_tech + permissible_values: + flow cytometric cell sorting: {} + lazer-tweezing: {} + microfluidics: {} + micromanipulation: {} + optical manipulation: {} + other: {} + SpaceTypStateEnum: + description: Permissible values, used by term space_typ_state + permissible_values: + typically occupied: {} + typically unoccupied: {} + SpecificEnum: + description: Permissible values, used by term specific + permissible_values: + as built: {} + bid: {} + construction: {} + design: {} + operation: {} + photos: {} + SrDepEnvEnum: + description: Permissible values, used by term sr_dep_env + permissible_values: + Fluvioldeltaic: {} + Fluviomarine: {} + Lacustine: {} + Marine: {} + other: {} + SrKerogTypeEnum: + description: Permissible values, used by term sr_kerog_type + permissible_values: + Type I: {} + Type II: {} + Type III: {} + Type IV: {} + other: {} + SrLithologyEnum: + description: Permissible values, used by term sr_lithology + permissible_values: + Biosilicieous: {} + Carbonate: {} + Clastic: {} + Coal: {} + other: {} + SubstructureTypeEnum: + description: Permissible values, used by term substructure_type + permissible_values: + basement: {} + crawlspace: {} + slab on grade: {} + SurfAirContEnum: + description: Permissible values, used by term surf_air_cont + permissible_values: + biocides: {} + biological contaminants: {} + dust: {} + nutrients: {} + organic matter: {} + particulate matter: {} + radon: {} + volatile organic compounds: {} + SurfMaterialEnum: + description: Permissible values, used by term surf_material + permissible_values: + adobe: {} + carpet: {} + cinder blocks: {} + concrete: {} + glass: {} + hay bales: {} + metal: {} + paint: {} + plastic: {} + stainless steel: {} + stone: {} + stucco: {} + tile: {} + vinyl: {} + wood: {} + SymbiontHostRoleEnum: + description: Permissible values, used by term symbiont_host_role + permissible_values: + accidental: {} + dead-end: {} + definitive: {} + intermediate: {} + paratenic: {} + reservoir: {} + single host: {} + SymLifeCycleTypeEnum: + description: Permissible values, used by term sym_life_cycle_type + permissible_values: + complex life cycle: {} + simple life cycle: {} + TaxIdentEnum: + description: Permissible values, used by term tax_ident + permissible_values: + 16S rRNA gene: {} + multi-marker approach: {} + other: {} + TidalStageEnum: + description: Permissible values, used by term tidal_stage + permissible_values: + ebb tide: {} + flood tide: {} + high tide: {} + low tide: {} + TillageEnum: + description: Permissible values, used by term tillage + permissible_values: + chisel: {} + cutting disc: {} + disc plough: {} + drill: {} + mouldboard: {} + ridge till: {} + strip tillage: {} + tined: {} + zonal tillage: {} + TrainLineEnum: + description: Permissible values, used by term train_line + permissible_values: + green: {} + orange: {} + red: {} + TrainStatLocEnum: + description: Permissible values, used by term train_stat_loc + permissible_values: + forest hills: {} + riverside: {} + south station above ground: {} + south station amtrak: {} + south station underground: {} + TrainStopLocEnum: + description: Permissible values, used by term train_stop_loc + permissible_values: + downtown: {} + end: {} + mid: {} + TrophicLevelEnum: + description: Permissible values, used by term trophic_level + permissible_values: + autotroph: {} + carboxydotroph: {} + chemoautolithotroph: {} + chemoautotroph: {} + chemoheterotroph: {} + chemolithoautotroph: {} + chemolithotroph: {} + chemoorganoheterotroph: {} + chemoorganotroph: {} + chemosynthetic: {} + chemotroph: {} + copiotroph: {} + diazotroph: {} + facultative: {} + heterotroph: {} + lithoautotroph: {} + lithoheterotroph: {} + lithotroph: {} + methanotroph: {} + methylotroph: {} + mixotroph: {} + obligate: {} + oligotroph: {} + organoheterotroph: {} + organotroph: {} + photoautotroph: {} + photoheterotroph: {} + photolithoautotroph: {} + photolithotroph: {} + photosynthetic: {} + phototroph: {} + TypeOfSymbiosisEnum: + description: Permissible values, used by term type_of_symbiosis + permissible_values: + commensalistic: {} + mutualistic: {} + parasitic: {} + UrineCollectMethEnum: + description: Permissible values, used by term urine_collect_meth + permissible_values: + catheter: {} + clean catch: {} + UrobiomSexEnum: + description: Permissible values, used by term urobiom_sex + permissible_values: + female: {} + hermaphrodite: {} + male: {} + neuter: {} + VirusEnrichApprEnum: + description: Permissible values, used by term virus_enrich_appr + permissible_values: + CsCl density gradient: {} + DNAse: {} + FeCl Precipitation: {} + PEG Precipitation: {} + RNAse: {} + centrifugation: {} + filtration: {} + none: {} + other: {} + targeted sequence capture: {} + ultracentrifugation: {} + ultrafiltration: {} + WallConstTypeEnum: + description: Permissible values, used by term wall_const_type + permissible_values: + fire resistive: {} + frame construction: {} + joisted masonry: {} + light noncombustible: {} + masonry noncombustible: {} + modified fire resistive: {} + WallFinishMatEnum: + description: Permissible values, used by term wall_finish_mat + permissible_values: + acoustical treatment: {} + gypsum board: {} + gypsum plaster: {} + masonry: {} + metal: {} + plaster: {} + stone facing: {} + terrazzo: {} + tile: {} + veneer plaster: {} + wood: {} + WallSurfTreatmentEnum: + description: Permissible values, used by term wall_surf_treatment + permissible_values: + fabric: {} + no treatment: {} + painted: {} + paneling: {} + stucco: {} + wall paper: {} + WaterFeatTypeEnum: + description: Permissible values, used by term water_feat_type + permissible_values: + fountain: {} + pool: {} + standing feature: {} + stream: {} + waterfall: {} + WeekdayEnum: + description: Permissible values, used by term weekday + permissible_values: + Friday: {} + Monday: {} + Saturday: {} + Sunday: {} + Thursday: {} + Tuesday: {} + Wednesday: {} + WgaAmpApprEnum: + description: Permissible values, used by term wga_amp_appr + permissible_values: + mda based: {} + pcr based: {} + WindowCoverEnum: + description: Permissible values, used by term window_cover + permissible_values: + blinds: {} + curtains: {} + none: {} + WindowHorizPosEnum: + description: Permissible values, used by term window_horiz_pos + permissible_values: + left: {} + middle: {} + right: {} + WindowMatEnum: + description: Permissible values, used by term window_mat + permissible_values: + clad: {} + fiberglass: {} + metal: {} + vinyl: {} + wood: {} + WindowStatusEnum: + description: Permissible values, used by term window_status + permissible_values: + closed: {} + open: {} + WindowTypeEnum: + description: Permissible values, used by term window_type + permissible_values: + fixed window: {} + horizontal sash window: {} + single-hung sash window: {} + WindowVertPosEnum: + description: Permissible values, used by term window_vert_pos + permissible_values: + bottom: {} + high: {} + low: {} + middle: {} + top: {} +slots: + migs_ba_data: + description: Data that comply with checklist MigsBa + title: MigsBa data + slot_uri: MIXS:migs_ba_data + range: MigsBa + multivalued: true + inlined: true + inlined_as_list: true + agriculture_data: + description: Data that comply with Extension Agriculture + title: Agriculture data + slot_uri: MIXS:agriculture_data + range: Agriculture + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_agriculture_data: + description: Data that comply with MigsBa combined with Agriculture + title: MigsBaAgriculture data + slot_uri: MIXS:migs_ba_agriculture_data + range: MigsBaAgriculture + multivalued: true + inlined: true + inlined_as_list: true + air_data: + description: Data that comply with Extension Air + title: Air data + keywords: + - air + slot_uri: MIXS:air_data + range: Air + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_air_data: + description: Data that comply with MigsBa combined with Air + title: MigsBaAir data + slot_uri: MIXS:migs_ba_air_data + range: MigsBaAir + multivalued: true + inlined: true + inlined_as_list: true + built_environment_data: + description: Data that comply with Extension BuiltEnvironment + title: BuiltEnvironment data + slot_uri: MIXS:built_environment_data + range: BuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_built_environment_data: + description: Data that comply with MigsBa combined with BuiltEnvironment + title: MigsBaBuiltEnvironment data + slot_uri: MIXS:migs_ba_built_environment_data + range: MigsBaBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + food_animal_and_animal_feed_data: + description: Data that comply with Extension FoodAnimalAndAnimalFeed + title: FoodAnimalAndAnimalFeed data + slot_uri: MIXS:food_animal_and_animal_feed_data + range: FoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_food_animal_and_animal_feed_data: + description: Data that comply with MigsBa combined with FoodAnimalAndAnimalFeed + title: MigsBaFoodAnimalAndAnimalFeed data + slot_uri: MIXS:migs_ba_food_animal_and_animal_feed_data + range: MigsBaFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + food_farm_environment_data: + description: Data that comply with Extension FoodFarmEnvironment + title: FoodFarmEnvironment data + slot_uri: MIXS:food_farm_environment_data + range: FoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_food_farm_environment_data: + description: Data that comply with MigsBa combined with FoodFarmEnvironment + title: MigsBaFoodFarmEnvironment data + slot_uri: MIXS:migs_ba_food_farm_environment_data + range: MigsBaFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + food_food_production_facility_data: + description: Data that comply with Extension FoodFoodProductionFacility + title: FoodFoodProductionFacility data + slot_uri: MIXS:food_food_production_facility_data + range: FoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_food_food_production_facility_data: + description: Data that comply with MigsBa combined with FoodFoodProductionFacility + title: MigsBaFoodFoodProductionFacility data + slot_uri: MIXS:migs_ba_food_food_production_facility_data + range: MigsBaFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + food_human_foods_data: + description: Data that comply with Extension FoodHumanFoods + title: FoodHumanFoods data + slot_uri: MIXS:food_human_foods_data + range: FoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_food_human_foods_data: + description: Data that comply with MigsBa combined with FoodHumanFoods + title: MigsBaFoodHumanFoods data + slot_uri: MIXS:migs_ba_food_human_foods_data + range: MigsBaFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + host_associated_data: + description: Data that comply with Extension HostAssociated + title: HostAssociated data + slot_uri: MIXS:host_associated_data + range: HostAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_host_associated_data: + description: Data that comply with MigsBa combined with HostAssociated + title: MigsBaHostAssociated data + slot_uri: MIXS:migs_ba_host_associated_data + range: MigsBaHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + human_associated_data: + description: Data that comply with Extension HumanAssociated + title: HumanAssociated data + slot_uri: MIXS:human_associated_data + range: HumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_human_associated_data: + description: Data that comply with MigsBa combined with HumanAssociated + title: MigsBaHumanAssociated data + slot_uri: MIXS:migs_ba_human_associated_data + range: MigsBaHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + human_gut_data: + description: Data that comply with Extension HumanGut + title: HumanGut data + slot_uri: MIXS:human_gut_data + range: HumanGut + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_human_gut_data: + description: Data that comply with MigsBa combined with HumanGut + title: MigsBaHumanGut data + slot_uri: MIXS:migs_ba_human_gut_data + range: MigsBaHumanGut + multivalued: true + inlined: true + inlined_as_list: true + human_oral_data: + description: Data that comply with Extension HumanOral + title: HumanOral data + slot_uri: MIXS:human_oral_data + range: HumanOral + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_human_oral_data: + description: Data that comply with MigsBa combined with HumanOral + title: MigsBaHumanOral data + slot_uri: MIXS:migs_ba_human_oral_data + range: MigsBaHumanOral + multivalued: true + inlined: true + inlined_as_list: true + human_skin_data: + description: Data that comply with Extension HumanSkin + title: HumanSkin data + slot_uri: MIXS:human_skin_data + range: HumanSkin + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_human_skin_data: + description: Data that comply with MigsBa combined with HumanSkin + title: MigsBaHumanSkin data + slot_uri: MIXS:migs_ba_human_skin_data + range: MigsBaHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + human_vaginal_data: + description: Data that comply with Extension HumanVaginal + title: HumanVaginal data + slot_uri: MIXS:human_vaginal_data + range: HumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_human_vaginal_data: + description: Data that comply with MigsBa combined with HumanVaginal + title: MigsBaHumanVaginal data + slot_uri: MIXS:migs_ba_human_vaginal_data + range: MigsBaHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + hydrocarbon_resources_cores_data: + description: Data that comply with Extension HydrocarbonResourcesCores + title: HydrocarbonResourcesCores data + slot_uri: MIXS:hydrocarbon_resources_cores_data + range: HydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_hydrocarbon_resources_cores_data: + description: Data that comply with MigsBa combined with HydrocarbonResourcesCores + title: MigsBaHydrocarbonResourcesCores data + slot_uri: MIXS:migs_ba_hydrocarbon_resources_cores_data + range: MigsBaHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with Extension HydrocarbonResourcesFluidsSwabs + title: HydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:hydrocarbon_resources_fluids_swabs_data + range: HydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with MigsBa combined with HydrocarbonResourcesFluidsSwabs + title: MigsBaHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:migs_ba_hydrocarbon_resources_fluids_swabs_data + range: MigsBaHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + microbial_mat_biofilm_data: + description: Data that comply with Extension MicrobialMatBiofilm + title: MicrobialMatBiofilm data + slot_uri: MIXS:microbial_mat_biofilm_data + range: MicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_microbial_mat_biofilm_data: + description: Data that comply with MigsBa combined with MicrobialMatBiofilm + title: MigsBaMicrobialMatBiofilm data + slot_uri: MIXS:migs_ba_microbial_mat_biofilm_data + range: MigsBaMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with Extension MiscellaneousNaturalOrArtificialEnvironment + title: MiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:miscellaneous_natural_or_artificial_environment_data + range: MiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with MigsBa combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsBaMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:migs_ba_miscellaneous_natural_or_artificial_environment_data + range: MigsBaMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + plant_associated_data: + description: Data that comply with Extension PlantAssociated + title: PlantAssociated data + slot_uri: MIXS:plant_associated_data + range: PlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_plant_associated_data: + description: Data that comply with MigsBa combined with PlantAssociated + title: MigsBaPlantAssociated data + slot_uri: MIXS:migs_ba_plant_associated_data + range: MigsBaPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + sediment_data: + description: Data that comply with Extension Sediment + title: Sediment data + keywords: + - sediment + slot_uri: MIXS:sediment_data + range: Sediment + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_sediment_data: + description: Data that comply with MigsBa combined with Sediment + title: MigsBaSediment data + slot_uri: MIXS:migs_ba_sediment_data + range: MigsBaSediment + multivalued: true + inlined: true + inlined_as_list: true + soil_data: + description: Data that comply with Extension Soil + title: Soil data + keywords: + - soil + slot_uri: MIXS:soil_data + range: Soil + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_soil_data: + description: Data that comply with MigsBa combined with Soil + title: MigsBaSoil data + slot_uri: MIXS:migs_ba_soil_data + range: MigsBaSoil + multivalued: true + inlined: true + inlined_as_list: true + symbiont_associated_data: + description: Data that comply with Extension SymbiontAssociated + title: SymbiontAssociated data + slot_uri: MIXS:symbiont_associated_data + range: SymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_symbiont_associated_data: + description: Data that comply with MigsBa combined with SymbiontAssociated + title: MigsBaSymbiontAssociated data + slot_uri: MIXS:migs_ba_symbiont_associated_data + range: MigsBaSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + wastewater_sludge_data: + description: Data that comply with Extension WastewaterSludge + title: WastewaterSludge data + slot_uri: MIXS:wastewater_sludge_data + range: WastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_wastewater_sludge_data: + description: Data that comply with MigsBa combined with WastewaterSludge + title: MigsBaWastewaterSludge data + slot_uri: MIXS:migs_ba_wastewater_sludge_data + range: MigsBaWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + water_data: + description: Data that comply with Extension Water + title: Water data + keywords: + - water + slot_uri: MIXS:water_data + range: Water + multivalued: true + inlined: true + inlined_as_list: true + migs_ba_water_data: + description: Data that comply with MigsBa combined with Water + title: MigsBaWater data + slot_uri: MIXS:migs_ba_water_data + range: MigsBaWater + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_data: + description: Data that comply with checklist MigsEu + title: MigsEu data + slot_uri: MIXS:migs_eu_data + range: MigsEu + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_agriculture_data: + description: Data that comply with MigsEu combined with Agriculture + title: MigsEuAgriculture data + slot_uri: MIXS:migs_eu_agriculture_data + range: MigsEuAgriculture + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_air_data: + description: Data that comply with MigsEu combined with Air + title: MigsEuAir data + slot_uri: MIXS:migs_eu_air_data + range: MigsEuAir + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_built_environment_data: + description: Data that comply with MigsEu combined with BuiltEnvironment + title: MigsEuBuiltEnvironment data + slot_uri: MIXS:migs_eu_built_environment_data + range: MigsEuBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_food_animal_and_animal_feed_data: + description: Data that comply with MigsEu combined with FoodAnimalAndAnimalFeed + title: MigsEuFoodAnimalAndAnimalFeed data + slot_uri: MIXS:migs_eu_food_animal_and_animal_feed_data + range: MigsEuFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_food_farm_environment_data: + description: Data that comply with MigsEu combined with FoodFarmEnvironment + title: MigsEuFoodFarmEnvironment data + slot_uri: MIXS:migs_eu_food_farm_environment_data + range: MigsEuFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_food_food_production_facility_data: + description: Data that comply with MigsEu combined with FoodFoodProductionFacility + title: MigsEuFoodFoodProductionFacility data + slot_uri: MIXS:migs_eu_food_food_production_facility_data + range: MigsEuFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_food_human_foods_data: + description: Data that comply with MigsEu combined with FoodHumanFoods + title: MigsEuFoodHumanFoods data + slot_uri: MIXS:migs_eu_food_human_foods_data + range: MigsEuFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_host_associated_data: + description: Data that comply with MigsEu combined with HostAssociated + title: MigsEuHostAssociated data + slot_uri: MIXS:migs_eu_host_associated_data + range: MigsEuHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_human_associated_data: + description: Data that comply with MigsEu combined with HumanAssociated + title: MigsEuHumanAssociated data + slot_uri: MIXS:migs_eu_human_associated_data + range: MigsEuHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_human_gut_data: + description: Data that comply with MigsEu combined with HumanGut + title: MigsEuHumanGut data + slot_uri: MIXS:migs_eu_human_gut_data + range: MigsEuHumanGut + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_human_oral_data: + description: Data that comply with MigsEu combined with HumanOral + title: MigsEuHumanOral data + slot_uri: MIXS:migs_eu_human_oral_data + range: MigsEuHumanOral + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_human_skin_data: + description: Data that comply with MigsEu combined with HumanSkin + title: MigsEuHumanSkin data + slot_uri: MIXS:migs_eu_human_skin_data + range: MigsEuHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_human_vaginal_data: + description: Data that comply with MigsEu combined with HumanVaginal + title: MigsEuHumanVaginal data + slot_uri: MIXS:migs_eu_human_vaginal_data + range: MigsEuHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_hydrocarbon_resources_cores_data: + description: Data that comply with MigsEu combined with HydrocarbonResourcesCores + title: MigsEuHydrocarbonResourcesCores data + slot_uri: MIXS:migs_eu_hydrocarbon_resources_cores_data + range: MigsEuHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with MigsEu combined with HydrocarbonResourcesFluidsSwabs + title: MigsEuHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:migs_eu_hydrocarbon_resources_fluids_swabs_data + range: MigsEuHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_microbial_mat_biofilm_data: + description: Data that comply with MigsEu combined with MicrobialMatBiofilm + title: MigsEuMicrobialMatBiofilm data + slot_uri: MIXS:migs_eu_microbial_mat_biofilm_data + range: MigsEuMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with MigsEu combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsEuMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:migs_eu_miscellaneous_natural_or_artificial_environment_data + range: MigsEuMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_plant_associated_data: + description: Data that comply with MigsEu combined with PlantAssociated + title: MigsEuPlantAssociated data + slot_uri: MIXS:migs_eu_plant_associated_data + range: MigsEuPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_sediment_data: + description: Data that comply with MigsEu combined with Sediment + title: MigsEuSediment data + slot_uri: MIXS:migs_eu_sediment_data + range: MigsEuSediment + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_soil_data: + description: Data that comply with MigsEu combined with Soil + title: MigsEuSoil data + slot_uri: MIXS:migs_eu_soil_data + range: MigsEuSoil + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_symbiont_associated_data: + description: Data that comply with MigsEu combined with SymbiontAssociated + title: MigsEuSymbiontAssociated data + slot_uri: MIXS:migs_eu_symbiont_associated_data + range: MigsEuSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_wastewater_sludge_data: + description: Data that comply with MigsEu combined with WastewaterSludge + title: MigsEuWastewaterSludge data + slot_uri: MIXS:migs_eu_wastewater_sludge_data + range: MigsEuWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + migs_eu_water_data: + description: Data that comply with MigsEu combined with Water + title: MigsEuWater data + slot_uri: MIXS:migs_eu_water_data + range: MigsEuWater + multivalued: true + inlined: true + inlined_as_list: true + migs_org_data: + description: Data that comply with checklist MigsOrg + title: MigsOrg data + slot_uri: MIXS:migs_org_data + range: MigsOrg + multivalued: true + inlined: true + inlined_as_list: true + migs_org_agriculture_data: + description: Data that comply with MigsOrg combined with Agriculture + title: MigsOrgAgriculture data + slot_uri: MIXS:migs_org_agriculture_data + range: MigsOrgAgriculture + multivalued: true + inlined: true + inlined_as_list: true + migs_org_air_data: + description: Data that comply with MigsOrg combined with Air + title: MigsOrgAir data + slot_uri: MIXS:migs_org_air_data + range: MigsOrgAir + multivalued: true + inlined: true + inlined_as_list: true + migs_org_built_environment_data: + description: Data that comply with MigsOrg combined with BuiltEnvironment + title: MigsOrgBuiltEnvironment data + slot_uri: MIXS:migs_org_built_environment_data + range: MigsOrgBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_org_food_animal_and_animal_feed_data: + description: Data that comply with MigsOrg combined with FoodAnimalAndAnimalFeed + title: MigsOrgFoodAnimalAndAnimalFeed data + slot_uri: MIXS:migs_org_food_animal_and_animal_feed_data + range: MigsOrgFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + migs_org_food_farm_environment_data: + description: Data that comply with MigsOrg combined with FoodFarmEnvironment + title: MigsOrgFoodFarmEnvironment data + slot_uri: MIXS:migs_org_food_farm_environment_data + range: MigsOrgFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_org_food_food_production_facility_data: + description: Data that comply with MigsOrg combined with FoodFoodProductionFacility + title: MigsOrgFoodFoodProductionFacility data + slot_uri: MIXS:migs_org_food_food_production_facility_data + range: MigsOrgFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + migs_org_food_human_foods_data: + description: Data that comply with MigsOrg combined with FoodHumanFoods + title: MigsOrgFoodHumanFoods data + slot_uri: MIXS:migs_org_food_human_foods_data + range: MigsOrgFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + migs_org_host_associated_data: + description: Data that comply with MigsOrg combined with HostAssociated + title: MigsOrgHostAssociated data + slot_uri: MIXS:migs_org_host_associated_data + range: MigsOrgHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_org_human_associated_data: + description: Data that comply with MigsOrg combined with HumanAssociated + title: MigsOrgHumanAssociated data + slot_uri: MIXS:migs_org_human_associated_data + range: MigsOrgHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_org_human_gut_data: + description: Data that comply with MigsOrg combined with HumanGut + title: MigsOrgHumanGut data + slot_uri: MIXS:migs_org_human_gut_data + range: MigsOrgHumanGut + multivalued: true + inlined: true + inlined_as_list: true + migs_org_human_oral_data: + description: Data that comply with MigsOrg combined with HumanOral + title: MigsOrgHumanOral data + slot_uri: MIXS:migs_org_human_oral_data + range: MigsOrgHumanOral + multivalued: true + inlined: true + inlined_as_list: true + migs_org_human_skin_data: + description: Data that comply with MigsOrg combined with HumanSkin + title: MigsOrgHumanSkin data + slot_uri: MIXS:migs_org_human_skin_data + range: MigsOrgHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + migs_org_human_vaginal_data: + description: Data that comply with MigsOrg combined with HumanVaginal + title: MigsOrgHumanVaginal data + slot_uri: MIXS:migs_org_human_vaginal_data + range: MigsOrgHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + migs_org_hydrocarbon_resources_cores_data: + description: Data that comply with MigsOrg combined with HydrocarbonResourcesCores + title: MigsOrgHydrocarbonResourcesCores data + slot_uri: MIXS:migs_org_hydrocarbon_resources_cores_data + range: MigsOrgHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + migs_org_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with MigsOrg combined with HydrocarbonResourcesFluidsSwabs + title: MigsOrgHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:migs_org_hydrocarbon_resources_fluids_swabs_data + range: MigsOrgHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + migs_org_microbial_mat_biofilm_data: + description: Data that comply with MigsOrg combined with MicrobialMatBiofilm + title: MigsOrgMicrobialMatBiofilm data + slot_uri: MIXS:migs_org_microbial_mat_biofilm_data + range: MigsOrgMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + migs_org_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with MigsOrg combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsOrgMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:migs_org_miscellaneous_natural_or_artificial_environment_data + range: MigsOrgMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_org_plant_associated_data: + description: Data that comply with MigsOrg combined with PlantAssociated + title: MigsOrgPlantAssociated data + slot_uri: MIXS:migs_org_plant_associated_data + range: MigsOrgPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_org_sediment_data: + description: Data that comply with MigsOrg combined with Sediment + title: MigsOrgSediment data + slot_uri: MIXS:migs_org_sediment_data + range: MigsOrgSediment + multivalued: true + inlined: true + inlined_as_list: true + migs_org_soil_data: + description: Data that comply with MigsOrg combined with Soil + title: MigsOrgSoil data + slot_uri: MIXS:migs_org_soil_data + range: MigsOrgSoil + multivalued: true + inlined: true + inlined_as_list: true + migs_org_symbiont_associated_data: + description: Data that comply with MigsOrg combined with SymbiontAssociated + title: MigsOrgSymbiontAssociated data + slot_uri: MIXS:migs_org_symbiont_associated_data + range: MigsOrgSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_org_wastewater_sludge_data: + description: Data that comply with MigsOrg combined with WastewaterSludge + title: MigsOrgWastewaterSludge data + slot_uri: MIXS:migs_org_wastewater_sludge_data + range: MigsOrgWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + migs_org_water_data: + description: Data that comply with MigsOrg combined with Water + title: MigsOrgWater data + slot_uri: MIXS:migs_org_water_data + range: MigsOrgWater + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_data: + description: Data that comply with checklist MigsPl + title: MigsPl data + slot_uri: MIXS:migs_pl_data + range: MigsPl + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_agriculture_data: + description: Data that comply with MigsPl combined with Agriculture + title: MigsPlAgriculture data + slot_uri: MIXS:migs_pl_agriculture_data + range: MigsPlAgriculture + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_air_data: + description: Data that comply with MigsPl combined with Air + title: MigsPlAir data + slot_uri: MIXS:migs_pl_air_data + range: MigsPlAir + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_built_environment_data: + description: Data that comply with MigsPl combined with BuiltEnvironment + title: MigsPlBuiltEnvironment data + slot_uri: MIXS:migs_pl_built_environment_data + range: MigsPlBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_food_animal_and_animal_feed_data: + description: Data that comply with MigsPl combined with FoodAnimalAndAnimalFeed + title: MigsPlFoodAnimalAndAnimalFeed data + slot_uri: MIXS:migs_pl_food_animal_and_animal_feed_data + range: MigsPlFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_food_farm_environment_data: + description: Data that comply with MigsPl combined with FoodFarmEnvironment + title: MigsPlFoodFarmEnvironment data + slot_uri: MIXS:migs_pl_food_farm_environment_data + range: MigsPlFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_food_food_production_facility_data: + description: Data that comply with MigsPl combined with FoodFoodProductionFacility + title: MigsPlFoodFoodProductionFacility data + slot_uri: MIXS:migs_pl_food_food_production_facility_data + range: MigsPlFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_food_human_foods_data: + description: Data that comply with MigsPl combined with FoodHumanFoods + title: MigsPlFoodHumanFoods data + slot_uri: MIXS:migs_pl_food_human_foods_data + range: MigsPlFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_host_associated_data: + description: Data that comply with MigsPl combined with HostAssociated + title: MigsPlHostAssociated data + slot_uri: MIXS:migs_pl_host_associated_data + range: MigsPlHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_human_associated_data: + description: Data that comply with MigsPl combined with HumanAssociated + title: MigsPlHumanAssociated data + slot_uri: MIXS:migs_pl_human_associated_data + range: MigsPlHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_human_gut_data: + description: Data that comply with MigsPl combined with HumanGut + title: MigsPlHumanGut data + slot_uri: MIXS:migs_pl_human_gut_data + range: MigsPlHumanGut + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_human_oral_data: + description: Data that comply with MigsPl combined with HumanOral + title: MigsPlHumanOral data + slot_uri: MIXS:migs_pl_human_oral_data + range: MigsPlHumanOral + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_human_skin_data: + description: Data that comply with MigsPl combined with HumanSkin + title: MigsPlHumanSkin data + slot_uri: MIXS:migs_pl_human_skin_data + range: MigsPlHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_human_vaginal_data: + description: Data that comply with MigsPl combined with HumanVaginal + title: MigsPlHumanVaginal data + slot_uri: MIXS:migs_pl_human_vaginal_data + range: MigsPlHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_hydrocarbon_resources_cores_data: + description: Data that comply with MigsPl combined with HydrocarbonResourcesCores + title: MigsPlHydrocarbonResourcesCores data + slot_uri: MIXS:migs_pl_hydrocarbon_resources_cores_data + range: MigsPlHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with MigsPl combined with HydrocarbonResourcesFluidsSwabs + title: MigsPlHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:migs_pl_hydrocarbon_resources_fluids_swabs_data + range: MigsPlHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_microbial_mat_biofilm_data: + description: Data that comply with MigsPl combined with MicrobialMatBiofilm + title: MigsPlMicrobialMatBiofilm data + slot_uri: MIXS:migs_pl_microbial_mat_biofilm_data + range: MigsPlMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with MigsPl combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsPlMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:migs_pl_miscellaneous_natural_or_artificial_environment_data + range: MigsPlMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_plant_associated_data: + description: Data that comply with MigsPl combined with PlantAssociated + title: MigsPlPlantAssociated data + slot_uri: MIXS:migs_pl_plant_associated_data + range: MigsPlPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_sediment_data: + description: Data that comply with MigsPl combined with Sediment + title: MigsPlSediment data + slot_uri: MIXS:migs_pl_sediment_data + range: MigsPlSediment + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_soil_data: + description: Data that comply with MigsPl combined with Soil + title: MigsPlSoil data + slot_uri: MIXS:migs_pl_soil_data + range: MigsPlSoil + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_symbiont_associated_data: + description: Data that comply with MigsPl combined with SymbiontAssociated + title: MigsPlSymbiontAssociated data + slot_uri: MIXS:migs_pl_symbiont_associated_data + range: MigsPlSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_wastewater_sludge_data: + description: Data that comply with MigsPl combined with WastewaterSludge + title: MigsPlWastewaterSludge data + slot_uri: MIXS:migs_pl_wastewater_sludge_data + range: MigsPlWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + migs_pl_water_data: + description: Data that comply with MigsPl combined with Water + title: MigsPlWater data + slot_uri: MIXS:migs_pl_water_data + range: MigsPlWater + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_data: + description: Data that comply with checklist MigsVi + title: MigsVi data + slot_uri: MIXS:migs_vi_data + range: MigsVi + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_agriculture_data: + description: Data that comply with MigsVi combined with Agriculture + title: MigsViAgriculture data + slot_uri: MIXS:migs_vi_agriculture_data + range: MigsViAgriculture + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_air_data: + description: Data that comply with MigsVi combined with Air + title: MigsViAir data + slot_uri: MIXS:migs_vi_air_data + range: MigsViAir + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_built_environment_data: + description: Data that comply with MigsVi combined with BuiltEnvironment + title: MigsViBuiltEnvironment data + slot_uri: MIXS:migs_vi_built_environment_data + range: MigsViBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_food_animal_and_animal_feed_data: + description: Data that comply with MigsVi combined with FoodAnimalAndAnimalFeed + title: MigsViFoodAnimalAndAnimalFeed data + slot_uri: MIXS:migs_vi_food_animal_and_animal_feed_data + range: MigsViFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_food_farm_environment_data: + description: Data that comply with MigsVi combined with FoodFarmEnvironment + title: MigsViFoodFarmEnvironment data + slot_uri: MIXS:migs_vi_food_farm_environment_data + range: MigsViFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_food_food_production_facility_data: + description: Data that comply with MigsVi combined with FoodFoodProductionFacility + title: MigsViFoodFoodProductionFacility data + slot_uri: MIXS:migs_vi_food_food_production_facility_data + range: MigsViFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_food_human_foods_data: + description: Data that comply with MigsVi combined with FoodHumanFoods + title: MigsViFoodHumanFoods data + slot_uri: MIXS:migs_vi_food_human_foods_data + range: MigsViFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_host_associated_data: + description: Data that comply with MigsVi combined with HostAssociated + title: MigsViHostAssociated data + slot_uri: MIXS:migs_vi_host_associated_data + range: MigsViHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_human_associated_data: + description: Data that comply with MigsVi combined with HumanAssociated + title: MigsViHumanAssociated data + slot_uri: MIXS:migs_vi_human_associated_data + range: MigsViHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_human_gut_data: + description: Data that comply with MigsVi combined with HumanGut + title: MigsViHumanGut data + slot_uri: MIXS:migs_vi_human_gut_data + range: MigsViHumanGut + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_human_oral_data: + description: Data that comply with MigsVi combined with HumanOral + title: MigsViHumanOral data + slot_uri: MIXS:migs_vi_human_oral_data + range: MigsViHumanOral + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_human_skin_data: + description: Data that comply with MigsVi combined with HumanSkin + title: MigsViHumanSkin data + slot_uri: MIXS:migs_vi_human_skin_data + range: MigsViHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_human_vaginal_data: + description: Data that comply with MigsVi combined with HumanVaginal + title: MigsViHumanVaginal data + slot_uri: MIXS:migs_vi_human_vaginal_data + range: MigsViHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_hydrocarbon_resources_cores_data: + description: Data that comply with MigsVi combined with HydrocarbonResourcesCores + title: MigsViHydrocarbonResourcesCores data + slot_uri: MIXS:migs_vi_hydrocarbon_resources_cores_data + range: MigsViHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with MigsVi combined with HydrocarbonResourcesFluidsSwabs + title: MigsViHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:migs_vi_hydrocarbon_resources_fluids_swabs_data + range: MigsViHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_microbial_mat_biofilm_data: + description: Data that comply with MigsVi combined with MicrobialMatBiofilm + title: MigsViMicrobialMatBiofilm data + slot_uri: MIXS:migs_vi_microbial_mat_biofilm_data + range: MigsViMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with MigsVi combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsViMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:migs_vi_miscellaneous_natural_or_artificial_environment_data + range: MigsViMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_plant_associated_data: + description: Data that comply with MigsVi combined with PlantAssociated + title: MigsViPlantAssociated data + slot_uri: MIXS:migs_vi_plant_associated_data + range: MigsViPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_sediment_data: + description: Data that comply with MigsVi combined with Sediment + title: MigsViSediment data + slot_uri: MIXS:migs_vi_sediment_data + range: MigsViSediment + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_soil_data: + description: Data that comply with MigsVi combined with Soil + title: MigsViSoil data + slot_uri: MIXS:migs_vi_soil_data + range: MigsViSoil + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_symbiont_associated_data: + description: Data that comply with MigsVi combined with SymbiontAssociated + title: MigsViSymbiontAssociated data + slot_uri: MIXS:migs_vi_symbiont_associated_data + range: MigsViSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_wastewater_sludge_data: + description: Data that comply with MigsVi combined with WastewaterSludge + title: MigsViWastewaterSludge data + slot_uri: MIXS:migs_vi_wastewater_sludge_data + range: MigsViWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + migs_vi_water_data: + description: Data that comply with MigsVi combined with Water + title: MigsViWater data + slot_uri: MIXS:migs_vi_water_data + range: MigsViWater + multivalued: true + inlined: true + inlined_as_list: true + mimag_data: + description: Data that comply with checklist Mimag + title: Mimag data + slot_uri: MIXS:mimag_data + range: Mimag + multivalued: true + inlined: true + inlined_as_list: true + mimag_agriculture_data: + description: Data that comply with Mimag combined with Agriculture + title: MimagAgriculture data + slot_uri: MIXS:mimag_agriculture_data + range: MimagAgriculture + multivalued: true + inlined: true + inlined_as_list: true + mimag_air_data: + description: Data that comply with Mimag combined with Air + title: MimagAir data + slot_uri: MIXS:mimag_air_data + range: MimagAir + multivalued: true + inlined: true + inlined_as_list: true + mimag_built_environment_data: + description: Data that comply with Mimag combined with BuiltEnvironment + title: MimagBuiltEnvironment data + slot_uri: MIXS:mimag_built_environment_data + range: MimagBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimag_food_animal_and_animal_feed_data: + description: Data that comply with Mimag combined with FoodAnimalAndAnimalFeed + title: MimagFoodAnimalAndAnimalFeed data + slot_uri: MIXS:mimag_food_animal_and_animal_feed_data + range: MimagFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + mimag_food_farm_environment_data: + description: Data that comply with Mimag combined with FoodFarmEnvironment + title: MimagFoodFarmEnvironment data + slot_uri: MIXS:mimag_food_farm_environment_data + range: MimagFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimag_food_food_production_facility_data: + description: Data that comply with Mimag combined with FoodFoodProductionFacility + title: MimagFoodFoodProductionFacility data + slot_uri: MIXS:mimag_food_food_production_facility_data + range: MimagFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + mimag_food_human_foods_data: + description: Data that comply with Mimag combined with FoodHumanFoods + title: MimagFoodHumanFoods data + slot_uri: MIXS:mimag_food_human_foods_data + range: MimagFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + mimag_host_associated_data: + description: Data that comply with Mimag combined with HostAssociated + title: MimagHostAssociated data + slot_uri: MIXS:mimag_host_associated_data + range: MimagHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimag_human_associated_data: + description: Data that comply with Mimag combined with HumanAssociated + title: MimagHumanAssociated data + slot_uri: MIXS:mimag_human_associated_data + range: MimagHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimag_human_gut_data: + description: Data that comply with Mimag combined with HumanGut + title: MimagHumanGut data + slot_uri: MIXS:mimag_human_gut_data + range: MimagHumanGut + multivalued: true + inlined: true + inlined_as_list: true + mimag_human_oral_data: + description: Data that comply with Mimag combined with HumanOral + title: MimagHumanOral data + slot_uri: MIXS:mimag_human_oral_data + range: MimagHumanOral + multivalued: true + inlined: true + inlined_as_list: true + mimag_human_skin_data: + description: Data that comply with Mimag combined with HumanSkin + title: MimagHumanSkin data + slot_uri: MIXS:mimag_human_skin_data + range: MimagHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + mimag_human_vaginal_data: + description: Data that comply with Mimag combined with HumanVaginal + title: MimagHumanVaginal data + slot_uri: MIXS:mimag_human_vaginal_data + range: MimagHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + mimag_hydrocarbon_resources_cores_data: + description: Data that comply with Mimag combined with HydrocarbonResourcesCores + title: MimagHydrocarbonResourcesCores data + slot_uri: MIXS:mimag_hydrocarbon_resources_cores_data + range: MimagHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + mimag_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with Mimag combined with HydrocarbonResourcesFluidsSwabs + title: MimagHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:mimag_hydrocarbon_resources_fluids_swabs_data + range: MimagHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + mimag_microbial_mat_biofilm_data: + description: Data that comply with Mimag combined with MicrobialMatBiofilm + title: MimagMicrobialMatBiofilm data + slot_uri: MIXS:mimag_microbial_mat_biofilm_data + range: MimagMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + mimag_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with Mimag combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimagMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:mimag_miscellaneous_natural_or_artificial_environment_data + range: MimagMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimag_plant_associated_data: + description: Data that comply with Mimag combined with PlantAssociated + title: MimagPlantAssociated data + slot_uri: MIXS:mimag_plant_associated_data + range: MimagPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimag_sediment_data: + description: Data that comply with Mimag combined with Sediment + title: MimagSediment data + slot_uri: MIXS:mimag_sediment_data + range: MimagSediment + multivalued: true + inlined: true + inlined_as_list: true + mimag_soil_data: + description: Data that comply with Mimag combined with Soil + title: MimagSoil data + slot_uri: MIXS:mimag_soil_data + range: MimagSoil + multivalued: true + inlined: true + inlined_as_list: true + mimag_symbiont_associated_data: + description: Data that comply with Mimag combined with SymbiontAssociated + title: MimagSymbiontAssociated data + slot_uri: MIXS:mimag_symbiont_associated_data + range: MimagSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimag_wastewater_sludge_data: + description: Data that comply with Mimag combined with WastewaterSludge + title: MimagWastewaterSludge data + slot_uri: MIXS:mimag_wastewater_sludge_data + range: MimagWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + mimag_water_data: + description: Data that comply with Mimag combined with Water + title: MimagWater data + slot_uri: MIXS:mimag_water_data + range: MimagWater + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_data: + description: Data that comply with checklist MimarksC + title: MimarksC data + slot_uri: MIXS:mimarks_c_data + range: MimarksC + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_agriculture_data: + description: Data that comply with MimarksC combined with Agriculture + title: MimarksCAgriculture data + slot_uri: MIXS:mimarks_c_agriculture_data + range: MimarksCAgriculture + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_air_data: + description: Data that comply with MimarksC combined with Air + title: MimarksCAir data + slot_uri: MIXS:mimarks_c_air_data + range: MimarksCAir + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_built_environment_data: + description: Data that comply with MimarksC combined with BuiltEnvironment + title: MimarksCBuiltEnvironment data + slot_uri: MIXS:mimarks_c_built_environment_data + range: MimarksCBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_food_animal_and_animal_feed_data: + description: Data that comply with MimarksC combined with FoodAnimalAndAnimalFeed + title: MimarksCFoodAnimalAndAnimalFeed data + slot_uri: MIXS:mimarks_c_food_animal_and_animal_feed_data + range: MimarksCFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_food_farm_environment_data: + description: Data that comply with MimarksC combined with FoodFarmEnvironment + title: MimarksCFoodFarmEnvironment data + slot_uri: MIXS:mimarks_c_food_farm_environment_data + range: MimarksCFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_food_food_production_facility_data: + description: Data that comply with MimarksC combined with FoodFoodProductionFacility + title: MimarksCFoodFoodProductionFacility data + slot_uri: MIXS:mimarks_c_food_food_production_facility_data + range: MimarksCFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_food_human_foods_data: + description: Data that comply with MimarksC combined with FoodHumanFoods + title: MimarksCFoodHumanFoods data + slot_uri: MIXS:mimarks_c_food_human_foods_data + range: MimarksCFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_host_associated_data: + description: Data that comply with MimarksC combined with HostAssociated + title: MimarksCHostAssociated data + slot_uri: MIXS:mimarks_c_host_associated_data + range: MimarksCHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_human_associated_data: + description: Data that comply with MimarksC combined with HumanAssociated + title: MimarksCHumanAssociated data + slot_uri: MIXS:mimarks_c_human_associated_data + range: MimarksCHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_human_gut_data: + description: Data that comply with MimarksC combined with HumanGut + title: MimarksCHumanGut data + slot_uri: MIXS:mimarks_c_human_gut_data + range: MimarksCHumanGut + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_human_oral_data: + description: Data that comply with MimarksC combined with HumanOral + title: MimarksCHumanOral data + slot_uri: MIXS:mimarks_c_human_oral_data + range: MimarksCHumanOral + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_human_skin_data: + description: Data that comply with MimarksC combined with HumanSkin + title: MimarksCHumanSkin data + slot_uri: MIXS:mimarks_c_human_skin_data + range: MimarksCHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_human_vaginal_data: + description: Data that comply with MimarksC combined with HumanVaginal + title: MimarksCHumanVaginal data + slot_uri: MIXS:mimarks_c_human_vaginal_data + range: MimarksCHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_hydrocarbon_resources_cores_data: + description: Data that comply with MimarksC combined with HydrocarbonResourcesCores + title: MimarksCHydrocarbonResourcesCores data + slot_uri: MIXS:mimarks_c_hydrocarbon_resources_cores_data + range: MimarksCHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with MimarksC combined with HydrocarbonResourcesFluidsSwabs + title: MimarksCHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:mimarks_c_hydrocarbon_resources_fluids_swabs_data + range: MimarksCHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_microbial_mat_biofilm_data: + description: Data that comply with MimarksC combined with MicrobialMatBiofilm + title: MimarksCMicrobialMatBiofilm data + slot_uri: MIXS:mimarks_c_microbial_mat_biofilm_data + range: MimarksCMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with MimarksC combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimarksCMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:mimarks_c_miscellaneous_natural_or_artificial_environment_data + range: MimarksCMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_plant_associated_data: + description: Data that comply with MimarksC combined with PlantAssociated + title: MimarksCPlantAssociated data + slot_uri: MIXS:mimarks_c_plant_associated_data + range: MimarksCPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_sediment_data: + description: Data that comply with MimarksC combined with Sediment + title: MimarksCSediment data + slot_uri: MIXS:mimarks_c_sediment_data + range: MimarksCSediment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_soil_data: + description: Data that comply with MimarksC combined with Soil + title: MimarksCSoil data + slot_uri: MIXS:mimarks_c_soil_data + range: MimarksCSoil + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_symbiont_associated_data: + description: Data that comply with MimarksC combined with SymbiontAssociated + title: MimarksCSymbiontAssociated data + slot_uri: MIXS:mimarks_c_symbiont_associated_data + range: MimarksCSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_wastewater_sludge_data: + description: Data that comply with MimarksC combined with WastewaterSludge + title: MimarksCWastewaterSludge data + slot_uri: MIXS:mimarks_c_wastewater_sludge_data + range: MimarksCWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + mimarks_c_water_data: + description: Data that comply with MimarksC combined with Water + title: MimarksCWater data + slot_uri: MIXS:mimarks_c_water_data + range: MimarksCWater + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_data: + description: Data that comply with checklist MimarksS + title: MimarksS data + slot_uri: MIXS:mimarks_s_data + range: MimarksS + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_agriculture_data: + description: Data that comply with MimarksS combined with Agriculture + title: MimarksSAgriculture data + slot_uri: MIXS:mimarks_s_agriculture_data + range: MimarksSAgriculture + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_air_data: + description: Data that comply with MimarksS combined with Air + title: MimarksSAir data + slot_uri: MIXS:mimarks_s_air_data + range: MimarksSAir + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_built_environment_data: + description: Data that comply with MimarksS combined with BuiltEnvironment + title: MimarksSBuiltEnvironment data + slot_uri: MIXS:mimarks_s_built_environment_data + range: MimarksSBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_food_animal_and_animal_feed_data: + description: Data that comply with MimarksS combined with FoodAnimalAndAnimalFeed + title: MimarksSFoodAnimalAndAnimalFeed data + slot_uri: MIXS:mimarks_s_food_animal_and_animal_feed_data + range: MimarksSFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_food_farm_environment_data: + description: Data that comply with MimarksS combined with FoodFarmEnvironment + title: MimarksSFoodFarmEnvironment data + slot_uri: MIXS:mimarks_s_food_farm_environment_data + range: MimarksSFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_food_food_production_facility_data: + description: Data that comply with MimarksS combined with FoodFoodProductionFacility + title: MimarksSFoodFoodProductionFacility data + slot_uri: MIXS:mimarks_s_food_food_production_facility_data + range: MimarksSFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_food_human_foods_data: + description: Data that comply with MimarksS combined with FoodHumanFoods + title: MimarksSFoodHumanFoods data + slot_uri: MIXS:mimarks_s_food_human_foods_data + range: MimarksSFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_host_associated_data: + description: Data that comply with MimarksS combined with HostAssociated + title: MimarksSHostAssociated data + slot_uri: MIXS:mimarks_s_host_associated_data + range: MimarksSHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_human_associated_data: + description: Data that comply with MimarksS combined with HumanAssociated + title: MimarksSHumanAssociated data + slot_uri: MIXS:mimarks_s_human_associated_data + range: MimarksSHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_human_gut_data: + description: Data that comply with MimarksS combined with HumanGut + title: MimarksSHumanGut data + slot_uri: MIXS:mimarks_s_human_gut_data + range: MimarksSHumanGut + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_human_oral_data: + description: Data that comply with MimarksS combined with HumanOral + title: MimarksSHumanOral data + slot_uri: MIXS:mimarks_s_human_oral_data + range: MimarksSHumanOral + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_human_skin_data: + description: Data that comply with MimarksS combined with HumanSkin + title: MimarksSHumanSkin data + slot_uri: MIXS:mimarks_s_human_skin_data + range: MimarksSHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_human_vaginal_data: + description: Data that comply with MimarksS combined with HumanVaginal + title: MimarksSHumanVaginal data + slot_uri: MIXS:mimarks_s_human_vaginal_data + range: MimarksSHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_hydrocarbon_resources_cores_data: + description: Data that comply with MimarksS combined with HydrocarbonResourcesCores + title: MimarksSHydrocarbonResourcesCores data + slot_uri: MIXS:mimarks_s_hydrocarbon_resources_cores_data + range: MimarksSHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with MimarksS combined with HydrocarbonResourcesFluidsSwabs + title: MimarksSHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:mimarks_s_hydrocarbon_resources_fluids_swabs_data + range: MimarksSHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_microbial_mat_biofilm_data: + description: Data that comply with MimarksS combined with MicrobialMatBiofilm + title: MimarksSMicrobialMatBiofilm data + slot_uri: MIXS:mimarks_s_microbial_mat_biofilm_data + range: MimarksSMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with MimarksS combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimarksSMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:mimarks_s_miscellaneous_natural_or_artificial_environment_data + range: MimarksSMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_plant_associated_data: + description: Data that comply with MimarksS combined with PlantAssociated + title: MimarksSPlantAssociated data + slot_uri: MIXS:mimarks_s_plant_associated_data + range: MimarksSPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_sediment_data: + description: Data that comply with MimarksS combined with Sediment + title: MimarksSSediment data + slot_uri: MIXS:mimarks_s_sediment_data + range: MimarksSSediment + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_soil_data: + description: Data that comply with MimarksS combined with Soil + title: MimarksSSoil data + slot_uri: MIXS:mimarks_s_soil_data + range: MimarksSSoil + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_symbiont_associated_data: + description: Data that comply with MimarksS combined with SymbiontAssociated + title: MimarksSSymbiontAssociated data + slot_uri: MIXS:mimarks_s_symbiont_associated_data + range: MimarksSSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_wastewater_sludge_data: + description: Data that comply with MimarksS combined with WastewaterSludge + title: MimarksSWastewaterSludge data + slot_uri: MIXS:mimarks_s_wastewater_sludge_data + range: MimarksSWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + mimarks_s_water_data: + description: Data that comply with MimarksS combined with Water + title: MimarksSWater data + slot_uri: MIXS:mimarks_s_water_data + range: MimarksSWater + multivalued: true + inlined: true + inlined_as_list: true + mims_data: + description: Data that comply with checklist Mims + title: Mims data + slot_uri: MIXS:mims_data + range: Mims + multivalued: true + inlined: true + inlined_as_list: true + mims_agriculture_data: + description: Data that comply with Mims combined with Agriculture + title: MimsAgriculture data + slot_uri: MIXS:mims_agriculture_data + range: MimsAgriculture + multivalued: true + inlined: true + inlined_as_list: true + mims_air_data: + description: Data that comply with Mims combined with Air + title: MimsAir data + slot_uri: MIXS:mims_air_data + range: MimsAir + multivalued: true + inlined: true + inlined_as_list: true + mims_built_environment_data: + description: Data that comply with Mims combined with BuiltEnvironment + title: MimsBuiltEnvironment data + slot_uri: MIXS:mims_built_environment_data + range: MimsBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mims_food_animal_and_animal_feed_data: + description: Data that comply with Mims combined with FoodAnimalAndAnimalFeed + title: MimsFoodAnimalAndAnimalFeed data + slot_uri: MIXS:mims_food_animal_and_animal_feed_data + range: MimsFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + mims_food_farm_environment_data: + description: Data that comply with Mims combined with FoodFarmEnvironment + title: MimsFoodFarmEnvironment data + slot_uri: MIXS:mims_food_farm_environment_data + range: MimsFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mims_food_food_production_facility_data: + description: Data that comply with Mims combined with FoodFoodProductionFacility + title: MimsFoodFoodProductionFacility data + slot_uri: MIXS:mims_food_food_production_facility_data + range: MimsFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + mims_food_human_foods_data: + description: Data that comply with Mims combined with FoodHumanFoods + title: MimsFoodHumanFoods data + slot_uri: MIXS:mims_food_human_foods_data + range: MimsFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + mims_host_associated_data: + description: Data that comply with Mims combined with HostAssociated + title: MimsHostAssociated data + slot_uri: MIXS:mims_host_associated_data + range: MimsHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + mims_human_associated_data: + description: Data that comply with Mims combined with HumanAssociated + title: MimsHumanAssociated data + slot_uri: MIXS:mims_human_associated_data + range: MimsHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + mims_human_gut_data: + description: Data that comply with Mims combined with HumanGut + title: MimsHumanGut data + slot_uri: MIXS:mims_human_gut_data + range: MimsHumanGut + multivalued: true + inlined: true + inlined_as_list: true + mims_human_oral_data: + description: Data that comply with Mims combined with HumanOral + title: MimsHumanOral data + slot_uri: MIXS:mims_human_oral_data + range: MimsHumanOral + multivalued: true + inlined: true + inlined_as_list: true + mims_human_skin_data: + description: Data that comply with Mims combined with HumanSkin + title: MimsHumanSkin data + slot_uri: MIXS:mims_human_skin_data + range: MimsHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + mims_human_vaginal_data: + description: Data that comply with Mims combined with HumanVaginal + title: MimsHumanVaginal data + slot_uri: MIXS:mims_human_vaginal_data + range: MimsHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + mims_hydrocarbon_resources_cores_data: + description: Data that comply with Mims combined with HydrocarbonResourcesCores + title: MimsHydrocarbonResourcesCores data + slot_uri: MIXS:mims_hydrocarbon_resources_cores_data + range: MimsHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + mims_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with Mims combined with HydrocarbonResourcesFluidsSwabs + title: MimsHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:mims_hydrocarbon_resources_fluids_swabs_data + range: MimsHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + mims_microbial_mat_biofilm_data: + description: Data that comply with Mims combined with MicrobialMatBiofilm + title: MimsMicrobialMatBiofilm data + slot_uri: MIXS:mims_microbial_mat_biofilm_data + range: MimsMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + mims_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with Mims combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimsMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:mims_miscellaneous_natural_or_artificial_environment_data + range: MimsMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + mims_plant_associated_data: + description: Data that comply with Mims combined with PlantAssociated + title: MimsPlantAssociated data + slot_uri: MIXS:mims_plant_associated_data + range: MimsPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + mims_sediment_data: + description: Data that comply with Mims combined with Sediment + title: MimsSediment data + slot_uri: MIXS:mims_sediment_data + range: MimsSediment + multivalued: true + inlined: true + inlined_as_list: true + mims_soil_data: + description: Data that comply with Mims combined with Soil + title: MimsSoil data + slot_uri: MIXS:mims_soil_data + range: MimsSoil + multivalued: true + inlined: true + inlined_as_list: true + mims_symbiont_associated_data: + description: Data that comply with Mims combined with SymbiontAssociated + title: MimsSymbiontAssociated data + slot_uri: MIXS:mims_symbiont_associated_data + range: MimsSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + mims_wastewater_sludge_data: + description: Data that comply with Mims combined with WastewaterSludge + title: MimsWastewaterSludge data + slot_uri: MIXS:mims_wastewater_sludge_data + range: MimsWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + mims_water_data: + description: Data that comply with Mims combined with Water + title: MimsWater data + slot_uri: MIXS:mims_water_data + range: MimsWater + multivalued: true + inlined: true + inlined_as_list: true + misag_data: + description: Data that comply with checklist Misag + title: Misag data + slot_uri: MIXS:misag_data + range: Misag + multivalued: true + inlined: true + inlined_as_list: true + misag_agriculture_data: + description: Data that comply with Misag combined with Agriculture + title: MisagAgriculture data + slot_uri: MIXS:misag_agriculture_data + range: MisagAgriculture + multivalued: true + inlined: true + inlined_as_list: true + misag_air_data: + description: Data that comply with Misag combined with Air + title: MisagAir data + slot_uri: MIXS:misag_air_data + range: MisagAir + multivalued: true + inlined: true + inlined_as_list: true + misag_built_environment_data: + description: Data that comply with Misag combined with BuiltEnvironment + title: MisagBuiltEnvironment data + slot_uri: MIXS:misag_built_environment_data + range: MisagBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + misag_food_animal_and_animal_feed_data: + description: Data that comply with Misag combined with FoodAnimalAndAnimalFeed + title: MisagFoodAnimalAndAnimalFeed data + slot_uri: MIXS:misag_food_animal_and_animal_feed_data + range: MisagFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + misag_food_farm_environment_data: + description: Data that comply with Misag combined with FoodFarmEnvironment + title: MisagFoodFarmEnvironment data + slot_uri: MIXS:misag_food_farm_environment_data + range: MisagFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + misag_food_food_production_facility_data: + description: Data that comply with Misag combined with FoodFoodProductionFacility + title: MisagFoodFoodProductionFacility data + slot_uri: MIXS:misag_food_food_production_facility_data + range: MisagFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + misag_food_human_foods_data: + description: Data that comply with Misag combined with FoodHumanFoods + title: MisagFoodHumanFoods data + slot_uri: MIXS:misag_food_human_foods_data + range: MisagFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + misag_host_associated_data: + description: Data that comply with Misag combined with HostAssociated + title: MisagHostAssociated data + slot_uri: MIXS:misag_host_associated_data + range: MisagHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + misag_human_associated_data: + description: Data that comply with Misag combined with HumanAssociated + title: MisagHumanAssociated data + slot_uri: MIXS:misag_human_associated_data + range: MisagHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + misag_human_gut_data: + description: Data that comply with Misag combined with HumanGut + title: MisagHumanGut data + slot_uri: MIXS:misag_human_gut_data + range: MisagHumanGut + multivalued: true + inlined: true + inlined_as_list: true + misag_human_oral_data: + description: Data that comply with Misag combined with HumanOral + title: MisagHumanOral data + slot_uri: MIXS:misag_human_oral_data + range: MisagHumanOral + multivalued: true + inlined: true + inlined_as_list: true + misag_human_skin_data: + description: Data that comply with Misag combined with HumanSkin + title: MisagHumanSkin data + slot_uri: MIXS:misag_human_skin_data + range: MisagHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + misag_human_vaginal_data: + description: Data that comply with Misag combined with HumanVaginal + title: MisagHumanVaginal data + slot_uri: MIXS:misag_human_vaginal_data + range: MisagHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + misag_hydrocarbon_resources_cores_data: + description: Data that comply with Misag combined with HydrocarbonResourcesCores + title: MisagHydrocarbonResourcesCores data + slot_uri: MIXS:misag_hydrocarbon_resources_cores_data + range: MisagHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + misag_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with Misag combined with HydrocarbonResourcesFluidsSwabs + title: MisagHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:misag_hydrocarbon_resources_fluids_swabs_data + range: MisagHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + misag_microbial_mat_biofilm_data: + description: Data that comply with Misag combined with MicrobialMatBiofilm + title: MisagMicrobialMatBiofilm data + slot_uri: MIXS:misag_microbial_mat_biofilm_data + range: MisagMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + misag_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with Misag combined with MiscellaneousNaturalOrArtificialEnvironment + title: MisagMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:misag_miscellaneous_natural_or_artificial_environment_data + range: MisagMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + misag_plant_associated_data: + description: Data that comply with Misag combined with PlantAssociated + title: MisagPlantAssociated data + slot_uri: MIXS:misag_plant_associated_data + range: MisagPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + misag_sediment_data: + description: Data that comply with Misag combined with Sediment + title: MisagSediment data + slot_uri: MIXS:misag_sediment_data + range: MisagSediment + multivalued: true + inlined: true + inlined_as_list: true + misag_soil_data: + description: Data that comply with Misag combined with Soil + title: MisagSoil data + slot_uri: MIXS:misag_soil_data + range: MisagSoil + multivalued: true + inlined: true + inlined_as_list: true + misag_symbiont_associated_data: + description: Data that comply with Misag combined with SymbiontAssociated + title: MisagSymbiontAssociated data + slot_uri: MIXS:misag_symbiont_associated_data + range: MisagSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + misag_wastewater_sludge_data: + description: Data that comply with Misag combined with WastewaterSludge + title: MisagWastewaterSludge data + slot_uri: MIXS:misag_wastewater_sludge_data + range: MisagWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + misag_water_data: + description: Data that comply with Misag combined with Water + title: MisagWater data + slot_uri: MIXS:misag_water_data + range: MisagWater + multivalued: true + inlined: true + inlined_as_list: true + miuvig_data: + description: Data that comply with checklist Miuvig + title: Miuvig data + slot_uri: MIXS:miuvig_data + range: Miuvig + multivalued: true + inlined: true + inlined_as_list: true + miuvig_agriculture_data: + description: Data that comply with Miuvig combined with Agriculture + title: MiuvigAgriculture data + slot_uri: MIXS:miuvig_agriculture_data + range: MiuvigAgriculture + multivalued: true + inlined: true + inlined_as_list: true + miuvig_air_data: + description: Data that comply with Miuvig combined with Air + title: MiuvigAir data + slot_uri: MIXS:miuvig_air_data + range: MiuvigAir + multivalued: true + inlined: true + inlined_as_list: true + miuvig_built_environment_data: + description: Data that comply with Miuvig combined with BuiltEnvironment + title: MiuvigBuiltEnvironment data + slot_uri: MIXS:miuvig_built_environment_data + range: MiuvigBuiltEnvironment + multivalued: true + inlined: true + inlined_as_list: true + miuvig_food_animal_and_animal_feed_data: + description: Data that comply with Miuvig combined with FoodAnimalAndAnimalFeed + title: MiuvigFoodAnimalAndAnimalFeed data + slot_uri: MIXS:miuvig_food_animal_and_animal_feed_data + range: MiuvigFoodAnimalAndAnimalFeed + multivalued: true + inlined: true + inlined_as_list: true + miuvig_food_farm_environment_data: + description: Data that comply with Miuvig combined with FoodFarmEnvironment + title: MiuvigFoodFarmEnvironment data + slot_uri: MIXS:miuvig_food_farm_environment_data + range: MiuvigFoodFarmEnvironment + multivalued: true + inlined: true + inlined_as_list: true + miuvig_food_food_production_facility_data: + description: Data that comply with Miuvig combined with FoodFoodProductionFacility + title: MiuvigFoodFoodProductionFacility data + slot_uri: MIXS:miuvig_food_food_production_facility_data + range: MiuvigFoodFoodProductionFacility + multivalued: true + inlined: true + inlined_as_list: true + miuvig_food_human_foods_data: + description: Data that comply with Miuvig combined with FoodHumanFoods + title: MiuvigFoodHumanFoods data + slot_uri: MIXS:miuvig_food_human_foods_data + range: MiuvigFoodHumanFoods + multivalued: true + inlined: true + inlined_as_list: true + miuvig_host_associated_data: + description: Data that comply with Miuvig combined with HostAssociated + title: MiuvigHostAssociated data + slot_uri: MIXS:miuvig_host_associated_data + range: MiuvigHostAssociated + multivalued: true + inlined: true + inlined_as_list: true + miuvig_human_associated_data: + description: Data that comply with Miuvig combined with HumanAssociated + title: MiuvigHumanAssociated data + slot_uri: MIXS:miuvig_human_associated_data + range: MiuvigHumanAssociated + multivalued: true + inlined: true + inlined_as_list: true + miuvig_human_gut_data: + description: Data that comply with Miuvig combined with HumanGut + title: MiuvigHumanGut data + slot_uri: MIXS:miuvig_human_gut_data + range: MiuvigHumanGut + multivalued: true + inlined: true + inlined_as_list: true + miuvig_human_oral_data: + description: Data that comply with Miuvig combined with HumanOral + title: MiuvigHumanOral data + slot_uri: MIXS:miuvig_human_oral_data + range: MiuvigHumanOral + multivalued: true + inlined: true + inlined_as_list: true + miuvig_human_skin_data: + description: Data that comply with Miuvig combined with HumanSkin + title: MiuvigHumanSkin data + slot_uri: MIXS:miuvig_human_skin_data + range: MiuvigHumanSkin + multivalued: true + inlined: true + inlined_as_list: true + miuvig_human_vaginal_data: + description: Data that comply with Miuvig combined with HumanVaginal + title: MiuvigHumanVaginal data + slot_uri: MIXS:miuvig_human_vaginal_data + range: MiuvigHumanVaginal + multivalued: true + inlined: true + inlined_as_list: true + miuvig_hydrocarbon_resources_cores_data: + description: Data that comply with Miuvig combined with HydrocarbonResourcesCores + title: MiuvigHydrocarbonResourcesCores data + slot_uri: MIXS:miuvig_hydrocarbon_resources_cores_data + range: MiuvigHydrocarbonResourcesCores + multivalued: true + inlined: true + inlined_as_list: true + miuvig_hydrocarbon_resources_fluids_swabs_data: + description: Data that comply with Miuvig combined with HydrocarbonResourcesFluidsSwabs + title: MiuvigHydrocarbonResourcesFluidsSwabs data + slot_uri: MIXS:miuvig_hydrocarbon_resources_fluids_swabs_data + range: MiuvigHydrocarbonResourcesFluidsSwabs + multivalued: true + inlined: true + inlined_as_list: true + miuvig_microbial_mat_biofilm_data: + description: Data that comply with Miuvig combined with MicrobialMatBiofilm + title: MiuvigMicrobialMatBiofilm data + slot_uri: MIXS:miuvig_microbial_mat_biofilm_data + range: MiuvigMicrobialMatBiofilm + multivalued: true + inlined: true + inlined_as_list: true + miuvig_miscellaneous_natural_or_artificial_environment_data: + description: Data that comply with Miuvig combined with MiscellaneousNaturalOrArtificialEnvironment + title: MiuvigMiscellaneousNaturalOrArtificialEnvironment data + slot_uri: MIXS:miuvig_miscellaneous_natural_or_artificial_environment_data + range: MiuvigMiscellaneousNaturalOrArtificialEnvironment + multivalued: true + inlined: true + inlined_as_list: true + miuvig_plant_associated_data: + description: Data that comply with Miuvig combined with PlantAssociated + title: MiuvigPlantAssociated data + slot_uri: MIXS:miuvig_plant_associated_data + range: MiuvigPlantAssociated + multivalued: true + inlined: true + inlined_as_list: true + miuvig_sediment_data: + description: Data that comply with Miuvig combined with Sediment + title: MiuvigSediment data + slot_uri: MIXS:miuvig_sediment_data + range: MiuvigSediment + multivalued: true + inlined: true + inlined_as_list: true + miuvig_soil_data: + description: Data that comply with Miuvig combined with Soil + title: MiuvigSoil data + slot_uri: MIXS:miuvig_soil_data + range: MiuvigSoil + multivalued: true + inlined: true + inlined_as_list: true + miuvig_symbiont_associated_data: + description: Data that comply with Miuvig combined with SymbiontAssociated + title: MiuvigSymbiontAssociated data + slot_uri: MIXS:miuvig_symbiont_associated_data + range: MiuvigSymbiontAssociated + multivalued: true + inlined: true + inlined_as_list: true + miuvig_wastewater_sludge_data: + description: Data that comply with Miuvig combined with WastewaterSludge + title: MiuvigWastewaterSludge data + slot_uri: MIXS:miuvig_wastewater_sludge_data + range: MiuvigWastewaterSludge + multivalued: true + inlined: true + inlined_as_list: true + miuvig_water_data: + description: Data that comply with Miuvig combined with Water + title: MiuvigWater data + slot_uri: MIXS:miuvig_water_data + range: MiuvigWater + multivalued: true + inlined: true + inlined_as_list: true + HACCP_term: + description: Hazard Analysis Critical Control Points (HACCP) food safety terms; This field accepts terms listed under HACCP guide food safety term (http://purl.obolibrary.org/obo/FOODON_03530221) + title: Hazard Analysis Critical Control Points (HACCP) guide food safety term + examples: + - value: tetrodotoxic poisoning [FOODON:03530249] + keywords: + - food + - term + slot_uri: MIXS:0001215 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + IFSAC_category: + annotations: + Expected_value: IFSAC term + description: 'The IFSAC food categorization scheme has five distinct levels to which foods can be assigned, depending upon the type of food. First, foods are assigned to one of four food groups (aquatic animals, land animals, plants, and other). Food groups include increasingly specific food categories; dairy, eggs, meat and poultry, and game are in the land animal food group, and the category meat and poultry is further subdivided into more specific categories of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry). Finally, foods are differentiated by differences in food processing (such as pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized solid and semi-solid dairy products, and unpasteurized solid and semi-solid dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html PMID: 28926300' + title: Interagency Food Safety Analytics Collaboration (IFSAC) category + examples: + - value: Plants:Produce:Vegetables:Herbs:Dried Herbs + keywords: + - food + slot_uri: MIXS:0001179 + range: string + required: true + multivalued: true + abs_air_humidity: + annotations: + Preferred_unit: gram per gram, kilogram per kilogram, kilogram, pound + description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + title: absolute air humidity + examples: + - value: 9 gram per gram + keywords: + - absolute + - air + - humidity + slot_uri: MIXS:0000122 + range: string + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + adapters: + description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + title: adapters + examples: + - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT + in_subset: + - sequencing + slot_uri: MIXS:0000048 + pattern: ^[ACGTRKSYMWBHDVN]+;[ACGTRKSYMWBHDVN]+$ + structured_pattern: + syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$ + interpolated: true + partial_match: true + add_recov_method: + description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field + title: secondary and tertiary recovery methods and start date + examples: + - value: Polymer Addition;2018-06-21T14:30Z + keywords: + - date + - method + - recover + - secondary + - start + slot_uri: MIXS:0001009 + required: true + pattern: ^(Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other);(\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\d|3[01])(T([01]\d|2[0-3]):([0-5]\d):([0-5]\d)(\.\d+)?(Z|([+-][01]\d:[0-5]\d))?)?)?)?$$ + structured_pattern: + syntax: ^({add_recov_methods});{date_time_stamp}$ + interpolated: true + partial_match: true + additional_info: + description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary + title: additional info + keywords: + - information + slot_uri: MIXS:0000300 + range: string + address: + description: The street name and building number where the sampling occurred + title: address + slot_uri: MIXS:0000218 + pattern: ^[1-9][0-9]* .*}$ + structured_pattern: + syntax: ^{integer} {text}}$ + interpolated: true + partial_match: true + adj_room: + description: List of rooms (room number, room name) immediately adjacent to the sampling room + title: adjacent rooms + keywords: + - adjacent + - room + slot_uri: MIXS:0000219 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + adjacent_environment: + annotations: + Expected_value: ENVO_01001110 or ENVO_00000070 + description: Description of the environmental system or features that are adjacent to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes + title: environment adjacent to site + examples: + - value: estuarine biome [ENVO:01000020] + keywords: + - adjacent + - environment + - site + string_serialization: '{termLabel}{[termID]}' + slot_uri: MIXS:0001121 + multivalued: true + aero_struc: + description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together + title: aerospace structure + examples: + - value: plane + slot_uri: MIXS:0000773 + range: AeroStrucEnum + agrochem_addition: + annotations: + Preferred_unit: gram, mole per liter, milligram per liter + description: Addition of fertilizers, pesticides, etc. - amount and time of applications + title: history/agrochemical additions + examples: + - value: roundup;5 milligram per liter;2018-06-21 + keywords: + - history + slot_uri: MIXS:0000639 + multivalued: true + pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+);(\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\d|3[01])(T([01]\d|2[0-3]):([0-5]\d):([0-5]\d)(\.\d+)?(Z|([+-][01]\d:[0-5]\d))?)?)?)?$$ + structured_pattern: + syntax: ^{agrochemical_name};{amount} {unit};{date_time_stamp}$ + interpolated: true + partial_match: true + air_PM_concen: + description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM + title: air particulate matter concentration + examples: + - value: PM2.5;10 microgram per cubic meter + keywords: + - air + - concentration + - particle + - particulate + slot_uri: MIXS:0000108 + multivalued: true + pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{particulate_matter_name};{float} {unit}$ + interpolated: true + partial_match: true + air_flow_impede: + annotations: + Expected_value: enumeration;obstruction type; distance from sampling device + description: Presence of objects in the area that would influence or impede air flow through the air filter + title: local air flow impediments + examples: + - value: obstructed;hay bales; 2 m + keywords: + - air + string_serialization: '[obstructed|unobstructed]; {text}; {measurement value}' + slot_uri: MIXS:0001146 + multivalued: true + air_temp: + annotations: + Preferred_unit: degree Celsius + description: Temperature of the air at the time of sampling + title: air temperature + keywords: + - air + - temperature + slot_uri: MIXS:0000124 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + air_temp_regm: + annotations: + Expected_value: temperature value;treatment interval and duration + Preferred_unit: meter + description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens + title: air temperature regimen + examples: + - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - air + - regimen + - temperature + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000551 + multivalued: true + al_sat: + annotations: + Preferred_unit: percentage + description: Aluminum saturation (esp. For tropical soils) + title: extreme_unusual_properties/Al saturation + keywords: + - extreme + - properties + - saturation + - unusual + slot_uri: MIXS:0000607 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + al_sat_meth: + description: Reference or method used in determining Al saturation + title: extreme_unusual_properties/Al saturation method + keywords: + - extreme + - method + - properties + - saturation + - unusual + slot_uri: MIXS:0000324 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + alkalinity: + annotations: + Preferred_unit: milliequivalent per liter, milligram per liter + description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + title: alkalinity + examples: + - value: 50 milligram per liter + keywords: + - alkalinity + slot_uri: MIXS:0000421 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + alkalinity_method: + description: Method used for alkalinity measurement + title: alkalinity method + examples: + - value: titration + keywords: + - alkalinity + - method + slot_uri: MIXS:0000298 + range: string + alkyl_diethers: + description: Concentration of alkyl diethers + title: alkyl diethers + examples: + - value: 0.005 mole per liter + slot_uri: MIXS:0000490 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + alt: + annotations: + Preferred_unit: meter + description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air + title: altitude + examples: + - value: 100 meter + in_subset: + - environment + slot_uri: MIXS:0000094 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + aminopept_act: + annotations: + Preferred_unit: mole per liter per hour + description: Measurement of aminopeptidase activity + title: aminopeptidase activity + examples: + - value: 0.269 mole per liter per hour + slot_uri: MIXS:0000172 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ammonium: + annotations: + Preferred_unit: micromole per liter, milligram per liter, parts per million + description: Concentration of ammonium in the sample + title: ammonium + examples: + - value: 1.5 milligram per liter + slot_uri: MIXS:0000427 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + amniotic_fluid_color: + description: Specification of the color of the amniotic fluid sample + title: amniotic fluid/color + slot_uri: MIXS:0000276 + range: string + amount_light: + annotations: + Preferred_unit: lux, lumens per square meter + description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + title: amount of light + keywords: + - light + slot_uri: MIXS:0000140 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ances_data: + description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) + title: ancestral data + examples: + - value: A/3*B + slot_uri: MIXS:0000247 + range: string + anim_water_method: + description: Description of the equipment or method used to distribute water to livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes + title: animal water delivery method + examples: + - value: water trough [EOL:0001618] + keywords: + - animal + - delivery + - method + - water + slot_uri: MIXS:0001115 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + animal_am: + description: The name(s) (generic or brand) of the antimicrobial(s) given to the food animal within the last 30 days + title: food animal antimicrobial + examples: + - value: tetracycline + keywords: + - animal + - antimicrobial + - food + slot_uri: MIXS:0001243 + range: string + animal_am_dur: + description: The duration of time (days) that the antimicrobial was administered to the food animal + title: food animal antimicrobial duration + examples: + - value: 3 days + keywords: + - animal + - antimicrobial + - duration + - food + - period + slot_uri: MIXS:0001244 + pattern: ^[-+]?[0-9]*\.?[0-9]+ days$ + structured_pattern: + syntax: ^{float} days$ + interpolated: true + partial_match: true + animal_am_freq: + description: The frequency per day that the antimicrobial was administered to the food animal + title: food animal antimicrobial frequency + examples: + - value: '1.5' + keywords: + - animal + - antimicrobial + - food + - frequency + slot_uri: MIXS:0001245 + range: float + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + animal_am_route: + description: The route by which the antimicrobial is adminstered into the body of the food animal + title: food animal antimicrobial route of administration + examples: + - value: oral-feed + keywords: + - administration + - animal + - antimicrobial + - food + - route + slot_uri: MIXS:0001246 + range: string + animal_am_use: + description: The prescribed intended use of or the condition treated by the antimicrobial given to the food animal by any route of administration + title: food animal antimicrobial intended use + examples: + - value: shipping fever + keywords: + - animal + - antimicrobial + - food + - use + slot_uri: MIXS:0001247 + range: string + animal_body_cond: + description: Body condition scoring is a production management tool used to evaluate overall health and nutritional needs of a food animal. Because there are different scoring systems, this field is restricted to three categories + title: food animal body condition + examples: + - value: under conditioned + keywords: + - animal + - body + - condition + - food + slot_uri: MIXS:0001248 + range: AnimalBodyCondEnum + animal_diet: + annotations: + Expected_value: text or FOODON_03309997 + description: If the isolate is from a food animal, the type of diet eaten by the food animal. Please list the main food staple and the setting, if appropriate. For a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org. Multiple terms may apply and can be separated by pipes |Food product for animal covers foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997. If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes. If the proper descriptor is not listed please use text to describe the food product type + title: food animal source diet + examples: + - value: Hay [FOODON:03301763] + keywords: + - animal + - diet + - food + - source + slot_uri: MIXS:0001130 + range: string + multivalued: true + animal_feed_equip: + annotations: + Expected_value: EOL:0001757 + description: Description of the feeding equipment used for livestock. This field accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757). Multiple terms can be separated by pipes + title: animal feeding equipment + examples: + - value: self feeding [EOL:0001645]| straight feed trough [EOL:0001661] + keywords: + - animal + - equipment + slot_uri: MIXS:0001113 + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + animal_group_size: + description: The number of food animals of the same species that are maintained together as a unit, i.e. a herd or flock + title: food animal group size + examples: + - value: '80' + keywords: + - animal + - food + - size + slot_uri: MIXS:0001129 + range: integer + animal_housing: + description: Description of the housing system of the livestock. This field accepts terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605) + title: animal housing system + examples: + - value: pen rearing system [EOL:0001636] + keywords: + - animal + slot_uri: MIXS:0001180 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + animal_intrusion: + description: Identification of animals intruding on the sample or sample site including invertebrates (such as pests or pollinators) and vertebrates (such as wildlife or domesticated animals). This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes + title: animal intrusion near sample source + examples: + - value: Thripidae [NCBITaxon:45053] + keywords: + - animal + - sample + - source + slot_uri: MIXS:0001114 + range: string + multivalued: true + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + animal_sex: + description: The sex and reproductive status of the food animal + title: food animal source sex category + examples: + - value: castrated male + keywords: + - animal + - food + - source + slot_uri: MIXS:0001249 + range: AnimalSexEnum + annot: + annotations: + Expected_value: name of tool or pipeline used, or annotation source description + description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + title: annotation + examples: + - value: prokka + in_subset: + - sequencing + slot_uri: MIXS:0000059 + range: string + annual_precpt: + annotations: + Preferred_unit: millimeter + description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps + title: mean annual precipitation + keywords: + - mean + slot_uri: MIXS:0000644 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + annual_temp: + annotations: + Preferred_unit: degree Celsius + description: Mean annual temperature + title: mean annual temperature + examples: + - value: 12.5 degree Celsius + keywords: + - mean + - temperature + slot_uri: MIXS:0000642 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + antibiotic_regm: + annotations: + Expected_value: antibiotic name;antibiotic amount;treatment interval and duration + Preferred_unit: milligram + description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens + title: antibiotic regimen + examples: + - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000553 + multivalued: true + api: + annotations: + Preferred_unit: degrees API + description: 'API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1 API)' + title: API gravity + examples: + - value: 31.1 API + slot_uri: MIXS:0000157 + range: string + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + arch_struc: + description: An architectural structure is a human-made, free-standing, immobile outdoor construction + title: architectural structure + examples: + - value: shed + slot_uri: MIXS:0000774 + range: ArchStrucEnum + area_samp_size: + annotations: + Expected_value: measurement value + Preferred_unit: centimeter + description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected + title: area sampled size + examples: + - value: 12 centimeter x 12 centimeter + keywords: + - area + - sample + - size + string_serialization: '{integer} {unit} x {integer} {unit}' + slot_uri: MIXS:0001255 + aromatics_pc: + annotations: + Preferred_unit: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: aromatics wt% + slot_uri: MIXS:0000133 + range: string + recommended: true + pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + asphaltenes_pc: + annotations: + Preferred_unit: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: asphaltenes wt% + slot_uri: MIXS:0000135 + range: string + recommended: true + pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + assembly_name: + annotations: + Expected_value: name and version of assembly + description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + title: assembly name + examples: + - value: HuRef, JCVI_ISG_i3_1.0 + in_subset: + - sequencing + string_serialization: '{text} {text}' + slot_uri: MIXS:0000057 + assembly_qual: + description: 'The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the large subunit (LSU) RNA, small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated' + title: assembly quality + examples: + - value: High-quality draft genome + in_subset: + - sequencing + keywords: + - quality + slot_uri: MIXS:0000056 + range: AssemblyQualEnum + assembly_software: + description: Tool(s) used for assembly, including version number and parameters + title: assembly software + examples: + - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise + in_subset: + - sequencing + keywords: + - software + slot_uri: MIXS:0000058 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + associated_resource: + annotations: + Expected_value: reference to resource + description: A related resource that is referenced, cited, or otherwise associated to the sequence + title: relevant electronic resources + examples: + - value: http://www.earthmicrobiome.org/ + in_subset: + - sequencing + keywords: + - resource + string_serialization: '{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0000091 + recommended: true + multivalued: true + association_duration: + annotations: + Preferred_unit: year, day, hour + description: Time spent in host of the symbiotic organism at the time of sampling; relevant scale depends on symbiotic organism and study + title: duration of association with the host + keywords: + - duration + - host + - host. + - period + slot_uri: MIXS:0001299 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + atmospheric_data: + annotations: + Expected_value: atmospheric data name;measurement value + description: Measurement of atmospheric data; can include multiple data + title: atmospheric data + examples: + - value: wind speed;9 knots + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0001097 + multivalued: true + avg_dew_point: + annotations: + Preferred_unit: degree Celsius + description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day + title: average dew point + examples: + - value: 25.5 degree Celsius + keywords: + - average + slot_uri: MIXS:0000141 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + avg_occup: + description: Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room + title: average daily occupancy + keywords: + - average + slot_uri: MIXS:0000775 + range: float + avg_temp: + annotations: + Preferred_unit: degree Celsius + description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day + title: average temperature + examples: + - value: 12.5 degree Celsius + keywords: + - average + - temperature + slot_uri: MIXS:0000142 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bac_prod: + annotations: + Preferred_unit: milligram per cubic meter per day + description: Bacterial production in the water column measured by isotope uptake + title: bacterial production + examples: + - value: 5 milligram per cubic meter per day + keywords: + - production + slot_uri: MIXS:0000683 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bac_resp: + annotations: + Preferred_unit: milligram per cubic meter per day, micromole oxygen per liter per hour + description: Measurement of bacterial respiration in the water column + title: bacterial respiration + examples: + - value: 300 micromole oxygen per liter per hour + slot_uri: MIXS:0000684 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bacteria_carb_prod: + description: Measurement of bacterial carbon production + title: bacterial carbon production + examples: + - value: 2.53 microgram per liter per hour + keywords: + - carbon + - production + slot_uri: MIXS:0000173 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bacterial_density: + annotations: + Preferred_unit: colony forming units per milliliter; colony forming units per gram of dry weight + description: Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043) + title: bacteria density + examples: + - value: 10 colony forming units per gram dry weight + keywords: + - density + slot_uri: MIXS:0001194 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + barometric_press: + annotations: + Preferred_unit: millibar + description: Force per unit area exerted against a surface by the weight of air above that surface + title: barometric pressure + examples: + - value: 5 millibar + keywords: + - pressure + slot_uri: MIXS:0000096 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + basin: + description: Name of the basin (e.g. Campos) + title: basin name + examples: + - value: Campos + slot_uri: MIXS:0000290 + range: string + required: true + bathroom_count: + description: The number of bathrooms in the building + title: bathroom count + examples: + - value: '1' + keywords: + - count + slot_uri: MIXS:0000776 + range: integer + bedroom_count: + description: The number of bedrooms in the building + title: bedroom count + examples: + - value: '2' + keywords: + - count + slot_uri: MIXS:0000777 + range: integer + benzene: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of benzene in the sample + title: benzene + slot_uri: MIXS:0000153 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bin_param: + description: The parameters that have been applied during the extraction of genomes from metagenomic datasets + title: binning parameters + examples: + - value: coverage + description: was 'coverage and kmer' + - value: kmer + description: was coverage and kmer + in_subset: + - sequencing + keywords: + - parameter + slot_uri: MIXS:0000077 + range: BinParamEnum + bin_software: + annotations: + Expected_value: names and versions of software(s) used + description: Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used + title: binning software + examples: + - value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin) + in_subset: + - sequencing + keywords: + - software + string_serialization: '{software};{version}{PID}' + slot_uri: MIXS:0000078 + biochem_oxygen_dem: + annotations: + Preferred_unit: milligram per liter + description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period + title: biochemical oxygen demand + keywords: + - oxygen + slot_uri: MIXS:0000653 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + biocide: + annotations: + Expected_value: name;name;timestamp + description: List of biocides (commercial name of product and supplier) and date of administration + title: biocide administration + examples: + - value: ALPHA 1427;Baker Hughes;2008-01-23 + keywords: + - administration + string_serialization: '{text};{text};{timestamp}' + slot_uri: MIXS:0001011 + recommended: true + biocide_admin_method: + annotations: + Expected_value: measurement value;frequency;duration;duration + Preferred_unit: milligram per liter + description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) + title: biocide administration method + keywords: + - administration + - method + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' + slot_uri: MIXS:0000456 + recommended: true + biocide_used: + annotations: + Expected_value: commercial name of biocide, active ingredient in biocide or class of biocide + description: Substance intended for preventing, neutralizing, destroying, repelling, or mitigating the effects of any pest or microorganism; that inhibits the growth, reproduction, and activity of organisms, including fungal cells; decreases the number of fungi or pests present; deters microbial growth and degradation of other ingredients in the formulation. Indicate the biocide used on the location where the sample was taken. Multiple terms can be separated by pipes + title: biocide + examples: + - value: Quaternary ammonium compound|SterBac + slot_uri: MIXS:0001258 + range: string + multivalued: true + biol_stat: + description: The level of genome modification + title: biological status + examples: + - value: natural + keywords: + - status + slot_uri: MIXS:0000858 + range: BiolStatEnum + biomass: + annotations: + Expected_value: biomass type;measurement value + Preferred_unit: ton, kilogram, gram + description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements + title: biomass + examples: + - value: total;20 gram + keywords: + - biomass + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000174 + multivalued: true + biotic_regm: + description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi + title: biotic regimen + examples: + - value: sample inoculated with Rhizobium spp. Culture + keywords: + - regimen + slot_uri: MIXS:0001038 + range: string + multivalued: true + biotic_relationship: + description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object + title: observed biotic relationship + examples: + - value: free living + in_subset: + - nucleic acid sequence source + keywords: + - observed + - relationship + slot_uri: MIXS:0000028 + range: BioticRelationshipEnum + birth_control: + annotations: + Expected_value: medication name + description: Specification of birth control medication used + title: birth control + slot_uri: MIXS:0000286 + range: string + bishomohopanol: + annotations: + Preferred_unit: microgram per liter, microgram per gram + description: Concentration of bishomohopanol + title: bishomohopanol + examples: + - value: 14 microgram per liter + slot_uri: MIXS:0000175 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + blood_blood_disord: + description: History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74) + title: blood/blood disorder + keywords: + - disorder + slot_uri: MIXS:0000271 + range: string + multivalued: true + blood_press_diast: + annotations: + Preferred_unit: millimeter mercury + description: Resting diastolic blood pressure, measured as mm mercury + title: host blood pressure diastolic + keywords: + - host + - host. + - pressure + slot_uri: MIXS:0000258 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + blood_press_syst: + annotations: + Preferred_unit: millimeter mercury + description: Resting systolic blood pressure, measured as mm mercury + title: host blood pressure systolic + keywords: + - host + - host. + - pressure + slot_uri: MIXS:0000259 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bromide: + annotations: + Preferred_unit: parts per million + description: Concentration of bromide + title: bromide + examples: + - value: 0.05 parts per million + slot_uri: MIXS:0000176 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + build_docs: + description: The building design, construction and operation documents + title: design, construction, and operation documents + examples: + - value: maintenance plans + keywords: + - documents + slot_uri: MIXS:0000787 + range: BuildDocsEnum + build_occup_type: + description: The primary function for which a building or discrete part of a building is intended to be used + title: building occupancy type + examples: + - value: market + keywords: + - type + slot_uri: MIXS:0000761 + range: BuildOccupTypeEnum + required: true + multivalued: true + building_setting: + description: A location (geography) where a building is set + title: building setting + examples: + - value: rural + slot_uri: MIXS:0000768 + range: BuildingSettingEnum + required: true + built_struc_age: + annotations: + Preferred_unit: year + description: The age of the built structure since construction + title: built structure age + examples: + - value: 15 years + keywords: + - age + slot_uri: MIXS:0000145 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + built_struc_set: + description: The characterization of the location of the built structure as high or low human density + title: built structure setting + examples: + - value: rural + slot_uri: MIXS:0000778 + range: BuiltStrucSetEnum + built_struc_type: + description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads + title: built structure type + keywords: + - type + slot_uri: MIXS:0000721 + range: string + calcium: + annotations: + Preferred_unit: milligram per liter, micromole per liter, parts per million + description: Concentration of calcium in the sample + title: calcium + examples: + - value: 0.2 micromole per liter + slot_uri: MIXS:0000432 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + carb_dioxide: + annotations: + Preferred_unit: micromole per liter, parts per million + description: Carbon dioxide (gas) amount or concentration at the time of sampling + title: carbon dioxide + examples: + - value: 410 parts per million + keywords: + - carbon + slot_uri: MIXS:0000097 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + carb_monoxide: + annotations: + Preferred_unit: micromole per liter, parts per million + description: Carbon monoxide (gas) amount or concentration at the time of sampling + title: carbon monoxide + examples: + - value: 0.1 parts per million + keywords: + - carbon + slot_uri: MIXS:0000098 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + carb_nitro_ratio: + annotations: + Expected_value: measurement value + description: Ratio of amount or concentrations of carbon to nitrogen + title: carbon/nitrogen ratio + examples: + - value: '0.417361111' + keywords: + - carbon + - nitrogen + - ratio + string_serialization: '{float}:{float}' + slot_uri: MIXS:0000310 + range: float + ceil_area: + annotations: + Preferred_unit: square meter + description: The area of the ceiling space within the room + title: ceiling area + examples: + - value: 25 square meter + keywords: + - area + - ceiling + slot_uri: MIXS:0000148 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ceil_cond: + description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + title: ceiling condition + examples: + - value: damaged + keywords: + - ceiling + - condition + slot_uri: MIXS:0000779 + range: DamagedEnum + ceil_finish_mat: + description: The type of material used to finish a ceiling + title: ceiling finish material + examples: + - value: stucco + keywords: + - ceiling + - material + slot_uri: MIXS:0000780 + range: CeilFinishMatEnum + ceil_struc: + description: The construction format of the ceiling + title: ceiling structure + examples: + - value: concrete + keywords: + - ceiling + slot_uri: MIXS:0000782 + range: CeilStrucEnum + ceil_texture: + description: The feel, appearance, or consistency of a ceiling surface + title: ceiling texture + examples: + - value: popcorn + keywords: + - ceiling + - texture + slot_uri: MIXS:0000783 + range: CeilingWallTextureEnum + ceil_thermal_mass: + annotations: + Preferred_unit: joule per degree Celsius + description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow + title: ceiling thermal mass + keywords: + - ceiling + - mass + slot_uri: MIXS:0000143 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ceil_type: + description: The type of ceiling according to the ceiling's appearance or construction + title: ceiling type + examples: + - value: coffered + keywords: + - ceiling + - type + slot_uri: MIXS:0000784 + range: CeilTypeEnum + ceil_water_mold: + description: Signs of the presence of mold or mildew on the ceiling + title: ceiling signs of water/mold + examples: + - value: presence of mold visible + keywords: + - ceiling + slot_uri: MIXS:0000781 + range: MoldVisibilityEnum + chem_administration: + annotations: + Expected_value: CHEBI;timestamp + description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + title: chemical administration + examples: + - value: agar [CHEBI:2509];2018-05-11T20:00Z + keywords: + - administration + string_serialization: '{termLabel} [{termID}];{timestamp}' + slot_uri: MIXS:0000751 + multivalued: true + chem_mutagen: + annotations: + Expected_value: mutagen name;mutagen amount;treatment interval and duration + Preferred_unit: milligram per liter + description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens + title: chemical mutagen + examples: + - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000555 + multivalued: true + chem_oxygen_dem: + annotations: + Preferred_unit: milligram per liter + description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite + title: chemical oxygen demand + keywords: + - oxygen + slot_uri: MIXS:0000656 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + chem_treat_method: + annotations: + Expected_value: measurement value;frequency;duration;duration + Preferred_unit: milligram per liter + description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) + title: chemical treatment method + keywords: + - method + - treatment + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' + slot_uri: MIXS:0000457 + chem_treatment: + annotations: + Expected_value: name;name;timestamp + description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included + title: chemical treatment + examples: + - value: ACCENT 1125;DOW;2010-11-17 + keywords: + - treatment + string_serialization: '{text};{text};{timestamp}' + slot_uri: MIXS:0001012 + chimera_check: + description: Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences + title: chimera check software + examples: + - value: uchime;v4.1;default parameters + in_subset: + - sequencing + keywords: + - software + slot_uri: MIXS:0000052 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + chloride: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of chloride in the sample + title: chloride + examples: + - value: 5000 milligram per liter + slot_uri: MIXS:0000429 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + chlorophyll: + annotations: + Preferred_unit: milligram per cubic meter, microgram per liter + description: Concentration of chlorophyll + title: chlorophyll + examples: + - value: 5 milligram per cubic meter + slot_uri: MIXS:0000177 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + climate_environment: + description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates + title: climate environment + examples: + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - environment + slot_uri: MIXS:0001040 + range: string + multivalued: true + coll_site_geo_feat: + annotations: + Expected_value: ENVO:00000002 or ENVO:00000070 + description: 'Text or terms that describe the geographic feature where the food sample was obtained by the researcher. This field accepts selected terms listed under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002), for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011} or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002]; or human construction (http://purl.obolibrary.org/obo/ENVO_00000070)' + title: collection site geographic feature + examples: + - value: farm [ENVO:00000078] + keywords: + - feature + - geographic + - site + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001183 + required: true + collection_date: + description: 'The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' + title: collection date + examples: + - value: '2013-03-25T12:42:31+01:00' + in_subset: + - environment + keywords: + - date + slot_uri: MIXS:0000011 + range: datetime + required: true + compl_appr: + annotations: + Expected_value: text + description: The approach used to determine the completeness of a given genomic assembly, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome + title: completeness approach + examples: + - value: other + description: was other UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) + in_subset: + - sequencing + slot_uri: MIXS:0000071 + range: ComplApprEnum + compl_score: + annotations: + Expected_value: quality;percent completeness + description: 'Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores' + title: completeness score + examples: + - value: med;60% + in_subset: + - sequencing + keywords: + - score + string_serialization: '[high|med|low];{percentage}' + slot_uri: MIXS:0000069 + compl_software: + annotations: + Expected_value: names and versions of software(s) used + description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + title: completeness software + examples: + - value: checkm + in_subset: + - sequencing + keywords: + - software + string_serialization: '{software};{version}' + slot_uri: MIXS:0000070 + conduc: + annotations: + Preferred_unit: milliSiemens per centimeter + description: Electrical conductivity of water + title: conductivity + examples: + - value: 10 milliSiemens per centimeter + slot_uri: MIXS:0000692 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + cons_food_stor_dur: + annotations: + Preferred_unit: hours or days + description: The storage duration of the food commodity by the consumer, prior to onset of illness or sample collection. Indicate the timepoint written in ISO 8601 format + title: food stored by consumer (storage duration) + examples: + - value: P5D + keywords: + - consumer + - duration) + - food + - storage + slot_uri: MIXS:0001195 + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + cons_food_stor_temp: + annotations: + Expected_value: text or measurement value + Preferred_unit: degree Celsius + description: Temperature at which food commodity was stored by the consumer, prior to onset of illness or sample collection + title: food stored by consumer (storage temperature) + examples: + - value: 4 degree Celsius + keywords: + - consumer + - food + - storage + - temperature + string_serialization: '{float} {unit}|{text}' + slot_uri: MIXS:0001196 + cons_purch_date: + description: The date a food product was purchased by consumer + title: purchase date + examples: + - value: '2013-03-25T12:42:31+01:00' + keywords: + - date + slot_uri: MIXS:0001197 + range: datetime + cons_qty_purchased: + description: The quantity of food purchased by consumer + title: quantity purchased + examples: + - value: 5 cans + keywords: + - quantity + slot_uri: MIXS:0001198 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + contam_score: + description: 'The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases' + title: contamination score + examples: + - value: '0.01' + in_subset: + - sequencing + keywords: + - score + slot_uri: MIXS:0000072 + range: float + contam_screen_input: + description: The type of sequence data used as input + title: contamination screening input + examples: + - value: contigs + in_subset: + - sequencing + slot_uri: MIXS:0000005 + range: ContamScreenInputEnum + contam_screen_param: + annotations: + Expected_value: enumeration;value or name + description: Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer + title: contamination screening parameters + examples: + - value: kmer + in_subset: + - sequencing + keywords: + - parameter + string_serialization: '[ref db|kmer|coverage|combination];{text|integer}' + slot_uri: MIXS:0000073 + cool_syst_id: + description: The cooling system identifier + title: cooling system identifier + examples: + - value: '12345' + keywords: + - identifier + slot_uri: MIXS:0000785 + range: integer + crop_rotation: + annotations: + Expected_value: crop rotation status;schedule + description: Whether or not crop is rotated, and if yes, rotation schedule + title: history/crop rotation + examples: + - value: yes;R2/2017-01-01/2018-12-31/P6M + keywords: + - history + slot_uri: MIXS:0000318 + crop_yield: + annotations: + Preferred_unit: kilogram per metre square + description: Amount of crop produced per unit or area of land + title: crop yield + examples: + - value: 570 kilogram per metre square + keywords: + - crop + slot_uri: MIXS:0001116 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + cult_isol_date: + description: The datetime marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies + title: culture isolation date + examples: + - value: '2018-05-11T10:00:00+01:00' + keywords: + - culture + - date + - isolation + slot_uri: MIXS:0001181 + range: datetime + cult_result: + description: Any result of a bacterial culture experiment reported as a binary assessment such as positive/negative, active/inactive + title: culture result + examples: + - value: positive + keywords: + - culture + slot_uri: MIXS:0001117 + range: CultResultEnum + cult_result_org: + description: Taxonomic information about the cultured organism(s) + title: culture result organism + examples: + - value: Listeria monocytogenes [NCIT:C86502] + keywords: + - culture + - organism + slot_uri: MIXS:0001118 + range: string + multivalued: true + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + cult_root_med: + annotations: + Expected_value: name, PMID,DOI or url + description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors + title: culture rooting medium + examples: + - value: http://himedialabs.com/TD/PT158.pdf + keywords: + - culture + string_serialization: '{text}|{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0001041 + cult_target: + annotations: + Expected_value: NCIT:C14250 or NCBI taxid or culture independent + description: The target microbial analyte in terms of investigation scope. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy + title: culture target microbial analyte + examples: + - value: Listeria monocytogenes [NCIT:C86502] + keywords: + - culture + - microbial + - target + string_serialization: '{termLabel} [{termID}]|{integer}' + slot_uri: MIXS:0001119 + multivalued: true + cur_land_use: + annotations: + Expected_value: enumeration + description: Present state of sample site + title: current land use + examples: + - value: conifers + keywords: + - land + - use + string_serialization: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)]' + slot_uri: MIXS:0001080 + cur_vegetation: + annotations: + Expected_value: current vegetation type + description: Vegetation classification from one or more standard classification systems, or agricultural crop + title: current vegetation + keywords: + - vegetation + slot_uri: MIXS:0000312 + range: string + cur_vegetation_meth: + description: Reference or method used in vegetation classification + title: current vegetation method + keywords: + - method + - vegetation + slot_uri: MIXS:0000314 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + date_extr_weath: + description: Date of unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order + title: extreme weather date + examples: + - value: '2013-03-25T12:42:31+01:00' + keywords: + - date + - extreme + - weather + slot_uri: MIXS:0001142 + range: datetime + multivalued: true + date_last_rain: + description: The date of the last time it rained + title: date last rain + examples: + - value: '2013-03-25T12:42:31+01:00' + keywords: + - date + - rain + slot_uri: MIXS:0000786 + range: datetime + decontam_software: + annotations: + Expected_value: enumeration + description: Tool(s) used in contamination screening + title: decontamination software + examples: + - value: anvi'o + in_subset: + - sequencing + keywords: + - software + string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]' + slot_uri: MIXS:0000074 + density: + annotations: + Preferred_unit: gram per cubic meter, gram per cubic centimeter + description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + title: density + examples: + - value: 1000 kilogram per cubic meter + keywords: + - density + slot_uri: MIXS:0000435 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + depos_env: + description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field + title: depositional environment + keywords: + - environment + slot_uri: MIXS:0000992 + range: DeposEnvEnum + recommended: true + depth: + annotations: + Preferred_unit: meter + description: The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples + title: depth + in_subset: + - environment + keywords: + - depth + slot_uri: MIXS:0000018 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + dermatology_disord: + description: History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37) + title: dermatology disorder + keywords: + - disorder + slot_uri: MIXS:0000284 + range: string + multivalued: true + detec_type: + annotations: + Expected_value: enumeration + description: Type of UViG detection + title: detection type + examples: + - value: independent sequence (UViG) + in_subset: + - sequencing + keywords: + - type + string_serialization: '[independent sequence (UViG)|provirus (UpViG)]' + slot_uri: MIXS:0000084 + dew_point: + annotations: + Preferred_unit: degree Celsius + description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water + title: dew point + examples: + - value: 22 degree Celsius + slot_uri: MIXS:0000129 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diet_last_six_month: + annotations: + Expected_value: diet change;current diet + description: Specification of major diet changes in the last six months, if yes the change should be specified + title: major diet change in last six months + examples: + - value: yes;vegetarian diet + keywords: + - diet + - months + string_serialization: '{boolean};{text}' + slot_uri: MIXS:0000266 + dietary_claim_use: + annotations: + Expected_value: FOODON:03510023 + description: These descriptors are used either for foods intended for special dietary use as defined in 21 CFR 105 or for foods that have special characteristics indicated in the name or labeling. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the most prominent dietary claim or use + title: dietary claim or use + examples: + - value: No preservatives [FOODON:03510113] + keywords: + - diet + - use + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001199 + multivalued: true + diether_lipids: + annotations: + Expected_value: diether lipid name;measurement value + Preferred_unit: nanogram per liter + description: Concentration of diether lipids; can include multiple types of diether lipids + title: diether lipids + examples: + - value: 0.2 nanogram per liter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000178 + multivalued: true + diss_carb_dioxide: + annotations: + Preferred_unit: micromole per liter, milligram per liter + description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + title: dissolved carbon dioxide + examples: + - value: 5 milligram per liter + keywords: + - carbon + - dissolved + slot_uri: MIXS:0000436 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_hydrogen: + annotations: + Preferred_unit: micromole per liter + description: Concentration of dissolved hydrogen + title: dissolved hydrogen + examples: + - value: 0.3 micromole per liter + keywords: + - dissolved + slot_uri: MIXS:0000179 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_inorg_carb: + annotations: + Preferred_unit: microgram per liter, milligram per liter, parts per million + description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter + title: dissolved inorganic carbon + examples: + - value: 2059 micromole per kilogram + keywords: + - carbon + - dissolved + - inorganic + slot_uri: MIXS:0000434 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_inorg_nitro: + annotations: + Preferred_unit: microgram per liter, micromole per liter + description: Concentration of dissolved inorganic nitrogen + title: dissolved inorganic nitrogen + examples: + - value: 761 micromole per liter + keywords: + - dissolved + - inorganic + - nitrogen + slot_uri: MIXS:0000698 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_inorg_phosp: + description: Concentration of dissolved inorganic phosphorus in the sample + title: dissolved inorganic phosphorus + examples: + - value: 56.5 micromole per liter + keywords: + - dissolved + - inorganic + - phosphorus + slot_uri: MIXS:0000106 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_iron: + annotations: + Preferred_unit: milligram per liter + description: Concentration of dissolved iron in the sample + title: dissolved iron + keywords: + - dissolved + slot_uri: MIXS:0000139 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_org_carb: + annotations: + Preferred_unit: micromole per liter, milligram per liter + description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid + title: dissolved organic carbon + examples: + - value: 197 micromole per liter + keywords: + - carbon + - dissolved + - organic + slot_uri: MIXS:0000433 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_org_nitro: + description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + title: dissolved organic nitrogen + examples: + - value: 0.05 micromole per liter + keywords: + - dissolved + - nitrogen + - organic + slot_uri: MIXS:0000162 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_oxygen: + annotations: + Preferred_unit: micromole per kilogram, milligram per liter + description: Concentration of dissolved oxygen + title: dissolved oxygen + examples: + - value: 175 micromole per kilogram + keywords: + - dissolved + - oxygen + slot_uri: MIXS:0000119 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_oxygen_fluid: + annotations: + Preferred_unit: micromole per kilogram, milligram per liter + description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic) + title: dissolved oxygen in fluids + keywords: + - dissolved + - oxygen + slot_uri: MIXS:0000438 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + dominant_hand: + description: Dominant hand of the subject + title: dominant hand + examples: + - value: right + slot_uri: MIXS:0000944 + range: DominantHandEnum + door_comp_type: + description: The composite type of the door + title: door type, composite + examples: + - value: revolving + keywords: + - door + - type + slot_uri: MIXS:0000795 + range: DoorCompTypeEnum + door_cond: + description: The phsical condition of the door + title: door condition + examples: + - value: new + keywords: + - condition + - door + slot_uri: MIXS:0000788 + range: DamagedRupturedEnum + door_direct: + description: The direction the door opens + title: door direction of opening + examples: + - value: inward + keywords: + - direction + - door + slot_uri: MIXS:0000789 + range: DoorDirectEnum + door_loc: + description: The relative location of the door in the room + title: door location + examples: + - value: north + keywords: + - door + - location + slot_uri: MIXS:0000790 + range: CompassDirections8Enum + door_mat: + description: The material the door is composed of + title: door material + examples: + - value: wood + keywords: + - door + - material + slot_uri: MIXS:0000791 + range: DoorMatEnum + door_move: + description: The type of movement of the door + title: door movement + examples: + - value: swinging + keywords: + - door + slot_uri: MIXS:0000792 + range: DoorMoveEnum + door_size: + annotations: + Preferred_unit: square meter + description: The size of the door + title: door area or size + examples: + - value: 2.5 square meter + keywords: + - area + - door + - size + slot_uri: MIXS:0000158 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + door_type: + description: The type of door material + title: door type + examples: + - value: wooden + keywords: + - door + - type + slot_uri: MIXS:0000794 + range: DoorTypeEnum + door_type_metal: + description: The type of metal door + title: door type, metal + examples: + - value: hollow + keywords: + - door + - type + slot_uri: MIXS:0000796 + range: DoorTypeMetalEnum + door_type_wood: + annotations: + Expected_value: enumeration + description: The type of wood door + title: door type, wood + examples: + - value: battened + keywords: + - door + - type + string_serialization: '[bettened and ledged|battened|ledged and braced|battened|ledged and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire gauged]' + slot_uri: MIXS:0000797 + door_water_mold: + description: Signs of the presence of mold or mildew on a door + title: door signs of water/mold + examples: + - value: presence of mold visible + keywords: + - door + slot_uri: MIXS:0000793 + range: MoldVisibilityEnum + douche: + description: Date of most recent douche + title: douche + examples: + - value: '2013-03-25T12:42:31+01:00' + slot_uri: MIXS:0000967 + range: datetime + down_par: + annotations: + Preferred_unit: microEinstein per square meter per second, microEinstein per square centimeter per second + description: Visible waveband radiance and irradiance measurements in the water column + title: downward PAR + examples: + - value: 28.71 microEinstein per square meter per second + slot_uri: MIXS:0000703 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + drainage_class: + description: Drainage classification from a standard system such as the USDA system + title: drainage classification + examples: + - value: well + keywords: + - classification + slot_uri: MIXS:0001085 + range: DrainageClassEnum + drawings: + description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + title: drawings + examples: + - value: sketch + keywords: + - drawings + slot_uri: MIXS:0000798 + range: DrawingsEnum + drug_usage: + annotations: + Expected_value: drug name;frequency + description: Any drug used by subject and the frequency of usage; can include multiple drugs used + title: drug usage + examples: + - value: Lipitor;2/day + keywords: + - drug + - use + string_serialization: '{text};{integer}/[year|month|week|day|hour]' + slot_uri: MIXS:0000894 + multivalued: true + efficiency_percent: + annotations: + Preferred_unit: micromole per liter + description: Percentage of volatile solids removed from the anaerobic digestor + title: efficiency percent + keywords: + - percent + slot_uri: MIXS:0000657 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + elev: + annotations: + Preferred_unit: meter + description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit + title: elevation + examples: + - value: 100 meter + in_subset: + - environment + keywords: + - elevation + slot_uri: MIXS:0000093 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + elevator: + description: The number of elevators within the built structure + title: elevator count + examples: + - value: '2' + keywords: + - count + slot_uri: MIXS:0000799 + range: integer + emulsions: + annotations: + Expected_value: emulsion name;measurement value + Preferred_unit: gram per liter + description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types + title: emulsions + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000660 + multivalued: true + encoded_traits: + annotations: + Expected_value: 'for plasmid: antibiotic resistance; for phage: converting genes' + description: Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage + title: encoded traits + examples: + - value: beta-lactamase class A + in_subset: + - nucleic acid sequence source + slot_uri: MIXS:0000034 + range: string + enrichment_protocol: + description: The microbiological workflow or protocol followed to test for the presence or enumeration of the target microbial analyte(s). Please provide a PubMed or DOI reference for published protocols + title: enrichment protocol + examples: + - value: 'BAM Chapter 4: Enumeration of Escherichia coli and the Coliform Bacteria' + keywords: + - enrichment + - protocol + slot_uri: MIXS:0001177 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|.*$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + env_broad_scale: + description: 'Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' + title: broad-scale environmental context + examples: + - value: rangeland biome [ENVO:01000247] + in_subset: + - environment + keywords: + - context + - environmental + slot_uri: MIXS:0000012 + range: string + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + env_local_scale: + annotations: + Expected_value: Environmental entities having causal influences upon the entity at time of sampling + description: 'Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' + title: local environmental context + examples: + - value: hillside [ENVO:01000333] + in_subset: + - environment + keywords: + - context + - environmental + slot_uri: MIXS:0000013 + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + env_medium: + description: 'Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)' + title: environmental medium + examples: + - value: bluegrass field soil [ENVO:00005789] + in_subset: + - environment + keywords: + - environmental + slot_uri: MIXS:0000014 + range: string + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + env_monitoring_zone: + annotations: + Expected_value: ENVO + description: An environmental monitoring zone is a formal designation as part of an environmental monitoring program, in which areas of a food production facility are categorized, commonly as zones 1-4, based on likelihood or risk of foodborne pathogen contamination. This field accepts terms listed under food production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO). Please add a term to indicate the environmental monitoring zone the sample was taken from + title: food production environmental monitoring zone + examples: + - value: Zone 1 + keywords: + - environmental + - food + - production + slot_uri: MIXS:0001254 + range: string + escalator: + description: The number of escalators within the built structure + title: escalator count + examples: + - value: '4' + keywords: + - count + slot_uri: MIXS:0000800 + range: integer + estimated_size: + annotations: + Expected_value: number of base pairs + description: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period + title: estimated size + examples: + - value: 300000 bp + in_subset: + - nucleic acid sequence source + keywords: + - size + string_serialization: '{integer} bp' + slot_uri: MIXS:0000024 + ethnicity: + annotations: + Expected_value: text recommend from Wikipedia list + description: A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups + title: ethnicity + examples: + - value: native american + slot_uri: MIXS:0000895 + range: string + multivalued: true + ethylbenzene: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of ethylbenzene in the sample + title: ethylbenzene + slot_uri: MIXS:0000155 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + exp_duct: + annotations: + Preferred_unit: square meter + description: The amount of exposed ductwork in the room + title: exposed ductwork + slot_uri: MIXS:0000144 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + exp_pipe: + description: The number of exposed pipes in the room + title: exposed pipes + keywords: + - pipes + slot_uri: MIXS:0000220 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + experimental_factor: + annotations: + Expected_value: text or EFO and/or OBI + description: Variable aspects of an experiment design that can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI) + title: experimental factor + examples: + - value: time series design [EFO:0001779] + in_subset: + - investigation + keywords: + - experimental + - factor + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0000008 + range: string + multivalued: true + pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ + ext_door: + description: The number of exterior doors in the built structure + title: exterior door count + keywords: + - count + - door + - exterior + slot_uri: MIXS:0000170 + range: integer + ext_wall_orient: + description: The orientation of the exterior wall + title: orientations of exterior wall + examples: + - value: northwest + keywords: + - exterior + - wall + slot_uri: MIXS:0000817 + range: CompassDirections8Enum + ext_window_orient: + description: The compass direction the exterior window of the room is facing + title: orientations of exterior window + examples: + - value: southwest + keywords: + - exterior + - window + slot_uri: MIXS:0000818 + range: CompassDirections8Enum + extr_weather_event: + description: Unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order + title: extreme weather event + examples: + - value: hail + keywords: + - event + - extreme + - weather + slot_uri: MIXS:0001141 + range: ExtrWeatherEventEnum + multivalued: true + extrachrom_elements: + description: Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) + title: extrachromosomal elements + examples: + - value: '5' + in_subset: + - nucleic acid sequence source + slot_uri: MIXS:0000023 + range: integer + extreme_event: + description: Unusual physical events that may have affected microbial populations + title: history/extreme events + keywords: + - event + - history + slot_uri: MIXS:0000320 + range: datetime + facility_type: + description: Establishment details about the type of facility where the sample was taken. This is independent of the specific product(s) within the facility + title: facility type + examples: + - value: manufacturing-processing + keywords: + - facility + - type + slot_uri: MIXS:0001252 + range: FacilityTypeEnum + multivalued: true + fao_class: + description: Soil classification from the FAO World soil distribution from International Soil Reference and Information Centre (ISRIC). The list of available soil classifications can be found at https://www.isric.org/explore/world-soil-distribution + title: soil_taxonomic/FAO classification + examples: + - value: Luvisols + keywords: + - classification + slot_uri: MIXS:0001083 + range: FaoClassEnum + farm_equip: + description: List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes + title: farm equipment used + examples: + - value: combine harvester [AGRO:00000473] + keywords: + - equipment + - farm + - use + slot_uri: MIXS:0001126 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + farm_equip_san: + annotations: + Expected_value: text or commercial name of sanitizer or class of sanitizer or active ingredient in sanitizer + Preferred_unit: parts per million + description: Method used to sanitize growing and harvesting equipment. This can including type and concentration of sanitizing solution. Multiple terms can be separated by one or more pipes + title: farm equipment sanitization + examples: + - value: hot water pressure wash, hypochlorite solution, 50 parts per million + keywords: + - equipment + - farm + string_serialization: '{text} {float} {unit}' + slot_uri: MIXS:0001124 + multivalued: true + farm_equip_san_freq: + description: The number of times farm equipment is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually + title: farm equipment sanitization frequency + examples: + - value: Biweekly + keywords: + - equipment + - farm + - frequency + slot_uri: MIXS:0001125 + range: string + farm_equip_shared: + description: List of planting, growing or harvesting equipment shared with other farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes + title: equipment shared with other farms + examples: + - value: combine harvester [AGRO:00000473] + keywords: + - equipment + - farm + slot_uri: MIXS:0001123 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + farm_water_source: + description: Source of water used on the farm for irrigation of crops or watering of livestock + title: farm watering water source + examples: + - value: well + description: was water well (ENVO:01000002) + keywords: + - farm + - source + - water + slot_uri: MIXS:0001110 + range: FarmWaterSourceEnum + recommended: true + feat_pred: + description: Method used to predict UViGs features such as ORFs, integration site, etc + title: feature prediction + examples: + - value: Prodigal;2.6.3;default parameters + in_subset: + - sequencing + keywords: + - feature + - predict + slot_uri: MIXS:0000061 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + ferm_chem_add: + annotations: + Expected_value: chemical ingredient + description: Any chemicals that are added to the fermentation process to achieve the desired final product + title: fermentation chemical additives + examples: + - value: salt + keywords: + - fermentation + string_serialization: '{float} {unit}' + slot_uri: MIXS:0001185 + recommended: true + multivalued: true + ferm_chem_add_perc: + annotations: + Preferred_unit: percentage + description: The amount of chemical added to the fermentation process + title: fermentation chemical additives percentage + examples: + - value: '0.01' + keywords: + - fermentation + - percent + slot_uri: MIXS:0001186 + range: float + recommended: true + multivalued: true + ferm_headspace_oxy: + annotations: + Preferred_unit: percentage + description: The amount of headspace oxygen in a fermentation vessel + title: fermentation headspace oxygen + examples: + - value: '0.05' + keywords: + - fermentation + - oxygen + slot_uri: MIXS:0001187 + range: float + recommended: true + ferm_medium: + description: The growth medium used for the fermented food fermentation process, which supplies the required nutrients. Usually this includes a carbon and nitrogen source, water, micronutrients and chemical additives + title: fermentation medium + examples: + - value: molasses + keywords: + - fermentation + slot_uri: MIXS:0001188 + range: string + recommended: true + ferm_pH: + description: The pH of the fermented food fermentation process + title: fermentation pH + examples: + - value: '4.5' + keywords: + - fermentation + - ph + slot_uri: MIXS:0001189 + range: float + recommended: true + ferm_rel_humidity: + annotations: + Preferred_unit: percentage + description: The relative humidity of the fermented food fermentation process + title: fermentation relative humidity + comments: + - percent or float? + examples: + - value: 95% + keywords: + - fermentation + - humidity + - relative + slot_uri: MIXS:0001190 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ferm_temp: + annotations: + Preferred_unit: degree Celsius + description: The temperature of the fermented food fermentation process + title: fermentation temperature + examples: + - value: 22 degrees Celsius + keywords: + - fermentation + - temperature + slot_uri: MIXS:0001191 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ferm_time: + annotations: + Preferred_unit: days + description: The time duration of the fermented food fermentation process + title: fermentation time + examples: + - value: P10D + keywords: + - fermentation + - time + slot_uri: MIXS:0001192 + range: string + recommended: true + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + ferm_vessel: + description: The type of vessel used for containment of the fermentation + title: fermentation vessel + examples: + - value: steel drum + keywords: + - fermentation + slot_uri: MIXS:0001193 + range: string + recommended: true + fertilizer_admin: + description: Type of fertilizer or amendment added to the soil or water for the purpose of improving substrate health and quality for plant growth. This field accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). Multiple terms may apply and can be separated by pipes, listing in reverse chronological order + title: fertilizer administration + examples: + - value: fish emulsion [AGRO:00000082] + keywords: + - administration + slot_uri: MIXS:0001127 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + fertilizer_date: + description: Date of administration of soil amendment or fertilizer. Multiple terms may apply and can be separated by pipes, listing in reverse chronological order + title: fertilizer administration date + examples: + - value: '2018-05-11T10:00:00+01:00' + keywords: + - administration + - date + slot_uri: MIXS:0001128 + range: datetime + fertilizer_regm: + annotations: + Expected_value: fertilizer name;fertilizer amount;treatment interval and duration + Preferred_unit: gram, mole per liter, milligram per liter + description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens + title: fertilizer regimen + examples: + - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000556 + multivalued: true + field: + description: Name of the hydrocarbon field (e.g. Albacora) + title: field name + slot_uri: MIXS:0000291 + range: string + recommended: true + filter_type: + description: A device which removes solid particulates or airborne molecular contaminants + title: filter type + examples: + - value: HEPA + keywords: + - filter + - type + slot_uri: MIXS:0000765 + range: FilterTypeEnum + required: true + multivalued: true + fire: + description: Historical and/or physical evidence of fire + title: history/fire + keywords: + - history + slot_uri: MIXS:0001086 + range: datetime + fireplace_type: + description: A firebox with chimney + title: fireplace type + examples: + - value: wood burning + keywords: + - type + slot_uri: MIXS:0000802 + range: FireplaceTypeEnum + flooding: + description: Historical and/or physical evidence of flooding + title: history/flooding + keywords: + - history + slot_uri: MIXS:0000319 + range: datetime + floor_age: + annotations: + Preferred_unit: years, weeks, days + description: The time period since installment of the carpet or flooring + title: floor age + keywords: + - age + - floor + slot_uri: MIXS:0000164 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + floor_area: + annotations: + Preferred_unit: square meter + description: The area of the floor space within the room + title: floor area + keywords: + - area + - floor + slot_uri: MIXS:0000165 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + floor_cond: + description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + title: floor condition + examples: + - value: new + keywords: + - condition + - floor + slot_uri: MIXS:0000803 + range: DamagedEnum + floor_count: + description: The number of floors in the building, including basements and mechanical penthouse + title: floor count + keywords: + - count + - floor + slot_uri: MIXS:0000225 + range: integer + floor_finish_mat: + annotations: + Expected_value: enumeration + description: The floor covering type; the finished surface that is walked on + title: floor finish material + examples: + - value: carpet + keywords: + - floor + - material + string_serialization: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify unfinished|sealed|clear finish|paint]' + slot_uri: MIXS:0000804 + floor_struc: + description: Refers to the structural elements and subfloor upon which the finish flooring is installed + title: floor structure + examples: + - value: concrete + keywords: + - floor + slot_uri: MIXS:0000806 + range: FloorStrucEnum + floor_thermal_mass: + annotations: + Preferred_unit: joule per degree Celsius + description: The ability of the floor to provide inertia against temperature fluctuations + title: floor thermal mass + keywords: + - floor + - mass + slot_uri: MIXS:0000166 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + floor_water_mold: + description: Signs of the presence of mold or mildew in a room + title: floor signs of water/mold + examples: + - value: ceiling discoloration + keywords: + - floor + slot_uri: MIXS:0000805 + range: FloorWaterMoldEnum + fluor: + annotations: + Preferred_unit: milligram chlorophyll a per cubic meter, volts + description: Raw or converted fluorescence of water + title: fluorescence + examples: + - value: 2.5 volts + slot_uri: MIXS:0000704 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + foetal_health_stat: + description: Specification of foetal health status, should also include abortion + title: amniotic fluid/foetal health status + keywords: + - status + slot_uri: MIXS:0000275 + range: string + food_additive: + annotations: + Expected_value: FOODON:03412972 + description: A substance or substances added to food to maintain or improve safety and freshness, to improve or maintain nutritional value, or improve taste, texture and appearance. This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the top 5 ingredients listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors + title: food additive + examples: + - value: xanthan gum [FOODON:03413321] + keywords: + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001200 + multivalued: true + food_allergen_label: + annotations: + Expected_value: FOODON:03510213 + description: A label indication that the product contains a recognized allergen. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213) + title: food allergen labeling + examples: + - value: food allergen labelling about crustaceans and products thereof [FOODON:03510215] + keywords: + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001201 + multivalued: true + food_clean_proc: + description: The process of cleaning food to separate other environmental materials from the food source. Multiple terms can be separated by pipes + title: food cleaning process + examples: + - value: rinsed with water + description: was rinsed with water|scrubbed with brush + - value: scrubbed with brush + description: was rinsed with water|scrubbed with brush + keywords: + - food + - process + slot_uri: MIXS:0001182 + range: FoodCleanProcEnum + food_contact_surf: + annotations: + Expected_value: FOODON:03500010 + description: The specific container or coating materials in direct contact with the food. Multiple values can be assigned. This field accepts terms listed under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010) + title: food contact surface + examples: + - value: cellulose acetate [FOODON:03500034] + keywords: + - food + - surface + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001131 + multivalued: true + food_contain_wrap: + annotations: + Expected_value: FOODON:03490100 + description: Type of container or wrapping defined by the main container material, the container form, and the material of the liner lids or ends. Also type of container or wrapping by form; prefer description by material first, then by form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100) + title: food container or wrapping + examples: + - value: Plastic shrink-pack [FOODON:03490137] + keywords: + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001132 + food_cooking_proc: + annotations: + Expected_value: FOODON:03450002 + description: The transformation of raw food by the application of heat. This field accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002) + title: food cooking process + examples: + - value: food blanching [FOODON:03470175] + keywords: + - food + - process + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001202 + multivalued: true + food_dis_point: + description: 'A reference to a place on the Earth, by its name or by its geographical location that refers to a distribution point along the food chain. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012' + title: food distribution point geographic location + examples: + - value: 'USA: Delmarva, Peninsula' + keywords: + - food + - geographic + - location + slot_uri: MIXS:0001203 + range: string + multivalued: true + pattern: '^.*: .*, .*$' + structured_pattern: + syntax: '^{text}: {text}, {text}$' + interpolated: true + partial_match: true + food_dis_point_city: + annotations: + Expected_value: GAZ:00000448 + description: 'A reference to a place on the Earth, by its name or by its geographical location that refers to a distribution point along the food chain. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012' + title: food distribution point geographic location (city) + examples: + - value: Atlanta[GAZ:00004445] + keywords: + - food + - geographic + - location + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001204 + multivalued: true + food_harvest_proc: + description: A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. This may include a part of an organism or the whole, and may involve killing the organism + title: Food harvesting process + examples: + - value: hand-picked + keywords: + - food + - process + slot_uri: MIXS:0001133 + range: string + multivalued: true + food_ingredient: + annotations: + Expected_value: FOODON + description: In this field, please list individual ingredients for multi-component food [FOODON:00002501] and simple foods that is not captured in food_type. Please use terms that are present in FoodOn. Multiple terms can be separated by one or more pipes |, but please consider limiting this list to the top 5 ingredients listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors + title: food ingredient + examples: + - value: bean (whole) [FOODON:00002753] + keywords: + - food + - ingredient + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001205 + multivalued: true + food_name_status: + description: A datum indicating that use of a food product name is regulated in some legal jurisdiction. This field accepts terms listed under food product name legal status (http://purl.obolibrary.org/obo/FOODON_03530087) + title: food product name legal status + examples: + - value: protected geographic indication [FOODON:03530256] + keywords: + - food + - product + - status + slot_uri: MIXS:0001206 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + food_origin: + description: A reference to a place on the Earth, by its name or by its geographical location that describes the origin of the food commodity, either in terms of its cultivation or production. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448) + title: food product origin geographic location + examples: + - value: 'USA: Delmarva, Peninsula' + keywords: + - food + - geographic + - location + - product + slot_uri: MIXS:0001207 + range: string + pattern: '^.*: .*, .*$' + structured_pattern: + syntax: '^{text}: {text}, {text}$' + interpolated: true + partial_match: true + food_pack_capacity: + annotations: + Preferred_unit: grams + description: The maximum number of product units within a package + title: food package capacity + examples: + - value: 454 grams + keywords: + - food + - package + slot_uri: MIXS:0001208 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + food_pack_integrity: + annotations: + Expected_value: FOODON:03530218 + description: A term label and term id to describe the state of the packing material and text to explain the exact condition. This field accepts terms listed under food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218) + title: food packing medium integrity + examples: + - value: food packing medium compromised [FOODON:00002517] + keywords: + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001209 + multivalued: true + food_pack_medium: + annotations: + Expected_value: FOODON:03480020 + description: The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal. This includes edible packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide), vacuum packed, or packed with aerosol propellant. This field accepts terms under food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple terms may apply and can be separated by pipes + title: food packing medium + keywords: + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001134 + multivalued: true + food_preserv_proc: + annotations: + Expected_value: FOODON:03470107 + description: The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. This field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107) + title: food preservation process + examples: + - value: food slow freezing [FOODON:03470128] + keywords: + - food + - process + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001135 + multivalued: true + food_prior_contact: + annotations: + Expected_value: FOODON:03530077 + description: The material the food contacted (e.g., was processed in) prior to packaging. This field accepts terms listed under material of contact prior to food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper descriptor is not listed please use text to describe the material of contact prior to food packaging + title: material of contact prior to food packaging + examples: + - value: processed in stainless steel container [FOODON:03530081] + keywords: + - food + - material + - prior + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001210 + multivalued: true + food_prod: + description: Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes + title: food production system characteristics + examples: + - value: organic plant cultivation [FOODON:03530253] + keywords: + - food + - production + slot_uri: MIXS:0001211 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + food_prod_char: + description: Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef + title: food production characteristics + examples: + - value: wild caught + keywords: + - food + - production + slot_uri: MIXS:0001136 + range: string + multivalued: true + food_prod_synonym: + description: Other names by which the food product is known by (e.g., regional or non-English names) + title: food product synonym + examples: + - value: pinot gris + keywords: + - food + - product + slot_uri: MIXS:0001212 + range: string + multivalued: true + food_product_qual: + description: Descriptors for describing food visually or via other senses, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. This field accepts terms listed under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454) + title: food product by quality + examples: + - value: raw [FOODON:03311126] + keywords: + - food + - product + - quality + slot_uri: MIXS:0001213 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + food_product_type: + annotations: + Expected_value: FOODON:00001002 or FOODON:03309997 + description: A food product type is a class of food products that is differentiated by its food composition (e.g., single- or multi-ingredient), processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. This field accepts terms under food product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997). If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes + title: food product type + keywords: + - food + - product + - type + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001184 + food_quality_date: + annotations: + Expected_value: enumeration, date + description: The date recommended for the use of the product while at peak quality, this date is not a reflection of safety unless used on infant formula this date is not a reflection of safety and is typically labeled on a food product as "best if used by," best by," "use by," or "freeze by." + title: food quality date + examples: + - value: best by 2020-05-24 + keywords: + - date + - food + - quality + string_serialization: '[best by|best if used by|freeze by|use by]; date' + slot_uri: MIXS:0001178 + food_source: + annotations: + Expected_value: FOODON term + description: Type of plant or animal from which the food product or its major ingredient is derived or a chemical food source [FDA CFSAN 1995] + title: food source + keywords: + - food + - source + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0001139 + food_source_age: + annotations: + Preferred_unit: days + description: The age of the food source host organim. Depending on the type of host organism, age may be more appropriate to report in days, weeks, or years + title: food source age + comments: + - ISO 8601 period or measurement value? + examples: + - value: 6 months + keywords: + - age + - food + - source + slot_uri: MIXS:0001251 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + food_trace_list: + description: The FDA is proposing to establish additional traceability recordkeeping requirements (beyond what is already required in existing regulations) for persons who manufacture, process, pack, or hold foods the Agency has designated for inclusion on the Food Traceability List. The Food Traceability List (FTL) identifies the foods for which the additional traceability records described in the proposed rule would be required. The term Food Traceability List (FTL) refers not only to the foods specifically listed (https://www.fda.gov/media/142303/download), but also to any foods that contain listed foods as ingredients + title: food traceability list category + examples: + - value: tropical tree fruits + keywords: + - food + slot_uri: MIXS:0001214 + range: FoodTraceListEnum + food_trav_mode: + description: A descriptor for the method of movement of food commodity along the food distribution system. This field accepts terms listed under travel mode (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes + title: food shipping transportation method + examples: + - value: train travel [GENEPIO:0001060] + keywords: + - food + - method + - transport + slot_uri: MIXS:0001137 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + food_trav_vehic: + annotations: + Expected_value: ENVO:01000604 + description: A descriptor for the mobile machine which is used to transport food commodities along the food distribution system. This field accepts terms listed under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes + title: food shipping transportation vehicle + examples: + - value: aircraft [ENVO:01001488]|car [ENVO:01000605] + keywords: + - food + - transport + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001138 + multivalued: true + food_treat_proc: + annotations: + Expected_value: FOODON:03460111 + description: Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned. This fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111) + title: food treatment process + examples: + - value: gluten removal process [FOODON:03460750] + keywords: + - food + - process + - treatment + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001140 + multivalued: true + freq_clean: + description: The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually + title: frequency of cleaning + examples: + - value: Daily + keywords: + - frequency + slot_uri: MIXS:0000226 + range: FreqCleanEnum + freq_cook: + description: The number of times a meal is cooked per week + title: frequency of cooking + keywords: + - frequency + slot_uri: MIXS:0000227 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + fungicide_regm: + annotations: + Preferred_unit: gram, mole per liter, milligram per liter + description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens + title: fungicide regimen + examples: + - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + slot_uri: MIXS:0000557 + range: string + multivalued: true + furniture: + description: The types of furniture present in the sampled room + title: furniture + examples: + - value: chair + slot_uri: MIXS:0000807 + range: FurnitureEnum + gaseous_environment: + annotations: + Preferred_unit: micromole per liter + description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens + title: gaseous environment + examples: + - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - environment + slot_uri: MIXS:0000558 + range: string + multivalued: true + gaseous_substances: + annotations: + Expected_value: gaseous substance name;measurement value + Preferred_unit: micromole per liter + description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + title: gaseous substances + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000661 + multivalued: true + gastrointest_disord: + description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77) + title: gastrointestinal tract disorder + keywords: + - disorder + slot_uri: MIXS:0000280 + range: string + multivalued: true + gender_restroom: + description: The gender type of the restroom + title: gender of restroom + examples: + - value: male + slot_uri: MIXS:0000808 + range: GenderRestroomEnum + genetic_mod: + annotations: + Expected_value: PMID, DOI, URL or text + description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection + title: genetic modification + examples: + - value: aox1A transgenic + string_serialization: '{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0000859 + geo_loc_name: + description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ) + title: geographic location (country and/or sea,region) + examples: + - value: 'USA: Maryland, Bethesda' + in_subset: + - environment + keywords: + - geographic + - location + slot_uri: MIXS:0000010 + range: string + required: true + pattern: '^.*: .*, .*$' + structured_pattern: + syntax: '^{text}: {text}, {text}$' + interpolated: true + partial_match: true + gestation_state: + description: Specification of the gestation state + title: amniotic fluid/gestation state + slot_uri: MIXS:0000272 + range: string + glucosidase_act: + annotations: + Preferred_unit: mol per liter per hour + description: Measurement of glucosidase activity + title: glucosidase activity + examples: + - value: 5 mol per liter per hour + slot_uri: MIXS:0000137 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + gravidity: + description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used + title: gravidity + examples: + - value: yes;due date:2018-05-11 + string_serialization: '{boolean};{timestamp}' + slot_uri: MIXS:0000875 + gravity: + annotations: + Expected_value: gravity factor value;treatment interval and duration + Preferred_unit: meter per square second, g + description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments + title: gravity + examples: + - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000559 + multivalued: true + growth_facil: + annotations: + Expected_value: free text or CO + description: 'Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' + title: growth facility + examples: + - value: Growth chamber [CO_715:0000189] + keywords: + - facility + - growth + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001043 + growth_habit: + description: Characteristic shape, appearance or growth form of a plant species + title: growth habit + examples: + - value: spreading + keywords: + - growth + slot_uri: MIXS:0001044 + range: GrowthHabitEnum + growth_hormone_regm: + annotations: + Expected_value: growth hormone name;growth hormone amount;treatment interval and duration + Preferred_unit: gram, mole per liter, milligram per liter + description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens + title: growth hormone regimen + examples: + - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - growth + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000560 + multivalued: true + growth_medium: + description: A liquid or gel containing nutrients, salts, and other factors formulated to support the growth of microorganisms, cells, or plants (National Cancer Institute Thesaurus). The name of the medium used to grow the microorganism + title: growth medium + examples: + - value: LB broth + keywords: + - growth + slot_uri: MIXS:0001108 + range: string + gynecologic_disord: + description: History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229) + title: gynecological disorder + keywords: + - disorder + slot_uri: MIXS:0000288 + range: string + multivalued: true + hall_count: + description: The total count of hallways and cooridors in the built structure + title: hallway/corridor count + keywords: + - corridor + - count + - hallway + slot_uri: MIXS:0000228 + range: integer + handidness: + description: The handidness of the individual sampled + title: handidness + examples: + - value: right handedness + slot_uri: MIXS:0000809 + range: HandidnessEnum + hc_produced: + description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field + title: hydrocarbon type produced + examples: + - value: Gas + keywords: + - hydrocarbon + - type + slot_uri: MIXS:0000989 + range: HcProducedEnum + required: true + hcr: + description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field + title: hydrocarbon resource type + examples: + - value: Oil Sand + keywords: + - hydrocarbon + - resource + - type + slot_uri: MIXS:0000988 + range: HcrEnum + required: true + hcr_fw_salinity: + annotations: + Preferred_unit: milligram per liter + description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + title: formation water salinity + keywords: + - salinity + - water + slot_uri: MIXS:0000406 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + hcr_geol_age: + description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' + title: hydrocarbon resource geological age + examples: + - value: Silurian + keywords: + - age + - hydrocarbon + - resource + slot_uri: MIXS:0000993 + range: GeolAgeEnum + recommended: true + hcr_pressure: + annotations: + Preferred_unit: atmosphere, kilopascal + description: Original pressure of the hydrocarbon resource + title: hydrocarbon resource original pressure + keywords: + - hydrocarbon + - pressure + - resource + slot_uri: MIXS:0000395 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true + hcr_temp: + annotations: + Preferred_unit: degree Celsius + description: Original temperature of the hydrocarbon resource + title: hydrocarbon resource original temperature + examples: + - value: 150-295 degree Celsius + keywords: + - hydrocarbon + - resource + - temperature + slot_uri: MIXS:0000393 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true + heat_cool_type: + description: Methods of conditioning or heating a room or building + title: heating and cooling system type + examples: + - value: heat pump + keywords: + - type + slot_uri: MIXS:0000766 + range: HeatCoolTypeEnum + required: true + multivalued: true + heat_deliv_loc: + description: The location of heat delivery within the room + title: heating delivery locations + examples: + - value: north + keywords: + - delivery + - location + - locations + slot_uri: MIXS:0000810 + range: CompassDirections8Enum + heat_sys_deliv_meth: + description: The method by which the heat is delivered through the system + title: heating system delivery method + examples: + - value: radiant + keywords: + - delivery + - method + slot_uri: MIXS:0000812 + range: HeatSysDelivMethEnum + heat_system_id: + description: The heating system identifier + title: heating system identifier + keywords: + - identifier + slot_uri: MIXS:0000833 + range: integer + heavy_metals: + annotations: + Expected_value: heavy metal name;measurement value unit + Preferred_unit: microgram per gram + description: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field + title: extreme_unusual_properties/heavy metals + examples: + - value: mercury;0.09 micrograms per gram + keywords: + - extreme + - properties + - unusual + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000652 + multivalued: true + heavy_metals_meth: + description: Reference or method used in determining heavy metals + title: extreme_unusual_properties/heavy metals method + keywords: + - extreme + - method + - properties + - unusual + slot_uri: MIXS:0000343 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + height_carper_fiber: + annotations: + Preferred_unit: centimeter + description: The average carpet fiber height in the indoor environment + title: height carpet fiber mat + keywords: + - height + slot_uri: MIXS:0000167 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + herbicide_regm: + annotations: + Preferred_unit: gram, mole per liter, milligram per liter + description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + title: herbicide regimen + examples: + - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + slot_uri: MIXS:0000561 + range: string + multivalued: true + horizon_meth: + description: Reference or method used in determining the horizon + title: horizon method + keywords: + - horizon + - method + slot_uri: MIXS:0000321 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + host_age: + annotations: + Preferred_unit: year, day, hour + description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees + title: host age + keywords: + - age + - host + - host. + slot_uri: MIXS:0000255 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_body_habitat: + description: Original body habitat where the sample was obtained from + title: host body habitat + keywords: + - body + - habitat + - host + - host. + slot_uri: MIXS:0000866 + range: string + host_body_mass_index: + annotations: + Preferred_unit: kilogram per square meter + description: Body mass index, calculated as weight/(height)squared + title: host body-mass index + examples: + - value: 22 kilogram per square meter + keywords: + - host + - host. + slot_uri: MIXS:0000317 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_body_product: + annotations: + Expected_value: FMA or UBERON + description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. Use terms from the foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) + title: host body product + examples: + - value: mucus [FMA:66938] + keywords: + - body + - host + - host. + - product + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000888 + host_body_site: + annotations: + Expected_value: FMA or UBERON + description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). Use terms from the foundational model of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON) + title: host body site + keywords: + - body + - host + - site + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000867 + host_body_temp: + annotations: + Preferred_unit: degree Celsius + description: Core body temperature of the host when sample was collected + title: host body temperature + keywords: + - body + - host + - host. + - temperature + slot_uri: MIXS:0000274 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_cellular_loc: + description: 'The localization of the symbiotic host organism within the host from which it was sampled: e.g. intracellular if the symbiotic host organism is localized within the cells or extracellular if the symbiotic host organism is localized outside of cells' + title: host cellular location + examples: + - value: extracellular + keywords: + - host + - host. + - location + slot_uri: MIXS:0001313 + range: HostCellularLocEnum + recommended: true + host_color: + description: The color of host + title: host color + keywords: + - host + - host. + slot_uri: MIXS:0000260 + range: string + host_common_name: + annotations: + Preferred_unit: '' + description: Common name of the host + title: host common name + keywords: + - host + - host. + slot_uri: MIXS:0000248 + range: string + host_dependence: + description: Type of host dependence for the symbiotic host organism to its host + title: host dependence + examples: + - value: obligate + keywords: + - host + - host. + slot_uri: MIXS:0001315 + range: HostDependenceEnum + required: true + host_diet: + description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types + title: host diet + keywords: + - diet + - host + - host. + slot_uri: MIXS:0000869 + range: string + multivalued: true + host_disease_stat: + annotations: + Expected_value: disease name or Disease Ontology term + description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + title: host disease status + in_subset: + - nucleic acid sequence source + keywords: + - disease + - host + - host. + - status + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0000031 + host_dry_mass: + annotations: + Preferred_unit: kilogram, gram + description: Measurement of dry mass + title: host dry mass + examples: + - value: 500 gram + keywords: + - dry + - host + - host. + - mass + slot_uri: MIXS:0000257 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_fam_rel: + annotations: + Expected_value: relationship type;arbitrary identifier + description: Relationships to other hosts in the same study; can include multiple relationships + title: host family relationship + keywords: + - family + - host + - host. + - relationship + string_serialization: '{text};{text}' + slot_uri: MIXS:0000872 + multivalued: true + host_genotype: + description: Observed genotype + title: host genotype + keywords: + - host + - host. + slot_uri: MIXS:0000365 + range: string + host_growth_cond: + description: Literature reference giving growth conditions of the host + title: host growth conditions + examples: + - value: https://academic.oup.com/icesjms/article/68/2/349/617247 + keywords: + - condition + - growth + - host + - host. + slot_uri: MIXS:0000871 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|.*$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + host_height: + annotations: + Preferred_unit: centimeter, millimeter, meter + description: The height of subject + title: host height + keywords: + - height + - host + - host. + slot_uri: MIXS:0000264 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_hiv_stat: + annotations: + Expected_value: HIV status;HAART initiation status + description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] + title: host HIV status + examples: + - value: yes;yes + keywords: + - host + - host. + - status + string_serialization: '{boolean};{boolean}' + slot_uri: MIXS:0000265 + host_infra_spec_name: + description: Taxonomic information about the host below subspecies level + title: host infra-specific name + keywords: + - host + - host. + slot_uri: MIXS:0000253 + range: string + host_infra_spec_rank: + description: Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc + title: host infra-specific rank + keywords: + - host + - host. + - rank + slot_uri: MIXS:0000254 + range: string + host_last_meal: + annotations: + Expected_value: content;duration + description: Content of last meal and time since feeding; can include multiple values + title: host last meal + keywords: + - host + - host. + string_serialization: '{text};{duration}' + slot_uri: MIXS:0000870 + multivalued: true + host_length: + annotations: + Preferred_unit: centimeter, millimeter, meter + description: The length of subject + title: host length + examples: + - value: 1 meter + keywords: + - host + - host. + - length + slot_uri: MIXS:0000256 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_life_stage: + annotations: + Expected_value: stage + description: Description of life stage of host + title: host life stage + keywords: + - host + - host. + - life + slot_uri: MIXS:0000251 + range: string + host_number: + annotations: + Expected_value: count + description: Number of symbiotic host individuals pooled at the time of collection + title: host number individual + examples: + - value: '3' + keywords: + - host + - host. + - number + string_serialization: '{float} m' + slot_uri: MIXS:0001305 + host_occupation: + description: Most frequent job performed by subject + title: host occupation + comments: + - Couldn't convert host_occupation with value veterinary to integer + - almost all host_occupation values in the NCBI biosample_set are strings, not integers + examples: + - value: veterinary + keywords: + - host + - host. + slot_uri: MIXS:0000896 + range: string + host_of_host_coinf: + annotations: + Expected_value: species name of coinfecting organism(s) + description: The taxonomic name of any coinfecting organism observed in a symbiotic relationship with the host of the sampled host organism. e.g. where a sample collected from a host trematode species (A) which was collected from a host_of_host fish (B) that was also infected with a nematode (C), the value here would be (C) the nematode {species name} or {common name}. Multiple co-infecting species may be added in a comma-separated list. For listing symbiotic organisms associated with the host (A) use the term Observed host symbiont + title: observed coinfecting organisms in host of host + examples: + - value: Maritrema novaezealandense + keywords: + - host + - host. + - observed + - organism + slot_uri: MIXS:0001310 + range: string + host_of_host_disease: + annotations: + Expected_value: disease name or Disease Ontology term + description: List of diseases with which the host of the symbiotic host organism has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + title: host of the symbiotic host disease status + examples: + - value: rabies [DOID:11260] + keywords: + - disease + - host + - host. + - status + - symbiosis + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0001319 + multivalued: true + host_of_host_env_loc: + annotations: + Expected_value: UBERON term(s), multiple values can be separated by pipes + description: For a symbiotic host organism the local anatomical environment within its host may have causal influences. Report the anatomical entity(s) which are in the direct environment of the symbiotic host organism being sampled and which you believe have significant causal influences on your sample or specimen. For example, if the symbiotic host organism being sampled is an intestinal worm, its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/) + title: host of the symbiotic host local environmental context + examples: + - value: small intestine[uberon:0002108] + keywords: + - context + - environmental + - host + - host. + - symbiosis + string_serialization: small intestine [UBERON:0002108] + slot_uri: MIXS:0001325 + multivalued: true + host_of_host_env_med: + annotations: + Expected_value: An ontology term for a material such as a tissue type or excreted substance + description: 'Report the environmental material(s) immediately surrounding the symbiotic host organism at the time of sampling. This usually will be a tissue or substance type from the host, but may be another material if the symbiont is external to the host. We recommend using classes from the UBERON ontology, but subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483) may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. intestines, heart).MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. intestines, heart)' + title: host of the symbiotic host environemental medium + examples: + - value: feces[uberon:0001988] + keywords: + - environmental + - host + - host. + - symbiosis + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0001326 + host_of_host_fam_rel: + annotations: + Expected_value: relationship type;arbitrary identifier + description: Familial relationship of the host of the symbiotic host organisms to other hosts of symbiotic host organism in the same study; can include multiple relationships + title: host of the symbiotic host family relationship + keywords: + - family + - host + - host. + - relationship + - symbiosis + string_serialization: '{text};{text}' + slot_uri: MIXS:0001328 + multivalued: true + host_of_host_geno: + description: Observed genotype of the host of the symbiotic host organism + title: host of the symbiotic host genotype + keywords: + - host + - host. + - symbiosis + slot_uri: MIXS:0001331 + range: string + host_of_host_gravid: + annotations: + Expected_value: gravidity status;timestamp + description: Whether or not the host of the symbiotic host organism is gravid, and if yes date due or date post-conception, specifying which is used + title: host of the symbiotic host gravidity + keywords: + - host + - host. + - symbiosis + string_serialization: '{boolean};{timestamp}' + slot_uri: MIXS:0001333 + host_of_host_infname: + description: Taxonomic name information of the host of the symbiotic host organism below subspecies level + title: host of the symbiotic host infra-specific name + keywords: + - host + - host. + - symbiosis + slot_uri: MIXS:0001329 + range: string + host_of_host_infrank: + description: Taxonomic rank information about the host of the symbiotic host organism below subspecies level, such as variety, form, rank etc + title: host of the symbiotic host infra-specific rank + keywords: + - host + - host. + - rank + - symbiosis + slot_uri: MIXS:0001330 + range: string + host_of_host_name: + description: Common name of the host of the symbiotic host organism + title: host of the symbiotic host common name + examples: + - value: snail + keywords: + - host + - host. + - symbiosis + slot_uri: MIXS:0001324 + range: string + host_of_host_pheno: + annotations: + Expected_value: phenotype of the host of the symbiotic organism; PATO + description: Phenotype of the host of the symbiotic host organism. For phenotypic quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato + title: host of the symbiotic host phenotype + keywords: + - host + - host. + - symbiosis + string_serialization: '{term}' + slot_uri: MIXS:0001332 + host_of_host_sub_id: + description: 'A unique identifier by which each host of the symbiotic host organism subject can be referred to, de-identified, e.g. #H14' + title: host of the symbiotic host subject id + examples: + - value: H3 + keywords: + - host + - host. + - identifier + - symbiosis + slot_uri: MIXS:0001327 + range: string + host_of_host_taxid: + annotations: + Expected_value: NCBI taxon identifier of the host of the symbiotic taxon organism + description: NCBI taxon id of the host of the symbiotic host organism + title: host of the symbiotic host taxon id + examples: + - value: '145637' + keywords: + - host + - host. + - identifier + - symbiosis + - taxon + string_serialization: '{integer}' + slot_uri: MIXS:0001306 + host_of_host_totmass: + description: Total mass of the host of the symbiotic host organism at collection, the unit depends on the host + title: host of the symbiotic host total mass + keywords: + - host + - host. + - mass + - symbiosis + - total + slot_uri: MIXS:0001334 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_phenotype: + annotations: + Expected_value: PATO or HP + description: Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP) + title: host phenotype + keywords: + - host + - host. + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000874 + host_pred_appr: + description: Tool or approach used for host prediction + title: host prediction approach + examples: + - value: CRISPR spacer match + in_subset: + - sequencing + keywords: + - host + - host. + - predict + slot_uri: MIXS:0000088 + range: HostPredApprEnum + host_pred_est_acc: + description: For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature + title: host prediction estimated accuracy + examples: + - value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)' + in_subset: + - sequencing + keywords: + - host + - host. + - predict + slot_uri: MIXS:0000089 + range: string + host_pulse: + annotations: + Preferred_unit: beats per minute + description: Resting pulse, measured as beats per minute + title: host pulse + examples: + - value: 65 beats per minute + keywords: + - host + - host. + slot_uri: MIXS:0000333 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_sex: + annotations: + Expected_value: enumeration + description: Gender or physical sex of the host + title: host sex + comments: + - example of non-binary from Excel sheets does not match any of the enumerated values + keywords: + - host + - host. + string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender (female to male)|transgender (male to female) + + |undeclared]' + slot_uri: MIXS:0000811 + host_shape: + description: Morphological shape of host + title: host shape + examples: + - value: round + keywords: + - host + - host. + slot_uri: MIXS:0000261 + range: string + host_spec_range: + annotations: + Expected_value: NCBI taxid + description: The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier + title: host specificity or range + examples: + - value: '9606' + in_subset: + - nucleic acid sequence source + keywords: + - host + - host. + - range + string_serialization: '{integer}' + slot_uri: MIXS:0000030 + multivalued: true + host_specificity: + description: 'Level of specificity of symbiont-host interaction: e.g. generalist (symbiont able to establish associations with distantly related hosts) or species-specific' + title: host specificity + examples: + - value: species-specific + keywords: + - host + - host. + slot_uri: MIXS:0001308 + range: HostSpecificityEnum + recommended: true + host_subject_id: + description: A unique identifier by which each subject can be referred to, de-identified + title: host subject id + keywords: + - host + - host. + - identifier + slot_uri: MIXS:0000861 + range: string + host_subspecf_genlin: + annotations: + Expected_value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar + description: Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123 + title: host subspecific genetic lineage + examples: + - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' + keywords: + - host + - host. + - lineage + string_serialization: '{rank name}:{text}' + slot_uri: MIXS:0001318 + multivalued: true + host_substrate: + description: The growth substrate of the host + title: host substrate + examples: + - value: rock + keywords: + - host + - host. + slot_uri: MIXS:0000252 + range: string + host_symbiont: + annotations: + Expected_value: species name or common name + description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite) + title: observed host symbionts + keywords: + - host + - host. + - observed + - symbiosis + slot_uri: MIXS:0001298 + range: string + multivalued: true + host_taxid: + annotations: + Expected_value: NCBI taxon identifier + description: NCBI taxon id of the host, e.g. 9606 + title: host taxid + keywords: + - host + - host. + - taxon + slot_uri: MIXS:0000250 + host_tot_mass: + annotations: + Preferred_unit: kilogram, gram + description: Total mass of the host at collection, the unit depends on host + title: host total mass + keywords: + - host + - host. + - mass + - total + slot_uri: MIXS:0000263 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_wet_mass: + annotations: + Preferred_unit: kilogram, gram + description: Measurement of wet mass + title: host wet mass + examples: + - value: 1500 gram + keywords: + - host + - host. + - mass + - wet + slot_uri: MIXS:0000567 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + hrt: + description: Whether subject had hormone replacement theraphy, and if yes start date + title: HRT + examples: + - value: '2013-03-25T12:42:31+01:00' + slot_uri: MIXS:0000969 + range: datetime + humidity: + description: Amount of water vapour in the air, at the time of sampling + title: humidity + keywords: + - humidity + slot_uri: MIXS:0000100 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + humidity_regm: + annotations: + Expected_value: humidity value;treatment interval and duration + Preferred_unit: gram per cubic meter + description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + title: humidity regimen + examples: + - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - humidity + - regimen + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000568 + multivalued: true + hygienic_area: + annotations: + Expected_value: Expected value + description: The subdivision of areas within a food production facility according to hygienic requirements. This field accepts terms listed under hygienic food production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that most accurately indicates the hygienic area your sample was taken from according to the definitions provided + title: hygienic food production area + examples: + - value: Low Hygiene Area + keywords: + - area + - food + - production + slot_uri: MIXS:0001253 + range: string + hysterectomy: + description: Specification of whether hysterectomy was performed + title: hysterectomy + examples: + - value: 'no' + slot_uri: MIXS:0000287 + range: boolean + ihmc_medication_code: + description: Can include multiple medication codes + title: IHMC medication code + examples: + - value: '810' + keywords: + - code + slot_uri: MIXS:0000884 + range: integer + multivalued: true + indoor_space: + description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + title: indoor space + examples: + - value: foyer + keywords: + - indoor + slot_uri: MIXS:0000763 + range: IndoorSpaceEnum + required: true + indoor_surf: + description: Type of indoor surface + title: indoor surface + examples: + - value: wall + keywords: + - indoor + - surface + slot_uri: MIXS:0000764 + range: IndoorSurfEnum + indust_eff_percent: + annotations: + Preferred_unit: percentage + description: Percentage of industrial effluents received by wastewater treatment plant + title: industrial effluent percent + keywords: + - percent + slot_uri: MIXS:0000662 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + inorg_particles: + annotations: + Expected_value: inorganic particle name;measurement value + Preferred_unit: mole per liter, milligram per liter + description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + title: inorganic particles + keywords: + - inorganic + - particle + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000664 + multivalued: true + inside_lux: + annotations: + Preferred_unit: kilowatt per square metre + description: The recorded value at sampling time (power density) + title: inside lux light + keywords: + - inside + - light + slot_uri: MIXS:0000168 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + int_wall_cond: + description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas + title: interior wall condition + examples: + - value: damaged + keywords: + - condition + - interior + - wall + slot_uri: MIXS:0000813 + range: DamagedEnum + intended_consumer: + annotations: + Expected_value: FOODON_03510136 or NCBI taxid + description: Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid + title: intended consumer + examples: + - value: 9606 o rsenior as food consumer [FOODON:03510254] + keywords: + - consumer + string_serialization: '{integer}|{termLabel} [{termID}]' + slot_uri: MIXS:0001144 + multivalued: true + isol_growth_condt: + description: Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material + title: isolation and growth condition + examples: + - value: doi:10.1016/j.syapm.2018.01.009 + in_subset: + - nucleic acid sequence source + keywords: + - condition + - growth + - isolation + slot_uri: MIXS:0000003 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + iw_bt_date_well: + description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + title: injection water breakthrough date of specific well + examples: + - value: '2013-03-25T12:42:31+01:00' + keywords: + - date + - water + slot_uri: MIXS:0001010 + range: datetime + iwf: + annotations: + Preferred_unit: percent + description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + title: injection water fraction + comments: + - pattern was "[0-9]*\\.?[0-9]+ ?%" + - percent or float? + examples: + - value: '0.79' + keywords: + - fraction + - water + slot_uri: MIXS:0000455 + range: float + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + kidney_disord: + description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557) + title: urine/kidney disorder + keywords: + - disorder + slot_uri: MIXS:0000277 + range: string + multivalued: true + last_clean: + description: The last time the floor was cleaned (swept, mopped, vacuumed) + title: last time swept/mopped/vacuumed + examples: + - value: '2013-03-25T12:42:31+01:00' + keywords: + - time + slot_uri: MIXS:0000814 + range: datetime + lat_lon: + description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees, limited to 8 decimal points, and in WGS84 system + title: geographic location (latitude and longitude) + examples: + - value: 50.586825 6.408977 + in_subset: + - environment + keywords: + - geographic + - location + slot_uri: MIXS:0000009 + required: true + pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$ + structured_pattern: + syntax: ^{lat} {lon}$ + interpolated: true + partial_match: true + lib_layout: + description: Specify whether to expect single, paired, or other configuration of reads + title: library layout + examples: + - value: paired + in_subset: + - sequencing + keywords: + - library + slot_uri: MIXS:0000041 + range: LibLayoutEnum + lib_reads_seqd: + description: Total number of clones sequenced from the library + title: library reads sequenced + examples: + - value: '20' + in_subset: + - sequencing + keywords: + - library + slot_uri: MIXS:0000040 + range: integer + lib_screen: + annotations: + Expected_value: screening strategy name + description: Specific enrichment or screening methods applied before and/or after creating libraries + title: library screening strategy + examples: + - value: enriched, screened, normalized + in_subset: + - sequencing + keywords: + - library + slot_uri: MIXS:0000043 + range: string + lib_size: + description: Total number of clones in the library prepared for the project + title: library size + examples: + - value: '50' + in_subset: + - sequencing + keywords: + - library + - size + slot_uri: MIXS:0000039 + range: integer + lib_vector: + annotations: + Expected_value: vector + description: Cloning vector type(s) used in construction of libraries + title: library vector + examples: + - value: Bacteriophage P1 + in_subset: + - sequencing + keywords: + - library + slot_uri: MIXS:0000042 + range: string + library_prep_kit: + annotations: + Expected_value: name of library preparation kit + description: Packaged kits (containing adapters, indexes, enzymes, buffers etc.), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids + title: library preparation kit + keywords: + - kit + - library + - preparation + slot_uri: MIXS:0001145 + range: string + light_intensity: + annotations: + Preferred_unit: lux + description: Measurement of light intensity + title: light intensity + examples: + - value: 0.3 lux + keywords: + - intensity + - light + slot_uri: MIXS:0000706 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + light_regm: + annotations: + Expected_value: exposure type;light intensity;light quality + Preferred_unit: lux; micrometer, nanometer, angstrom + description: Information about treatment(s) involving exposure to light, including both light intensity and quality + title: light regimen + examples: + - value: incandescant light;10 lux;450 nanometer + keywords: + - light + - regimen + string_serialization: '{text};{float} {unit};{float} {unit}' + slot_uri: MIXS:0000569 + light_type: + description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light + title: light type + examples: + - value: desk lamp + keywords: + - light + - type + slot_uri: MIXS:0000769 + range: LightTypeEnum + required: true + multivalued: true + link_addit_analys: + description: Link to additional analysis results performed on the sample + title: links to additional analysis + keywords: + - link + slot_uri: MIXS:0000340 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + link_class_info: + annotations: + Expected_value: PMID,DOI or url + description: Link to digitized soil maps or other soil classification information + title: link to classification information + keywords: + - classification + - information + - link + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000329 + link_climate_info: + description: Link to climate resource + title: link to climate information + keywords: + - information + - link + slot_uri: MIXS:0000328 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + lithology: + description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field' + title: lithology + examples: + - value: Volcanic + keywords: + - lithology + slot_uri: MIXS:0000990 + range: LithologyEnum + recommended: true + liver_disord: + description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409) + title: liver disorder + keywords: + - disorder + slot_uri: MIXS:0000282 + range: string + multivalued: true + local_class: + annotations: + Expected_value: local classification name + description: Soil classification based on local soil classification system + title: soil_taxonomic/local classification + keywords: + - classification + slot_uri: MIXS:0000330 + range: string + local_class_meth: + description: Reference or method used in determining the local soil classification + title: soil_taxonomic/local classification method + keywords: + - classification + - method + slot_uri: MIXS:0000331 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + lot_number: + annotations: + Expected_value: lot number, item + description: 'A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. Synonym: Batch Number. The submitter should provide lot number of the item followed by the item name for which the lot number was provided' + title: lot number + examples: + - value: 1239ABC01A, split Cornish hens + keywords: + - number + string_serialization: '{integer}, {text}' + slot_uri: MIXS:0001147 + multivalued: true + mag_cov_software: + description: Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets + title: MAG coverage software + examples: + - value: bbmap + in_subset: + - sequencing + keywords: + - software + slot_uri: MIXS:0000080 + range: MagCovSoftwareEnum + magnesium: + annotations: + Preferred_unit: mole per liter, milligram per liter, parts per million, micromole per kilogram + description: Concentration of magnesium in the sample + title: magnesium + examples: + - value: 52.8 micromole per kilogram + slot_uri: MIXS:0000431 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + maternal_health_stat: + description: Specification of the maternal health status + title: amniotic fluid/maternal health status + keywords: + - status + slot_uri: MIXS:0000273 + range: string + max_occup: + description: The maximum amount of people allowed in the indoor environment + title: maximum occupancy + keywords: + - maximum + slot_uri: MIXS:0000229 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + mean_frict_vel: + annotations: + Preferred_unit: meter per second + description: Measurement of mean friction velocity + title: mean friction velocity + examples: + - value: 0.5 meter per second + keywords: + - mean + - velocity + slot_uri: MIXS:0000498 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + mean_peak_frict_vel: + annotations: + Preferred_unit: meter per second + description: Measurement of mean peak friction velocity + title: mean peak friction velocity + examples: + - value: 1 meter per second + keywords: + - mean + - peak + - velocity + slot_uri: MIXS:0000502 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + mech_struc: + description: 'mechanical structure: a moving structure' + title: mechanical structure + examples: + - value: elevator + slot_uri: MIXS:0000815 + range: MechStrucEnum + mechanical_damage: + annotations: + Expected_value: damage type;body site + description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + title: mechanical damage + examples: + - value: pruning;bark + string_serialization: '{text};{text}' + slot_uri: MIXS:0001052 + multivalued: true + medic_hist_perform: + description: Whether full medical history was collected + title: medical history performed + examples: + - value: '1' + keywords: + - history + slot_uri: MIXS:0000897 + range: boolean + menarche: + description: Date of most recent menstruation + title: menarche + examples: + - value: '2013-03-25T12:42:31+01:00' + slot_uri: MIXS:0000965 + range: datetime + menopause: + description: Date of onset of menopause + title: menopause + examples: + - value: '2013-03-25T12:42:31+01:00' + slot_uri: MIXS:0000968 + range: datetime + methane: + annotations: + Preferred_unit: micromole per liter, parts per billion, parts per million + description: Methane (gas) amount or concentration at the time of sampling + title: methane + slot_uri: MIXS:0000101 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + micro_biomass_meth: + description: Reference or method used in determining microbial biomass + title: microbial biomass method + comments: + - slot name/scn was microbial_biomass_meth + examples: + - value: http://dx.doi.org/10.1016/j.soilbio.2005.01.021 + keywords: + - biomass + - method + - microbial + slot_uri: MIXS:0000339 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + microb_cult_med: + description: A culture medium used to select for, grow, and maintain prokaryotic microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) forms. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the culture medium + title: microbiological culture medium + examples: + - value: brain heart infusion agar [MICRO:0000566] + keywords: + - culture + - microbiological + slot_uri: MIXS:0001216 + range: string + pattern: ^.*|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + microb_start: + annotations: + Expected_value: FOODON:03544453 + description: Any type of microorganisms used in food production. This field accepts terms listed under live organisms for food production (http://purl.obolibrary.org/obo/FOODON_0344453) + title: microbial starter + examples: + - value: starter cultures [FOODON:03544454] + keywords: + - microbial + string_serialization: '{term label} [{termID}]|{text}' + slot_uri: MIXS:0001217 + microb_start_count: + annotations: + Expected_value: organism name; measurement value; enumeration + Preferred_unit: colony forming units per milliliter; colony forming units per gram of dry weight + description: 'Total cell count of starter culture per gram, volume or area of sample and the method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should also be provided. (example : total prokaryotes; 3.5e7 cells per ml; qPCR)' + title: microbial starter organism count + examples: + - value: total prokaryotes;3.5e9 colony forming units per milliliter;spread plate + keywords: + - count + - microbial + - organism + string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|spread plate|other]' + slot_uri: MIXS:0001218 + microb_start_inoc: + annotations: + Preferred_unit: milligram or gram + description: The amount of starter culture used to inoculate a new batch + title: microbial starter inoculation + examples: + - value: 100 milligrams + keywords: + - microbial + slot_uri: MIXS:0001219 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + microb_start_prep: + description: Information about the protocol or method used to prepare the starter inoculum + title: microbial starter preparation + examples: + - value: liquid starter culture, propagated 3 cycles in milk prior to inoculation + keywords: + - microbial + - preparation + slot_uri: MIXS:0001220 + range: string + microb_start_source: + description: The source from which the microbial starter culture was sourced. If commercially supplied, list supplier + title: microbial starter source + examples: + - value: backslopped, GetCulture + keywords: + - microbial + - source + slot_uri: MIXS:0001221 + range: string + microb_start_taxID: + description: Please include Genus species and strain ID, if known of microorganisms used in food production. For complex communities, pipes can be used to separate two or more microbes + title: microbial starter NCBI taxonomy ID + examples: + - value: Lactobacillus rhamnosus [NCIT:C123495] + keywords: + - identifier + - microbial + - ncbi + - taxon + slot_uri: MIXS:0001222 + range: string + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + microbial_biomass: + annotations: + Preferred_unit: ton, kilogram, gram per kilogram soil + description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units + title: microbial biomass + keywords: + - biomass + - microbial + slot_uri: MIXS:0000650 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + mid: + description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + title: multiplex identifiers + examples: + - value: GTGAATAT + in_subset: + - sequencing + keywords: + - identifier + slot_uri: MIXS:0000047 + range: string + pattern: ^[ACGTRKSYMWBHDVN]+$ + structured_pattern: + syntax: ^{ambiguous_nucleotides}$ + interpolated: true + partial_match: true + mineral_nutr_regm: + annotations: + Expected_value: mineral nutrient name;mineral nutrient amount;treatment interval and duration + Preferred_unit: gram, mole per liter, milligram per liter + description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens + title: mineral nutrient regimen + examples: + - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - mineral + - nutrient + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000570 + multivalued: true + misc_param: + annotations: + Expected_value: parameter name;measurement value + description: Any other measurement performed or parameter collected, that is not listed here + title: miscellaneous parameter + examples: + - value: Bicarbonate ion concentration;2075 micromole per kilogram + keywords: + - parameter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000752 + multivalued: true + mode_transmission: + description: The process through which the symbiotic host organism entered the host from which it was sampled + title: mode of transmission + examples: + - value: horizontal:castrator + slot_uri: MIXS:0001312 + range: ModeTransmissionEnum + recommended: true + n_alkanes: + annotations: + Expected_value: n-alkane name;measurement value + description: Concentration of n-alkanes; can include multiple n-alkanes + title: n-alkanes + examples: + - value: n-hexadecane;100 milligram per liter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000503 + multivalued: true + neg_cont_type: + annotations: + Expected_value: enumeration or text + description: The substance or equipment used as a negative control in an investigation + title: negative control type + in_subset: + - investigation + keywords: + - type + slot_uri: MIXS:0001321 + range: NegContTypeEnum + recommended: true + nitrate: + annotations: + Preferred_unit: micromole per liter, milligram per liter, parts per million + description: Concentration of nitrate in the sample + title: nitrate + examples: + - value: 65 micromole per liter + keywords: + - nitrate + slot_uri: MIXS:0000425 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + nitrite: + annotations: + Preferred_unit: micromole per liter, milligram per liter, parts per million + description: Concentration of nitrite in the sample + title: nitrite + examples: + - value: 0.5 micromole per liter + keywords: + - nitrite + slot_uri: MIXS:0000426 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + nitro: + annotations: + Preferred_unit: micromole per liter + description: Concentration of nitrogen (total) + title: nitrogen + examples: + - value: 4.2 micromole per liter + keywords: + - nitrogen + slot_uri: MIXS:0000504 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + non_min_nutr_regm: + annotations: + Preferred_unit: gram, mole per liter, milligram per liter + description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens + title: non-mineral nutrient regimen + examples: + - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ + keywords: + - non-mineral + - nutrient + - regimen + slot_uri: MIXS:0000571 + range: string + multivalued: true + nose_mouth_teeth_throat_disord: + description: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974) + title: nose/mouth/teeth/throat disorder + keywords: + - disorder + slot_uri: MIXS:0000283 + range: string + multivalued: true + nose_throat_disord: + description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974) + title: nose throat disorder + keywords: + - disorder + slot_uri: MIXS:0000270 + range: string + multivalued: true + nucl_acid_amp: + description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids + title: nucleic acid amplification + examples: + - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ + in_subset: + - sequencing + slot_uri: MIXS:0000038 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + nucl_acid_ext: + description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample + title: nucleic acid extraction + examples: + - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf + in_subset: + - sequencing + slot_uri: MIXS:0000037 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + nucl_acid_ext_kit: + annotations: + Expected_value: The name of an extraction kit + description: The name of the extraction kit used to recover the nucleic acid fraction of an input material is performed + title: nucleic acid extraction kit + examples: + - value: Qiagen PowerSoil Kit + keywords: + - kit + slot_uri: MIXS:0001223 + range: string + multivalued: true + num_replicons: + annotations: + Expected_value: 'for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments' + description: Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote + title: number of replicons + examples: + - value: '2' + in_subset: + - nucleic acid sequence source + keywords: + - number + string_serialization: '{integer}' + slot_uri: MIXS:0000022 + range: integer + num_samp_collect: + description: The number of samples collected during the current sampling event + title: number of samples collected + examples: + - value: 116 samples + keywords: + - number + - sample + slot_uri: MIXS:0001224 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + number_contig: + description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG + title: number of contigs + examples: + - value: '40' + in_subset: + - sequencing + keywords: + - number + slot_uri: MIXS:0000060 + range: integer + number_pets: + description: The number of pets residing in the sampled space + title: number of pets + keywords: + - number + slot_uri: MIXS:0000231 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + number_plants: + description: The number of plant(s) in the sampling space + title: number of houseplants + keywords: + - number + slot_uri: MIXS:0000230 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + number_resident: + description: The number of individuals currently occupying in the sampling location + title: number of residents + keywords: + - number + slot_uri: MIXS:0000232 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + occup_density_samp: + description: Average number of occupants at time of sampling per square footage + title: occupant density at sampling + examples: + - value: '0.1' + keywords: + - density + slot_uri: MIXS:0000217 + range: float + required: true + occup_document: + description: The type of documentation of occupancy + title: occupancy documentation + examples: + - value: estimate + keywords: + - documentation + slot_uri: MIXS:0000816 + range: OccupDocumentEnum + occup_samp: + description: Number of occupants present at time of sample within the given space + title: occupancy at sampling + examples: + - value: '10' + slot_uri: MIXS:0000772 + range: float + required: true + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + org_carb: + description: Concentration of organic carbon + title: organic carbon + examples: + - value: 1.5 microgram per liter + keywords: + - carbon + - organic + slot_uri: MIXS:0000508 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + org_count_qpcr_info: + annotations: + Expected_value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles + Preferred_unit: number of cells per gram (or ml or cm^2) + description: 'If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)' + title: organism count qPCR information + keywords: + - count + - information + - organism + string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles' + slot_uri: MIXS:0000099 + org_matter: + annotations: + Preferred_unit: microgram per liter + description: Concentration of organic matter + title: organic matter + examples: + - value: 1.75 milligram per cubic meter + keywords: + - organic + slot_uri: MIXS:0000204 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + org_nitro: + description: Concentration of organic nitrogen + title: organic nitrogen + examples: + - value: 4 micromole per liter + keywords: + - nitrogen + - organic + slot_uri: MIXS:0000205 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + org_particles: + annotations: + Expected_value: particle name;measurement value + Preferred_unit: gram per liter + description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc + title: organic particles + keywords: + - organic + - particle + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000665 + multivalued: true + organism_count: + annotations: + Expected_value: organism name;measurement value;enumeration + description: 'Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' + title: organism count + keywords: + - count + - organism + string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]' + slot_uri: MIXS:0000103 + multivalued: true + otu_class_appr: + annotations: + Expected_value: cutoffs and method used + description: Cutoffs and approach used when clustering species-level OTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside OTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis + title: OTU classification approach + examples: + - value: 95% ANI;85% AF; greedy incremental clustering + in_subset: + - sequencing + keywords: + - classification + - otu + string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}' + slot_uri: MIXS:0000085 + otu_db: + annotations: + Expected_value: database and version + description: Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" OTUs, if any + title: OTU database + examples: + - value: NCBI Viral RefSeq;83 + in_subset: + - sequencing + keywords: + - database + - otu + string_serialization: '{database};{version}' + slot_uri: MIXS:0000087 + otu_seq_comp_appr: + annotations: + Expected_value: software name, version and relevant parameters + description: Tool and thresholds used to compare sequences when computing "species-level" OTUs + title: OTU sequence comparison approach + examples: + - value: 'blastn;2.6.0+;e-value cutoff: 0.001' + in_subset: + - sequencing + keywords: + - otu + string_serialization: '{software};{version};{parameters}' + slot_uri: MIXS:0000086 + owc_tvdss: + annotations: + Preferred_unit: meter + description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + title: oil water contact depth + keywords: + - depth + - oil + - water + slot_uri: MIXS:0000405 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + oxy_stat_samp: + description: Oxygenation status of sample + title: oxygenation status of sample + examples: + - value: aerobic + keywords: + - oxygen + - sample + - status + slot_uri: MIXS:0000753 + range: OxyStatSampEnum + oxygen: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Oxygen (gas) amount or concentration at the time of sampling + title: oxygen + examples: + - value: 600 parts per million + keywords: + - oxygen + slot_uri: MIXS:0000104 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + part_org_carb: + description: Concentration of particulate organic carbon + title: particulate organic carbon + examples: + - value: 1.92 micromole per liter + keywords: + - carbon + - organic + - particle + - particulate + slot_uri: MIXS:0000515 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + part_org_nitro: + annotations: + Preferred_unit: microgram per liter, micromole per liter + description: Concentration of particulate organic nitrogen + title: particulate organic nitrogen + examples: + - value: 0.3 micromole per liter + keywords: + - nitrogen + - organic + - particle + - particulate + slot_uri: MIXS:0000719 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + part_plant_animal: + annotations: + Expected_value: FOODON:03420116 + description: The anatomical part of the organism being involved in food production or consumption; e.g., a carrot is the root of the plant (root vegetable). This field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116) + title: part of plant or animal + examples: + - value: chuck [FOODON:03530021] + keywords: + - animal + - plant + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001149 + multivalued: true + particle_class: + annotations: + Expected_value: particle name;measurement value + Preferred_unit: micrometer + description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values + title: particle classification + keywords: + - classification + - particle + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000206 + multivalued: true + pathogenicity: + annotations: + Expected_value: names of organisms that the entity is pathogenic to + description: To what is the entity pathogenic + title: known pathogenicity + examples: + - value: human, animal, plant, fungi, bacteria + in_subset: + - nucleic acid sequence source + slot_uri: MIXS:0000027 + range: string + pcr_cond: + annotations: + Expected_value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles + description: Description of reaction conditions and components of polymerase chain reaction performed during library preparation. + title: pcr conditions + examples: + - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 + - value: initial denaturation:94degC_1.5min + in_subset: + - sequencing + keywords: + - condition + - pcr + string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles + slot_uri: MIXS:0000049 + pcr_primers: + annotations: + Expected_value: 'FWD: forward primer sequence;REV:reverse primer sequence' + description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters + title: pcr primers + examples: + - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT + in_subset: + - sequencing + keywords: + - pcr + string_serialization: FWD:{dna};REV:{dna} + slot_uri: MIXS:0000046 + permeability: + annotations: + Expected_value: measurement value range + Preferred_unit: mD + description: 'Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' + title: permeability + string_serialization: '{integer} - {integer} {unit}' + slot_uri: MIXS:0000404 + perturbation: + annotations: + Expected_value: perturbation type name;perturbation interval and duration + description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types + title: perturbation + examples: + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M + keywords: + - perturbation + string_serialization: '{text};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000754 + multivalued: true + pesticide_regm: + annotations: + Preferred_unit: gram, mole per liter, milligram per liter + description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens + title: pesticide regimen + examples: + - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + slot_uri: MIXS:0000573 + range: string + multivalued: true + pet_farm_animal: + annotations: + Expected_value: presence status;type of animal or pet + description: Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present + title: presence of pets or farm animals + examples: + - value: yes; 5 cats + keywords: + - animal + - farm + - presence + string_serialization: '{boolean};{text}' + slot_uri: MIXS:0000267 + multivalued: true + petroleum_hydrocarb: + annotations: + Preferred_unit: micromole per liter + description: Concentration of petroleum hydrocarbon + title: petroleum hydrocarbon + examples: + - value: 0.05 micromole per liter + keywords: + - hydrocarbon + - petroleum + slot_uri: MIXS:0000516 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ph: + description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + title: pH + examples: + - value: '7.2' + keywords: + - ph + slot_uri: MIXS:0001001 + range: float + ph_meth: + description: Reference or method used in determining pH + title: pH method + examples: + - value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf + keywords: + - method + - ph + slot_uri: MIXS:0001106 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + ph_regm: + description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen + title: pH regimen + examples: + - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M + keywords: + - ph + - regimen + slot_uri: MIXS:0001056 + range: string + multivalued: true + phaeopigments: + annotations: + Expected_value: phaeopigment name;measurement value + Preferred_unit: milligram per cubic meter + description: Concentration of phaeopigments; can include multiple phaeopigments + title: phaeopigments + examples: + - value: 2.5 milligram per cubic meter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000180 + multivalued: true + phosphate: + annotations: + Preferred_unit: micromole per liter + description: Concentration of phosphate + title: phosphate + examples: + - value: 0.7 micromole per liter + keywords: + - phosphate + slot_uri: MIXS:0000505 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + phosplipid_fatt_acid: + annotations: + Expected_value: phospholipid fatty acid name;measurement value + description: Concentration of phospholipid fatty acids; can include multiple values + title: phospholipid fatty acid + examples: + - value: 2.98 milligram per liter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000181 + multivalued: true + photon_flux: + annotations: + Preferred_unit: number of photons per second per unit area + description: Measurement of photon flux + title: photon flux + examples: + - value: 3.926 micromole photons per second per square meter + slot_uri: MIXS:0000725 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + photosynt_activ: + annotations: + Preferred_unit: mol m-2 s-1 + description: Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll fluorescence emissions / reflectance / transpiration) Please also include the term method term detailing the method of activity measurement + title: photosynthetic activity + examples: + - value: 0.1 mol CO2 m-2 s-1 + description: added a magnitude to the example from the XLSX file, " mol CO2 m-2 s-1" + slot_uri: MIXS:0001296 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + photosynt_activ_meth: + description: Reference or method used in measurement of photosythetic activity + title: photosynthetic activity method + keywords: + - method + slot_uri: MIXS:0001336 + range: string + recommended: true + multivalued: true + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|.*$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + plant_growth_med: + annotations: + Expected_value: EO or enumeration + description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary + title: plant growth medium + keywords: + - growth + - plant + string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' + slot_uri: MIXS:0001057 + plant_part_maturity: + annotations: + Expected_value: FOODON:03530050 + description: A description of the stage of development of a plant or plant part based on maturity or ripeness. This field accepts terms listed under degree of plant maturity (http://purl.obolibrary.org/obo/FOODON_03530050) + title: degree of plant part maturity + examples: + - value: ripe or mature [FOODON:03530052] + keywords: + - degree + - plant + string_serialization: '{term label}{term ID}' + slot_uri: MIXS:0001120 + plant_product: + annotations: + Expected_value: product name + description: Substance produced by the plant, where the sample was obtained from + title: plant product + examples: + - value: xylem sap [PO:0025539] + keywords: + - plant + - product + slot_uri: MIXS:0001058 + range: string + plant_reprod_crop: + description: Plant reproductive part used in the field during planting to start the crop + title: plant reproductive part + examples: + - value: seedling + keywords: + - plant + slot_uri: MIXS:0001150 + range: PlantReprodCropEnum + multivalued: true + plant_sex: + description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite + title: plant sex + examples: + - value: Hermaphroditic + keywords: + - plant + slot_uri: MIXS:0001059 + range: PlantSexEnum + plant_struc: + description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here + title: plant structure + examples: + - value: epidermis [PO:0005679] + keywords: + - plant + slot_uri: MIXS:0001060 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + plant_water_method: + description: Description of the equipment or method used to distribute water to crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes + title: plant water delivery method + examples: + - value: drip irrigation process [AGRO:00000056] + keywords: + - delivery + - method + - plant + - water + slot_uri: MIXS:0001111 + range: string + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + ploidy: + description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO + title: ploidy + examples: + - value: allopolyploidy [PATO:0001379] + in_subset: + - nucleic acid sequence source + slot_uri: MIXS:0000021 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + pollutants: + annotations: + Expected_value: pollutant name;measurement value + Preferred_unit: gram, mole per liter, milligram per liter, microgram per cubic meter + description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant + title: pollutants + examples: + - value: lead;0.15 microgram per cubic meter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000107 + multivalued: true + pool_dna_extracts: + annotations: + Expected_value: pooling status;number of pooled extracts + Preferred_unit: gram, milliliter, microliter + description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given + title: pooling of DNA extracts (if done) + examples: + - value: yes, 5 + keywords: + - dna + - pooling + slot_uri: MIXS:0000325 + porosity: + annotations: + Expected_value: measurement value or range + Preferred_unit: percentage + description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + title: porosity + keywords: + - porosity + string_serialization: '{float} - {float} {unit}' + slot_uri: MIXS:0000211 + pos_cont_type: + description: The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive + title: positive control type + in_subset: + - investigation + keywords: + - type + string_serialization: '{term} or {text}' + slot_uri: MIXS:0001322 + recommended: true + potassium: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of potassium in the sample + title: potassium + examples: + - value: 463 milligram per liter + slot_uri: MIXS:0000430 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + pour_point: + annotations: + Preferred_unit: degree Celsius + description: 'Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' + title: pour point + slot_uri: MIXS:0000127 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + pre_treatment: + annotations: + Expected_value: pre-treatment type + description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + title: pre-treatment + slot_uri: MIXS:0000348 + range: string + pred_genome_struc: + description: Expected structure of the viral genome + title: predicted genome structure + examples: + - value: non-segmented + in_subset: + - sequencing + keywords: + - predict + slot_uri: MIXS:0000083 + range: PredGenomeStrucEnum + pred_genome_type: + annotations: + Expected_value: enumeration + description: Type of genome predicted for the UViG + title: predicted genome type + examples: + - value: dsDNA + in_subset: + - sequencing + keywords: + - predict + - type + string_serialization: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]' + slot_uri: MIXS:0000082 + pregnancy: + description: Date due of pregnancy + title: pregnancy + examples: + - value: '2013-03-25T12:42:31+01:00' + slot_uri: MIXS:0000966 + range: datetime + pres_animal_insect: + annotations: + Expected_value: enumeration;count + description: The type and number of animals or insects present in the sampling space + title: presence of pets, animals, or insects + examples: + - value: cat;5 + keywords: + - animal + - presence + string_serialization: '[cat|dog|rodent|snake|other];{integer}' + slot_uri: MIXS:0000819 + pressure: + annotations: + Preferred_unit: atmosphere + description: Pressure to which the sample is subject to, in atmospheres + title: pressure + examples: + - value: 50 atmosphere + keywords: + - pressure + slot_uri: MIXS:0000412 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + prev_land_use_meth: + description: Reference or method used in determining previous land use and dates + title: history/previous land use method + keywords: + - history + - land + - method + - use + slot_uri: MIXS:0000316 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + previous_land_use: + annotations: + Expected_value: land use name;date + description: Previous land use and dates + title: history/previous land use + examples: + - value: fallow; 2018-05-11:T14:30Z + keywords: + - history + - land + - use + string_serialization: '{text};{timestamp}' + slot_uri: MIXS:0000315 + primary_prod: + annotations: + Preferred_unit: milligram per cubic meter per day, gram per square meter per day + description: Measurement of primary production, generally measured as isotope uptake + title: primary production + examples: + - value: 100 milligram per cubic meter per day + keywords: + - primary + - production + slot_uri: MIXS:0000728 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + primary_treatment: + annotations: + Expected_value: primary treatment type + description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed + title: primary treatment + keywords: + - primary + - treatment + slot_uri: MIXS:0000349 + range: string + prod_label_claims: + description: Labeling claims containing descriptors such as wild caught, free-range, organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can include more than one term, separated by ";" + title: production labeling claims + examples: + - value: free range + keywords: + - production + slot_uri: MIXS:prod_label_claims + range: string + multivalued: true + prod_rate: + annotations: + Preferred_unit: cubic meter per day + description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + title: production rate + keywords: + - production + - rate + slot_uri: MIXS:0000452 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + prod_start_date: + description: Date of field's first production + title: production start date + examples: + - value: '2013-03-25T12:42:31+01:00' + keywords: + - date + - production + - start + slot_uri: MIXS:0001008 + range: datetime + recommended: true + profile_position: + description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + title: profile position + examples: + - value: summit + slot_uri: MIXS:0001084 + range: ProfilePositionEnum + project_name: + description: Name of the project within which the sequencing was organized + title: project name + examples: + - value: Forest soil metagenome + in_subset: + - investigation + keywords: + - project + slot_uri: MIXS:0000092 + range: string + required: true + propagation: + annotations: + Expected_value: 'for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual; other more specific values (e.g., incompatibility group) are allowed' + description: 'The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual' + title: propagation + examples: + - value: lytic + in_subset: + - nucleic acid sequence source + slot_uri: MIXS:0000033 + range: string + pulmonary_disord: + description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850) + title: lung/pulmonary disorder + keywords: + - disorder + slot_uri: MIXS:0000269 + range: string + multivalued: true + quad_pos: + description: The quadrant position of the sampling room within the building + title: quadrant position + examples: + - value: West side + slot_uri: MIXS:0000820 + range: QuadPosEnum + radiation_regm: + annotations: + Expected_value: radiation type name;radiation amount;treatment interval and duration + Preferred_unit: rad, gray + description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens + title: radiation regimen + examples: + - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000575 + multivalued: true + rainfall_regm: + annotations: + Expected_value: measurement value;treatment interval and duration + Preferred_unit: millimeter + description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + title: rainfall regimen + examples: + - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - rain + - regimen + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000576 + multivalued: true + reactor_type: + annotations: + Expected_value: reactor type name + description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage + title: reactor type + keywords: + - type + slot_uri: MIXS:0000350 + range: string + reassembly_bin: + description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly? + title: reassembly post binning + examples: + - value: 'no' + in_subset: + - sequencing + keywords: + - post + slot_uri: MIXS:0000079 + range: boolean + redox_potential: + annotations: + Preferred_unit: millivolt + description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + title: redox potential + examples: + - value: 300 millivolt + slot_uri: MIXS:0000182 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ref_biomaterial: + description: Primary publication if isolated before genome publication; otherwise, primary genome report + title: reference for biomaterial + examples: + - value: doi:10.1016/j.syapm.2018.01.009 + in_subset: + - nucleic acid sequence source + slot_uri: MIXS:0000025 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + ref_db: + annotations: + Expected_value: names, versions, and references of databases + description: List of database(s) used for ORF annotation, along with version number and reference to website or publication + title: reference database(s) + examples: + - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 + in_subset: + - sequencing + keywords: + - database + string_serialization: '{database};{version};{reference}' + slot_uri: MIXS:0000062 + rel_air_humidity: + annotations: + Preferred_unit: percentage + description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air + title: relative air humidity + comments: + - percent or float? + examples: + - value: '0.8' + keywords: + - air + - humidity + - relative + slot_uri: MIXS:0000121 + range: float + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + rel_humidity_out: + annotations: + Preferred_unit: gram of air, kilogram of air + description: The recorded outside relative humidity value at the time of sampling + title: outside relative humidity + examples: + - value: 12 per kilogram of air + keywords: + - humidity + - relative + slot_uri: MIXS:0000188 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + rel_location: + description: Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road + title: relative location of sample + examples: + - value: furrow + keywords: + - location + - relative + - sample + slot_uri: MIXS:0001161 + range: string + rel_samp_loc: + description: The sampling location within the train car + title: relative sampling location + examples: + - value: center of car + keywords: + - location + - relative + slot_uri: MIXS:0000821 + range: RelSampLocEnum + rel_to_oxygen: + description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments + title: relationship to oxygen + examples: + - value: aerobe + in_subset: + - nucleic acid sequence source + keywords: + - oxygen + - relationship + slot_uri: MIXS:0000015 + range: RelToOxygenEnum + repository_name: + annotations: + Expected_value: Institution + description: The name of the institution where the sample or DNA extract is held or "sample not available" if the sample was used in its entirety for analysis or otherwise not retained + title: repository name + examples: + - value: FDA CFSAN Microbiology Laboratories + slot_uri: MIXS:0001152 + range: string + multivalued: true + reservoir: + description: Name of the reservoir (e.g. Carapebus) + title: reservoir name + slot_uri: MIXS:0000303 + range: string + recommended: true + resins_pc: + annotations: + Preferred_unit: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: resins wt% + slot_uri: MIXS:0000134 + range: string + recommended: true + pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + room_air_exch_rate: + annotations: + Preferred_unit: liter per hour + description: The rate at which outside air replaces indoor air in a given space + title: room air exchange rate + keywords: + - air + - rate + - room + slot_uri: MIXS:0000169 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + room_architec_elem: + description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure + title: room architectural elements + keywords: + - room + slot_uri: MIXS:0000233 + range: string + room_condt: + description: The condition of the room at the time of sampling + title: room condition + examples: + - value: new + keywords: + - condition + - room + slot_uri: MIXS:0000822 + range: RoomCondtEnum + room_connected: + description: List of rooms connected to the sampling room by a doorway + title: rooms connected by a doorway + examples: + - value: office + keywords: + - doorway + - room + slot_uri: MIXS:0000826 + range: RoomConnectedEnum + room_count: + description: The total count of rooms in the built structure including all room types + title: room count + keywords: + - count + - room + slot_uri: MIXS:0000234 + range: integer + room_dim: + annotations: + Expected_value: measurement value + Preferred_unit: meter + description: The length, width and height of sampling room + title: room dimensions + examples: + - value: 4 meter x 4 meter x 4 meter + keywords: + - dimensions + - room + string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' + slot_uri: MIXS:0000192 + room_door_dist: + annotations: + Preferred_unit: meter + description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + title: room door distance + keywords: + - distance + - door + - room + slot_uri: MIXS:0000193 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_door_share: + description: List of room(s) (room number, room name) sharing a door with the sampling room + title: rooms that share a door with sampling room + keywords: + - door + - room + slot_uri: MIXS:0000242 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + room_hallway: + description: List of room(s) (room number, room name) located in the same hallway as sampling room + title: rooms that are on the same hallway + keywords: + - hallway + - room + slot_uri: MIXS:0000238 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + room_loc: + description: The position of the room within the building + title: room location in building + examples: + - value: interior room + keywords: + - location + - room + slot_uri: MIXS:0000823 + range: RoomLocEnum + room_moist_dam_hist: + description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed + title: room moisture damage or mold history + keywords: + - history + - moisture + - room + slot_uri: MIXS:0000235 + range: integer + room_net_area: + annotations: + Preferred_unit: square feet, square meter + description: The net floor area of sampling room. Net area excludes wall thicknesses + title: room net area + keywords: + - area + - room + slot_uri: MIXS:0000194 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_occup: + description: Count of room occupancy at time of sampling + title: room occupancy + keywords: + - room + slot_uri: MIXS:0000236 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_samp_pos: + description: The horizontal sampling position in the room relative to architectural elements + title: room sampling position + examples: + - value: south corner + keywords: + - room + slot_uri: MIXS:0000824 + range: RoomSampPosEnum + room_type: + annotations: + Expected_value: enumeration + description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + title: room type + examples: + - value: bathroom + keywords: + - room + - type + string_serialization: '[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' + slot_uri: MIXS:0000825 + room_vol: + annotations: + Preferred_unit: cubic feet, cubic meter + description: Volume of sampling room + title: room volume + keywords: + - room + - volume + slot_uri: MIXS:0000195 + range: string + pattern: ^[1-9][0-9]* .*$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_wall_share: + description: List of room(s) (room number, room name) sharing a wall with the sampling room + title: rooms that share a wall with sampling room + keywords: + - room + - wall + slot_uri: MIXS:0000243 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + room_window_count: + description: Number of windows in the room + title: room window count + keywords: + - count + - room + - window + slot_uri: MIXS:0000237 + range: integer + root_cond: + description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container + title: rooting conditions + examples: + - value: http://himedialabs.com/TD/PT158.pdf + keywords: + - condition + slot_uri: MIXS:0001061 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|.*$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + root_med_carbon: + annotations: + Expected_value: carbon source name;measurement value + Preferred_unit: milligram per liter + description: Source of organic carbon in the culture rooting medium; e.g. sucrose + title: rooting medium carbon + examples: + - value: sucrose + keywords: + - carbon + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000577 + root_med_macronutr: + annotations: + Expected_value: macronutrient name;measurement value + Preferred_unit: milligram per liter + description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L) + title: rooting medium macronutrients + examples: + - value: KH2PO4;170 milligram per liter + keywords: + - macronutrients + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000578 + root_med_micronutr: + annotations: + Expected_value: micronutrient name;measurement value + Preferred_unit: milligram per liter + description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L) + title: rooting medium micronutrients + examples: + - value: H3BO3;6.2 milligram per liter + keywords: + - micronutrients + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000579 + root_med_ph: + description: pH measurement of the culture rooting medium; e.g. 5.5 + title: rooting medium pH + examples: + - value: '7.5' + keywords: + - ph + slot_uri: MIXS:0001062 + range: float + root_med_regl: + annotations: + Expected_value: regulator name;measurement value + Preferred_unit: milligram per liter + description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA + title: rooting medium regulators + examples: + - value: abscisic acid;0.75 milligram per liter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000581 + root_med_solid: + description: Specification of the solidifying agent in the culture rooting medium; e.g. agar + title: rooting medium solidifier + examples: + - value: agar + slot_uri: MIXS:0001063 + range: string + root_med_suppl: + annotations: + Expected_value: supplement name;measurement value + Preferred_unit: milligram per liter + description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L) + title: rooting medium organic supplements + examples: + - value: nicotinic acid;0.5 milligram per liter + keywords: + - organic + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000580 + route_transmission: + description: Description of path taken by the symbiotic host organism being sampled in order to establish a symbiotic relationship with the host (with which it was observed at the time of sampling) via a mode of transmission (specified in mode_transmission) + title: route of transmission + keywords: + - route + slot_uri: MIXS:0001316 + range: RouteTransmissionEnum + salinity: + annotations: + Preferred_unit: practical salinity unit, percentage + description: The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater + title: salinity + examples: + - value: 25 practical salinity unit + keywords: + - salinity + slot_uri: MIXS:0000183 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + salt_regm: + annotations: + Preferred_unit: gram, microgram, mole per liter, gram per liter + description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens + title: salt regimen + examples: + - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + - salt + slot_uri: MIXS:0000582 + range: string + multivalued: true + samp_capt_status: + description: Reason for the sample + title: sample capture status + examples: + - value: farm sample + keywords: + - sample + - status + slot_uri: MIXS:0000860 + range: SampCaptStatusEnum + samp_collect_device: + annotations: + Expected_value: device name + description: The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094) + title: sample collection device + in_subset: + - nucleic acid sequence source + keywords: + - device + - sample + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0000002 + samp_collect_method: + description: The method employed for collecting the sample + title: sample collection method + in_subset: + - nucleic acid sequence source + keywords: + - method + - sample + slot_uri: MIXS:0001225 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|.*$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + samp_collect_point: + description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field + title: sample collection point + examples: + - value: well + keywords: + - sample + slot_uri: MIXS:0001015 + range: SampCollectPointEnum + required: true + samp_dis_stage: + description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen + title: sample disease stage + examples: + - value: infection + keywords: + - disease + - sample + slot_uri: MIXS:0000249 + range: SampDisStageEnum + samp_floor: + annotations: + Expected_value: enumeration + description: The floor of the building, where the sampling room is located + title: sampling floor + examples: + - value: 4th floor + keywords: + - floor + string_serialization: '[1st floor|2nd floor|{integer} floor|basement|lobby]' + slot_uri: MIXS:0000828 + samp_loc_condition: + description: The condition of the sample location at the time of sampling + title: sample location condition + examples: + - value: new + keywords: + - condition + - location + - sample + slot_uri: MIXS:0001257 + range: SampLocConditionEnum + samp_loc_corr_rate: + annotations: + Preferred_unit: millimeter per year + description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays + title: corrosion rate at sample location + keywords: + - location + - rate + - sample + slot_uri: MIXS:0000136 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true + samp_mat_process: + description: A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed + title: sample material processing + examples: + - value: filtering of seawater, storing samples in ethanol + in_subset: + - nucleic acid sequence source + keywords: + - material + - process + - sample + slot_uri: MIXS:0000016 + range: string + samp_md: + annotations: + Expected_value: measurement value;enumeration + Preferred_unit: meter + description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field + title: sample measured depth + examples: + - value: 1534 meter;MSL + keywords: + - depth + - measurement + - sample + string_serialization: '{float} {unit};[GL|DF|RT|KB|MSL|other]' + slot_uri: MIXS:0000413 + samp_name: + annotations: + Preferred_unit: '' + description: A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name + title: sample name + examples: + - value: ISDsoil1 + in_subset: + - investigation + keywords: + - sample + slot_uri: MIXS:0001107 + range: string + required: true + samp_pooling: + description: Physical combination of several instances of like material, e.g. RNA extracted from samples or dishes of cell cultures into one big aliquot of cells. Please provide a short description of the samples that were pooled + title: sample pooling + examples: + - value: 5uL of extracted genomic DNA from 5 leaves were pooled + keywords: + - pooling + - sample + slot_uri: MIXS:0001153 + range: string + multivalued: true + samp_preserv: + annotations: + Preferred_unit: milliliter + description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + title: preservative added to sample + keywords: + - sample + slot_uri: MIXS:0000463 + range: string + pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + samp_purpose: + annotations: + Expected_value: enumeration or {text} + description: The reason that the sample was collected + title: purpose of sampling + examples: + - value: field trial + keywords: + - purpose + string_serialization: '[active surveillance in response to an outbreak|active surveillance not initiated by an outbreak|clinical trial|cluster investigation|environmental assessment|farm sample|field trial|for cause|industry internal investigation|market sample|passive surveillance|population based studies|research|research and development] or {text}' + slot_uri: MIXS:0001151 + samp_rep_biol: + description: Measurements of biologically distinct samples that show biological variation + title: biological sample replicate + examples: + - value: 6 replicates + keywords: + - sample + slot_uri: MIXS:0001226 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_rep_tech: + description: Repeated measurements of the same sample that show independent measures of the noise associated with the equipment and the protocols + title: technical sample replicate + examples: + - value: 10 replicates + keywords: + - sample + slot_uri: MIXS:0001227 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_room_id: + description: Sampling room number. This ID should be consistent with the designations on the building floor plans + title: sampling room ID or name + keywords: + - identifier + - room + slot_uri: MIXS:0000244 + range: integer + samp_size: + description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected + title: amount or size of sample collected + examples: + - value: 5 liter + in_subset: + - nucleic acid sequence source + keywords: + - sample + - size + slot_uri: MIXS:0000001 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_sort_meth: + description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor + title: sample size sorting method + keywords: + - method + - sample + - size + slot_uri: MIXS:0000216 + range: string + multivalued: true + samp_source_mat_cat: + annotations: + Expected_value: GENEPIO:0001237 + description: This is the scientific role or category that the subject organism or material has with respect to an investigation. This field accepts terms listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237 or http://purl.obolibrary.org/obo/OBI_0100051) + title: sample source material category + examples: + - value: environmental (swab or sampling) [GENEPIO:0001732] + keywords: + - material + - sample + - source + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0001154 + samp_stor_device: + annotations: + Expected_value: NCIT:C4318 + description: The container used to store the sample. This field accepts terms listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the proper descriptor is not listed please use text to describe the storage device + title: sample storage device + examples: + - value: Whirl Pak sampling bag [GENEPIO:0002122] + keywords: + - device + - sample + - storage + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001228 + samp_stor_media: + description: The liquid that is added to the sample collection device prior to sampling. If the sample is pre-hydrated, indicate the liquid media the sample is pre-hydrated with for storage purposes. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the sample storage media + title: sample storage media + examples: + - value: peptone water medium [MICRO:0000548] + keywords: + - sample + - storage + slot_uri: MIXS:0001229 + range: string + pattern: ^.*|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + samp_store_dur: + description: Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format + title: sample storage duration + examples: + - value: P1Y6M + keywords: + - duration + - period + - sample + - storage + slot_uri: MIXS:0000116 + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + samp_store_loc: + annotations: + Expected_value: location name + description: Location at which sample was stored, usually name of a specific freezer/room + title: sample storage location + examples: + - value: Freezer no:5 + keywords: + - location + - sample + - storage + slot_uri: MIXS:0000755 + range: string + samp_store_sol: + annotations: + Expected_value: solution name + description: Solution within which sample was stored, if any + title: sample storage solution + examples: + - value: 5% ethanol + keywords: + - sample + - storage + slot_uri: MIXS:0001317 + range: string + samp_store_temp: + annotations: + Preferred_unit: degree Celsius + description: Temperature at which sample was stored, e.g. -80 degree Celsius + title: sample storage temperature + examples: + - value: -80 degree Celsius + keywords: + - sample + - storage + - temperature + slot_uri: MIXS:0000110 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_subtype: + description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field + title: sample subtype + examples: + - value: biofilm + keywords: + - sample + slot_uri: MIXS:0000999 + range: SampSubtypeEnum + recommended: true + samp_surf_moisture: + description: Degree of water held on a sampled surface. If present, user can state the degree of water held on surface (intermittent moisture, submerged). If no surface moisture is present indicate not present + title: sample surface moisture + examples: + - value: submerged + keywords: + - moisture + - sample + - surface + slot_uri: MIXS:0001256 + range: SampSurfMoistureEnum + multivalued: true + samp_taxon_id: + description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome for mock community/positive controls, or 'blank sample' for negative controls + title: taxonomy ID of DNA sample + examples: + - value: Gut Metagenome [NCBITaxon:749906] + in_subset: + - investigation + keywords: + - dna + - identifier + - sample + - taxon + slot_uri: MIXS:0001320 + range: string + required: true + pattern: ^.* \[NCBITaxon:\d+\]$ + structured_pattern: + syntax: ^{text} \[{NCBItaxon_id}\]$ + interpolated: true + partial_match: true + samp_time_out: + annotations: + Expected_value: time + Preferred_unit: hour + description: The recent and long term history of outside sampling + title: sampling time outside + keywords: + - time + string_serialization: '{float}' + slot_uri: MIXS:0000196 + samp_transport_cond: + annotations: + Expected_value: measurement value;measurement value + Preferred_unit: days;degree Celsius + description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 C) + title: sample transport conditions + examples: + - value: 5 days;-20 degree Celsius + keywords: + - condition + - sample + - transport + string_serialization: '{float} {unit};{float} {unit}' + slot_uri: MIXS:0000410 + samp_transport_cont: + description: Conatiner in which the sample was stored during transport. Indicate the location name + title: sample transport container + examples: + - value: cooler + keywords: + - sample + - transport + slot_uri: MIXS:0001230 + range: SampTransportContEnum + samp_transport_dur: + annotations: + Preferred_unit: days + description: The duration of time from when the sample was collected until processed. Indicate the duration for which the sample was stored written in ISO 8601 format + title: sample transport duration + examples: + - value: P10D + keywords: + - duration + - period + - sample + - transport + slot_uri: MIXS:0001231 + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + samp_transport_temp: + annotations: + Expected_value: text or measurement value + Preferred_unit: degree Celsius + description: Temperature at which sample was transported, e.g. -20 or 4 degree Celsius + title: sample transport temperature + examples: + - value: 4 degree Celsius + keywords: + - sample + - temperature + - transport + string_serialization: '{float} {unit} {text}' + slot_uri: MIXS:0001232 + samp_tvdss: + annotations: + Expected_value: measurement value or measurement value range + Preferred_unit: meter + description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m + title: sample true vertical depth subsea + keywords: + - depth + - sample + string_serialization: '{float}-{float} {unit}' + slot_uri: MIXS:0000409 + recommended: true + samp_type: + description: The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246) + title: sample type + examples: + - value: built environment sample [GENEPIO:0001248] + keywords: + - sample + - type + slot_uri: MIXS:0000998 + range: string + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + samp_vol_we_dna_ext: + annotations: + Preferred_unit: milliliter, gram, milligram, square centimeter + description: 'Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)' + title: sample volume or weight for DNA extraction + examples: + - value: 1500 milliliter + in_subset: + - nucleic acid sequence source + keywords: + - dna + - sample + - volume + - weight + slot_uri: MIXS:0000111 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_weather: + description: The weather on the sampling day + title: sampling day weather + examples: + - value: foggy + keywords: + - day + - weather + slot_uri: MIXS:0000827 + range: SampWeatherEnum + samp_well_name: + description: Name of the well (e.g. BXA1123) where sample was taken + title: sample well name + keywords: + - sample + slot_uri: MIXS:0000296 + range: string + recommended: true + saturates_pc: + annotations: + Preferred_unit: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: saturates wt% + slot_uri: MIXS:0000131 + range: string + recommended: true + pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + sc_lysis_approach: + description: Method used to free DNA from interior of the cell(s) or particle(s) + title: single cell or viral particle lysis approach + examples: + - value: enzymatic + in_subset: + - sequencing + keywords: + - particle + - single + slot_uri: MIXS:0000076 + range: ScLysisApproachEnum + sc_lysis_method: + annotations: + Expected_value: kit, protocol name + description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis + title: single cell or viral particle lysis kit protocol + examples: + - value: ambion single cell lysis kit + in_subset: + - sequencing + keywords: + - kit + - particle + - protocol + - single + slot_uri: MIXS:0000054 + range: string + season: + annotations: + Expected_value: autumn [NCIT:C94733], spring [NCIT:C94731], summer [NCIT:C94732], winter [NCIT:C94730] + description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729) + title: season + comments: + - autumn [NCIT:C94733] does not match ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$ + - would require ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:[a-zA-Z0-9]\\]$ + examples: + - value: autumn [NCIT:C94733] + keywords: + - season + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000829 + range: string + pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:[a-zA-Z0-9]+\]$ + season_environment: + description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment + title: seasonal environment + examples: + - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - environment + - season + slot_uri: MIXS:0001068 + range: string + multivalued: true + season_humidity: + description: Average humidity of the region throughout the growing season + title: mean seasonal humidity + comments: + - percent or float? + examples: + - value: '0.25' + keywords: + - humidity + - mean + - season + slot_uri: MIXS:0001148 + range: float + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + season_precpt: + annotations: + Preferred_unit: millimeter + description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps + title: mean seasonal precipitation + examples: + - value: 75 millimeters + keywords: + - mean + - season + slot_uri: MIXS:0000645 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + season_temp: + annotations: + Preferred_unit: degree Celsius + description: Mean seasonal temperature + title: mean seasonal temperature + examples: + - value: 18 degree Celsius + keywords: + - mean + - season + - temperature + slot_uri: MIXS:0000643 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + season_use: + description: The seasons the space is occupied + title: seasonal use + examples: + - value: Winter + keywords: + - season + - use + slot_uri: MIXS:0000830 + range: SeasonUseEnum + secondary_treatment: + annotations: + Expected_value: secondary treatment type + description: The process for substantially degrading the biological content of the sewage + title: secondary treatment + keywords: + - secondary + - treatment + slot_uri: MIXS:0000351 + range: string + sediment_type: + description: Information about the sediment type based on major constituents + title: sediment type + examples: + - value: biogenous + keywords: + - sediment + - type + slot_uri: MIXS:0001078 + range: SedimentTypeEnum + seq_meth: + description: Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103) + title: sequencing method + examples: + - value: 454 Genome Sequencer FLX [OBI:0000702] + in_subset: + - sequencing + keywords: + - method + slot_uri: MIXS:0000050 + range: string + required: true + pattern: ^.*|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + seq_quality_check: + annotations: + Expected_value: none or manually edited + description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA + title: sequence quality check + examples: + - value: none + in_subset: + - sequencing + keywords: + - quality + slot_uri: MIXS:0000051 + range: SeqQualityCheckEnum + sequencing_kit: + annotations: + Expected_value: name of sequencing kit used + description: Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. Indicate name of the sequencing kit + title: sequencing kit + examples: + - value: NextSeq 500/550 High Output Kit v2.5 (75 Cycles) + keywords: + - kit + slot_uri: MIXS:0001155 + range: string + sequencing_location: + description: The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced + title: sequencing location + examples: + - value: University of Maryland Genomics Resource Center + keywords: + - location + slot_uri: MIXS:0001156 + range: string + serovar_or_serotype: + description: A characterization of a cell or microorganism based on the antigenic properties of the molecules on its surface. Indicate the name of a serovar or serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy + title: serovar or serotype + examples: + - value: Escherichia coli strain O157:H7 [NCIT:C86883] + slot_uri: MIXS:0001157 + range: string + multivalued: true + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + sewage_type: + annotations: + Expected_value: sewage type name + description: Type of wastewater treatment plant as municipial or industrial + title: sewage type + keywords: + - type + slot_uri: MIXS:0000215 + range: string + sexual_act: + annotations: + Expected_value: partner sex;frequency + description: Current sexual partner and frequency of sex + title: sexual activity + slot_uri: MIXS:0000285 + range: string + shad_dev_water_mold: + description: Signs of the presence of mold or mildew on the shading device + title: shading device signs of water/mold + examples: + - value: no presence of mold visible + keywords: + - device + slot_uri: MIXS:0000834 + range: MoldVisibilityEnum + shading_device_cond: + description: The physical condition of the shading device at the time of sampling + title: shading device condition + examples: + - value: new + keywords: + - condition + - device + slot_uri: MIXS:0000831 + range: DamagedRupturedEnum + shading_device_loc: + description: The location of the shading device in relation to the built structure + title: shading device location + examples: + - value: exterior + keywords: + - device + - location + slot_uri: MIXS:0000832 + range: ShadingDeviceLocEnum + shading_device_mat: + annotations: + Expected_value: material name + description: The material the shading device is composed of + title: shading device material + keywords: + - device + - material + slot_uri: MIXS:0000245 + range: string + shading_device_type: + description: The type of shading device + title: shading device type + examples: + - value: slatted aluminum + description: was slatted aluminum awning + keywords: + - device + - type + slot_uri: MIXS:0000835 + range: ShadingDeviceTypeEnum + sieving: + annotations: + Expected_value: design name and/or size;amount + description: Collection design of pooled samples and/or sieve size and amount of sample sieved + title: sieving + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000322 + silicate: + annotations: + Preferred_unit: micromole per liter + description: Concentration of silicate + title: silicate + examples: + - value: 0.05 micromole per liter + slot_uri: MIXS:0000184 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sim_search_meth: + description: Tool used to compare ORFs with database, along with version and cutoffs used + title: similarity search method + examples: + - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score + in_subset: + - sequencing + keywords: + - method + slot_uri: MIXS:0000063 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + size_frac: + annotations: + Expected_value: filter size value range + description: Filtering pore size used in sample preparation + title: size fraction selected + examples: + - value: 0-0.22 micrometer + in_subset: + - nucleic acid sequence source + keywords: + - fraction + - size + string_serialization: '{float}-{float} {unit}' + slot_uri: MIXS:0000017 + size_frac_low: + annotations: + Preferred_unit: micrometer + description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials smaller than the size threshold are excluded from the sample + title: size-fraction lower threshold + examples: + - value: 0.2 micrometer + keywords: + - lower + slot_uri: MIXS:0000735 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + size_frac_up: + annotations: + Preferred_unit: micrometer + description: Mesh or pore size of the device used to retain the sample. Materials larger than the size threshold are excluded from the sample. + title: size-fraction upper threshold + examples: + - value: 20 micrometer + keywords: + - upper + slot_uri: MIXS:0000736 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + slope_aspect: + annotations: + Preferred_unit: degree + description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration + title: slope aspect + keywords: + - slope + slot_uri: MIXS:0000647 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + slope_gradient: + annotations: + Preferred_unit: percentage + description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer + title: slope gradient + keywords: + - slope + slot_uri: MIXS:0000646 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sludge_retent_time: + annotations: + Preferred_unit: hours + description: The time activated sludge remains in reactor + title: sludge retention time + keywords: + - time + slot_uri: MIXS:0000669 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + smoker: + description: Specification of smoking status + title: smoker + examples: + - value: 'yes' + slot_uri: MIXS:0000262 + range: boolean + sodium: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Sodium concentration in the sample + title: sodium + examples: + - value: 10.5 milligram per liter + slot_uri: MIXS:0000428 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_conductivity: + annotations: + Preferred_unit: milliSiemens per centimeter + title: soil conductivity + examples: + - value: 10 milliSiemens per centimeter + keywords: + - soil + slot_uri: MIXS:0001158 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_cover: + annotations: + Expected_value: subclass of 'environmental material', http://purl.obolibrary.org/obo/ENVO_00010483 + description: Material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material + title: soil cover + examples: + - value: bare soil [ENVO01001616] + keywords: + - soil + string_serialization: bare soil [ENVO:01001616] + slot_uri: MIXS:0001159 + soil_horizon: + description: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath + title: soil horizon + examples: + - value: A horizon + keywords: + - horizon + - soil + slot_uri: MIXS:0001082 + range: SoilHorizonEnum + soil_pH: + title: soil pH + examples: + - value: '7.2' + keywords: + - ph + - soil + slot_uri: MIXS:0001160 + range: float + soil_porosity: + annotations: + Expected_value: percent porosity + Preferred_unit: percentage + description: Porosity of soil or deposited sediment is volume of voids divided by the total volume of sample + title: soil sediment porosity + examples: + - value: '0.2' + keywords: + - porosity + - sediment + - soil + string_serialization: '{percentage}' + slot_uri: MIXS:0001162 + soil_temp: + annotations: + Preferred_unit: degree Celsius + description: Temperature of soil at the time of sampling + title: soil temperature + examples: + - value: 25 degrees Celsius + keywords: + - soil + - temperature + slot_uri: MIXS:0001163 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_texture: + description: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional + title: soil texture + keywords: + - soil + - texture + slot_uri: MIXS:0000335 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_texture_class: + description: One of the 12 soil texture classes use to describe soil texture based on the relative proportion of different grain sizes of mineral particles [sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil + title: soil texture classification + examples: + - value: silty clay loam + keywords: + - classification + - soil + - texture + slot_uri: MIXS:0001164 + range: SoilTextureClassEnum + soil_texture_meth: + description: Reference or method used in determining soil texture + title: soil texture method + examples: + - value: https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf + keywords: + - method + - soil + - texture + slot_uri: MIXS:0000336 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + soil_type: + annotations: + Expected_value: ENVO:00001998 + description: Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes + title: soil type + examples: + - value: plinthosol [ENVO:00002250] + keywords: + - soil + - type + slot_uri: MIXS:0000332 + soil_type_meth: + description: Reference or method used in determining soil series name or other lower-level classification + title: soil type method + examples: + - value: https://www.lrh.usace.army.mil/Portals/38/docs/PR/BluestoneSFEIS/Appendix%20K-Soil%20Descriptions.pdf + keywords: + - method + - soil + - type + slot_uri: MIXS:0000334 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + solar_irradiance: + annotations: + Preferred_unit: kilowatts per square meter per day, ergs per square centimeter per second + description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval + title: solar irradiance + examples: + - value: 1.36 kilowatts per square meter per day + slot_uri: MIXS:0000112 + range: string + multivalued: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soluble_inorg_mat: + annotations: + Expected_value: soluble inorganic material name;measurement value + Preferred_unit: gram, microgram, mole per liter, gram per liter, parts per million + description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc + title: soluble inorganic material + keywords: + - inorganic + - material + - soluble + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000672 + multivalued: true + soluble_org_mat: + annotations: + Expected_value: soluble organic material name;measurement value + Preferred_unit: gram, microgram, mole per liter, gram per liter, parts per million + description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc + title: soluble organic material + keywords: + - material + - organic + - soluble + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000673 + multivalued: true + soluble_react_phosp: + annotations: + Preferred_unit: micromole per liter, milligram per liter, parts per million + description: Concentration of soluble reactive phosphorus + title: soluble reactive phosphorus + examples: + - value: 0.1 milligram per liter + keywords: + - phosphorus + - soluble + slot_uri: MIXS:0000738 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sop: + annotations: + Expected_value: reference to SOP + description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences + title: relevant standard operating procedures + examples: + - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ + in_subset: + - sequencing + keywords: + - procedures + string_serialization: '{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0000090 + multivalued: true + sort_tech: + description: Method used to sort/isolate cells or particles of interest + title: sorting technology + examples: + - value: optical manipulation + in_subset: + - sequencing + slot_uri: MIXS:0000075 + range: SortTechEnum + source_mat_id: + annotations: + Expected_value: 'for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer' + description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2) + title: source material identifiers + examples: + - value: MPI012345 + in_subset: + - nucleic acid sequence source + keywords: + - identifier + - material + - source + slot_uri: MIXS:0000026 + range: string + multivalued: true + source_uvig: + annotations: + Expected_value: enumeration + description: Type of dataset from which the UViG was obtained + title: source of UViGs + examples: + - value: viral fraction metagenome (virome) + in_subset: + - nucleic acid sequence source + keywords: + - source + string_serialization: '[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]' + slot_uri: MIXS:0000035 + space_typ_state: + description: Customary or normal state of the space + title: space typical state + examples: + - value: typically occupied + slot_uri: MIXS:0000770 + range: SpaceTypStateEnum + required: true + spec_intended_cons: + description: Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136) + title: specific intended consumer + examples: + - value: senior as food consumer [FOODON:03510254] + keywords: + - consumer + slot_uri: MIXS:0001234 + range: string + multivalued: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + special_diet: + annotations: + Expected_value: enumeration + description: Specification of special diet; can include multiple special diets + title: special diet + examples: + - value: other:vegan + keywords: + - diet + string_serialization: '[low carb|reduced calorie|vegetarian|other(to be specified)]' + slot_uri: MIXS:0000905 + multivalued: true + specific: + description: 'The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents' + title: specifications + examples: + - value: construction + slot_uri: MIXS:0000836 + range: SpecificEnum + specific_host: + annotations: + Expected_value: host scientific name, taxonomy ID + description: Report the host's taxonomic name and/or NCBI taxonomy ID + title: host scientific name + examples: + - value: Homo sapiens and/or 9606 + in_subset: + - nucleic acid sequence source + keywords: + - host + - host. + string_serialization: '{text}|{NCBI taxid}' + slot_uri: MIXS:0000029 + specific_humidity: + annotations: + Preferred_unit: gram of air, kilogram of air + description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound + title: specific humidity + examples: + - value: 15 per kilogram of air + keywords: + - humidity + slot_uri: MIXS:0000214 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + spikein_AMR: + annotations: + Expected_value: measurement value ARO:3004299 + description: Qualitative description of a microbial response to antimicrobial agents. Bacteria may be susceptible or resistant to a broad range of antibiotic drugs or drug classes, with several intermediate states or phases. This field accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299) + title: antimicrobial phenotype of spike-in bacteria + examples: + - value: wild type [ARO:3004432] + keywords: + - antimicrobial + - spike + string_serialization: '{float} {unit};{termLabel} [{termID}]' + slot_uri: MIXS:0001235 + multivalued: true + spikein_antibiotic: + annotations: + Expected_value: drug name; concentration + description: Antimicrobials used in research study to assess effects of exposure on microbiome of a specific site. Please list antimicrobial, common name and/or class and concentration used for spike-in + title: spike-in with antibiotics + examples: + - value: Tetracycline at 5 mg/ml + keywords: + - spike + string_serialization: '{text} {integer}' + slot_uri: MIXS:0001171 + multivalued: true + spikein_count: + annotations: + Expected_value: organism name;measurement value;enumeration + Preferred_unit: colony forming units per milliliter; colony forming units per gram of dry weight + description: 'Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should also be provided (example: total prokaryotes; 3.5e7 cells per ml; qPCR)' + title: spike-in organism count + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + keywords: + - count + - organism + - spike + string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]' + slot_uri: MIXS:0001335 + spikein_growth_med: + description: A liquid or gel containing nutrients, salts, and other factors formulated to support the growth of microorganisms, cells, or plants (National Cancer Institute Thesaurus). A growth medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. In this case, list the culture medium used to propagate the spike-in bacteria during preparation of spike-in inoculum. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the spike in growth media + title: spike-in growth medium + examples: + - value: LB broth [MCO:0000036] + keywords: + - growth + - spike + slot_uri: MIXS:0001169 + range: string + multivalued: true + pattern: ^.*|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + spikein_metal: + annotations: + Expected_value: heavy metal name or chemical symbol; concentration + description: Heavy metals used in research study to assess effects of exposure on microbiome of a specific site. Please list heavy metals and concentration used for spike-in + title: spike-in with heavy metals + examples: + - value: Cd at 20 ppm + keywords: + - heavy + - spike + string_serialization: '{text} {integer}' + slot_uri: MIXS:0001172 + multivalued: true + spikein_org: + description: Taxonomic information about the spike-in organism(s). This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes + title: spike in organism + examples: + - value: Listeria monocytogenes [NCIT:C86502]|28901 + keywords: + - organism + - spike + slot_uri: MIXS:0001167 + range: string + multivalued: true + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + spikein_serovar: + annotations: + Expected_value: NCIT:C14250 or antigenic formula or serovar name + description: Taxonomic information about the spike-in organism(s) at the serovar or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes + title: spike-in bacterial serovar or serotype + examples: + - value: Escherichia coli strain O157:H7 [NCIT:C86883]|83334 + keywords: + - spike + string_serialization: '{termLabel} [{termID}]|{integer}' + slot_uri: MIXS:0001168 + multivalued: true + spikein_strain: + annotations: + Expected_value: NCIT:C14250 or NCBI taxid or text + description: Taxonomic information about the spike-in organism(s) at the strain level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes + title: spike-in microbial strain + examples: + - value: '169963' + keywords: + - microbial + - spike + string_serialization: '{termLabel} [{termID}]|{integer}' + slot_uri: MIXS:0001170 + multivalued: true + sr_dep_env: + description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + title: source rock depositional environment + examples: + - value: Marine + keywords: + - environment + - source + slot_uri: MIXS:0000996 + range: SrDepEnvEnum + sr_geol_age: + description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' + title: source rock geological age + examples: + - value: Silurian + keywords: + - age + - source + slot_uri: MIXS:0000997 + range: GeolAgeEnum + sr_kerog_type: + description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field' + title: source rock kerogen type + examples: + - value: Type IV + keywords: + - source + - type + slot_uri: MIXS:0000994 + range: SrKerogTypeEnum + sr_lithology: + description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field + title: source rock lithology + examples: + - value: Coal + keywords: + - lithology + - source + slot_uri: MIXS:0000995 + range: SrLithologyEnum + standing_water_regm: + description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + title: standing water regimen + examples: + - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + - water + slot_uri: MIXS:0001069 + range: string + multivalued: true + ster_meth_samp_room: + annotations: + Expected_value: ENVO:01001026 + description: The method used to sterilize the sampling room. This field accepts terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026). If the proper descriptor is not listed, please use text to describe the sampling room sterilization method. Multiple terms can be separated by pipes + title: sampling room sterilization method + examples: + - value: ultraviolet radiation [ENVO:21001216]|infrared radiation [ENVO:21001214] + keywords: + - method + - room + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001259 + multivalued: true + store_cond: + annotations: + Expected_value: storage condition type;duration + description: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) + title: storage conditions + examples: + - value: -20 degree Celsius freezer;P2Y10D + keywords: + - condition + - storage + string_serialization: '{text};{period}' + slot_uri: MIXS:0000327 + study_complt_stat: + annotations: + Expected_value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow up (4)other-specify + description: Specification of study completion status, if no the reason should be specified + title: study completion status + examples: + - value: no;non-compliance + keywords: + - status + string_serialization: '{boolean};[adverse event|non-compliance|lost to follow up|other-specify]' + slot_uri: MIXS:0000898 + study_design: + annotations: + Expected_value: OBI:0500000 + description: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. This field accepts terms under study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor is not listed please use text to describe the study design. Multiple terms can be separated by pipes + title: study design + examples: + - value: in vitro design [OBI:0001285] + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001236 + multivalued: true + study_inc_dur: + annotations: + Preferred_unit: hours or days + description: Sample incubation duration if unpublished or unvalidated method is used. Indicate the timepoint written in ISO 8601 format + title: study incubation duration + examples: + - value: PT24H + keywords: + - duration + - incubation + - period + slot_uri: MIXS:0001237 + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + study_inc_temp: + annotations: + Preferred_unit: degree Celsius + description: Sample incubation temperature if unpublished or unvalidated method is used + title: study incubation temperature + examples: + - value: 37 degree Celsius + keywords: + - incubation + - temperature + slot_uri: MIXS:0001238 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + study_timecourse: + annotations: + Preferred_unit: dpi + description: For time-course research studies involving samples of the food commodity, indicate the total duration of the time-course study + title: time-course duration + examples: + - value: 2 days post inoculation + keywords: + - duration + - period + - time + slot_uri: MIXS:0001239 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + study_tmnt: + annotations: + Expected_value: MCO:0000866 + description: A process in which the act is intended to modify or alter some other material entity. From the study design, each treatment is comprised of one level of one or multiple factors. This field accepts terms listed under treatment (http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not listed please use text to describe the study treatment. Multiple terms can be separated by one or more pipes + title: study treatment + examples: + - value: Factor A|spike-in|levels high, medium, low + keywords: + - treatment + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001240 + multivalued: true + subspecf_gen_lin: + annotations: + Expected_value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar + description: Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123 + title: subspecific genetic lineage + examples: + - value: serovar:Newport + in_subset: + - nucleic acid sequence source + keywords: + - lineage + string_serialization: '{rank name}:{text}' + slot_uri: MIXS:0000020 + substructure_type: + description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level + title: substructure type + examples: + - value: basement + keywords: + - type + slot_uri: MIXS:0000767 + range: SubstructureTypeEnum + multivalued: true + sulfate: + annotations: + Preferred_unit: micromole per liter, milligram per liter, parts per million + description: Concentration of sulfate in the sample + title: sulfate + examples: + - value: 5 micromole per liter + keywords: + - sulfate + slot_uri: MIXS:0000423 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sulfate_fw: + annotations: + Preferred_unit: milligram per liter + description: Original sulfate concentration in the hydrocarbon resource + title: sulfate in formation water + keywords: + - sulfate + - water + slot_uri: MIXS:0000407 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sulfide: + annotations: + Preferred_unit: micromole per liter, milligram per liter, parts per million + description: Concentration of sulfide in the sample + title: sulfide + examples: + - value: 2 micromole per liter + keywords: + - sulfide + slot_uri: MIXS:0000424 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + surf_air_cont: + description: Contaminant identified on surface + title: surface-air contaminant + examples: + - value: radon + slot_uri: MIXS:0000759 + range: SurfAirContEnum + recommended: true + multivalued: true + surf_humidity: + annotations: + Preferred_unit: percentage + description: 'Surfaces: water activity as a function of air and material moisture' + title: surface humidity + comments: + - percent or float? + examples: + - value: '0.1' + keywords: + - humidity + - surface + slot_uri: MIXS:0000123 + range: float + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + surf_material: + description: Surface materials at the point of sampling + title: surface material + examples: + - value: wood + keywords: + - material + - surface + slot_uri: MIXS:0000758 + range: SurfMaterialEnum + surf_moisture: + annotations: + Preferred_unit: parts per million, gram per cubic meter, gram per square meter + description: Water held on a surface + title: surface moisture + examples: + - value: 0.01 gram per square meter + keywords: + - moisture + - surface + slot_uri: MIXS:0000128 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + surf_moisture_ph: + description: ph measurement of surface + title: surface moisture pH + examples: + - value: '7' + keywords: + - moisture + - ph + - surface + slot_uri: MIXS:0000760 + range: float + recommended: true + surf_temp: + annotations: + Preferred_unit: degree Celsius + description: Temperature of the surface at the time of sampling + title: surface temperature + examples: + - value: 15 degree Celsius + keywords: + - surface + - temperature + slot_uri: MIXS:0000125 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + suspend_part_matter: + annotations: + Preferred_unit: milligram per liter + description: Concentration of suspended particulate matter + title: suspended particulate matter + examples: + - value: 0.5 milligram per liter + keywords: + - particle + - particulate + - suspended + slot_uri: MIXS:0000741 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + suspend_solids: + annotations: + Expected_value: suspended solid name;measurement value + Preferred_unit: gram, microgram, milligram per liter, mole per liter, gram per liter, part per million + description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances + title: suspended solids + keywords: + - solids + - suspended + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000150 + multivalued: true + sym_life_cycle_type: + annotations: + Expected_value: type of life cycle of the symbiotic organism (host of the samples) + description: Type of life cycle of the symbiotic host species (the thing being sampled). Simple life cycles occur within a single host, complex ones within multiple different hosts over the course of their normal life cycle + title: symbiotic host organism life cycle type + examples: + - value: complex life cycle + keywords: + - host + - host. + - life + - organism + - symbiosis + - type + slot_uri: MIXS:0001300 + range: SymLifeCycleTypeEnum + required: true + symbiont_host_role: + description: Role of the host in the life cycle of the symbiotic organism + title: host of the symbiont role + examples: + - value: intermediate + keywords: + - host + - host. + - symbiosis + slot_uri: MIXS:0001303 + range: SymbiontHostRoleEnum + recommended: true + tan: + annotations: + Preferred_unit: milligram per liter + description: 'Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' + title: total acid number + keywords: + - number + - total + slot_uri: MIXS:0000120 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + target_gene: + description: Targeted gene or locus name for marker gene studies + title: target gene + examples: + - value: 16S rRNA, 18S rRNA, nif, amoA, rpo + in_subset: + - sequencing + keywords: + - target + slot_uri: MIXS:0000044 + range: string + target_subfragment: + description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA + title: target subfragment + examples: + - value: V6, V9, ITS + in_subset: + - sequencing + keywords: + - target + slot_uri: MIXS:0000045 + range: string + tax_class: + description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes + title: taxonomic classification + examples: + - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) + in_subset: + - sequencing + keywords: + - classification + - taxon + slot_uri: MIXS:0000064 + range: string + tax_ident: + description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG + title: taxonomic identity marker + examples: + - value: other + description: was other rpoB gene + in_subset: + - sequencing + keywords: + - identifier + - marker + - taxon + slot_uri: MIXS:0000053 + range: TaxIdentEnum + temp: + annotations: + Preferred_unit: degree Celsius + description: Temperature of the sample at the time of sampling + title: temperature + examples: + - value: 25 degree Celsius + in_subset: + - environment + keywords: + - temperature + slot_uri: MIXS:0000113 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + temp_out: + annotations: + Preferred_unit: degree Celsius + description: The recorded temperature value at sampling time outside + title: temperature outside house + examples: + - value: 5 degree Celsius + keywords: + - house + - temperature + slot_uri: MIXS:0000197 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tertiary_treatment: + annotations: + Expected_value: tertiary treatment type + description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment + title: tertiary treatment + keywords: + - treatment + slot_uri: MIXS:0000352 + range: string + tidal_stage: + description: Stage of tide + title: tidal stage + examples: + - value: high tide + slot_uri: MIXS:0000750 + range: TidalStageEnum + tillage: + description: Note method(s) used for tilling + title: history/tillage + examples: + - value: chisel + keywords: + - history + slot_uri: MIXS:0001081 + range: TillageEnum + multivalued: true + time_last_toothbrush: + description: Specification of the time since last toothbrushing + title: time since last toothbrushing + comments: + - P2H45M does not match ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$ + - problematic ISO 8601 period validation + examples: + - value: PT2H45M + keywords: + - time + slot_uri: MIXS:0000924 + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + time_since_last_wash: + description: Specification of the time since last wash + title: time since last wash + examples: + - value: P1D + keywords: + - time + slot_uri: MIXS:0000943 + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + timepoint: + annotations: + Preferred_unit: hours or days + description: Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. Indicate the timepoint written in ISO 8601 format + title: timepoint + examples: + - value: PT24H + keywords: + - time + slot_uri: MIXS:0001173 + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + tiss_cult_growth_med: + description: Description of plant tissue culture growth media used + title: tissue culture growth media + examples: + - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf + keywords: + - culture + - growth + slot_uri: MIXS:0001070 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|.*$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + toluene: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of toluene in the sample + title: toluene + slot_uri: MIXS:0000154 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_carb: + description: Total carbon content + title: total carbon + keywords: + - carbon + - total + slot_uri: MIXS:0000525 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_depth_water_col: + annotations: + Preferred_unit: meter + description: Measurement of total depth of water column + title: total depth of water column + examples: + - value: 500 meter + keywords: + - depth + - total + - water + slot_uri: MIXS:0000634 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_diss_nitro: + annotations: + Preferred_unit: microgram per liter + description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' + title: total dissolved nitrogen + examples: + - value: 40 microgram per liter + keywords: + - dissolved + - nitrogen + - total + slot_uri: MIXS:0000744 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_inorg_nitro: + annotations: + Preferred_unit: microgram per liter + description: Total inorganic nitrogen content + title: total inorganic nitrogen + examples: + - value: 40 microgram per liter + keywords: + - inorganic + - nitrogen + - total + slot_uri: MIXS:0000745 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_iron: + annotations: + Preferred_unit: milligram per liter, milligram per kilogram + description: Concentration of total iron in the sample + title: total iron + keywords: + - total + slot_uri: MIXS:0000105 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_nitro: + annotations: + Preferred_unit: microgram per liter, micromole per liter, milligram per liter + description: 'Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen' + title: total nitrogen concentration + examples: + - value: 50 micromole per liter + keywords: + - concentration + - nitrogen + - total + slot_uri: MIXS:0000102 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_nitro_cont_meth: + description: Reference or method used in determining the total nitrogen + title: total nitrogen content method + examples: + - value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 + keywords: + - content + - method + - nitrogen + - total + slot_uri: MIXS:0000338 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + tot_nitro_content: + description: Total nitrogen content of the sample + title: total nitrogen content + examples: + - value: 35 milligrams Nitrogen per kilogram of soil + keywords: + - content + - nitrogen + - total + slot_uri: MIXS:0000530 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_org_c_meth: + description: Reference or method used in determining total organic carbon + title: total organic carbon method + examples: + - value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf + keywords: + - carbon + - method + - organic + - total + slot_uri: MIXS:0000337 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + tot_org_carb: + annotations: + Preferred_unit: gram Carbon per kilogram sample material + description: Total organic carbon content + title: total organic carbon + examples: + - value: '0.02' + keywords: + - carbon + - organic + - total + slot_uri: MIXS:0000533 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_part_carb: + annotations: + Preferred_unit: microgram per liter, micromole per liter + description: Total particulate carbon content + title: total particulate carbon + examples: + - value: 35 micromole per liter + keywords: + - carbon + - particle + - particulate + - total + slot_uri: MIXS:0000747 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_phosp: + annotations: + Preferred_unit: micromole per liter, milligram per liter, parts per million + description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' + title: total phosphorus + examples: + - value: 0.03 milligram per liter + keywords: + - phosphorus + - total + slot_uri: MIXS:0000117 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_phosphate: + annotations: + Preferred_unit: microgram per liter, micromole per liter + description: Total amount or concentration of phosphate + title: total phosphate + keywords: + - phosphate + - total + slot_uri: MIXS:0000689 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_sulfur: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of total sulfur in the sample + title: total sulfur + keywords: + - sulfur + - total + slot_uri: MIXS:0000419 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + train_line: + description: The subway line name + title: train line + examples: + - value: red + keywords: + - train + slot_uri: MIXS:0000837 + range: TrainLineEnum + train_stat_loc: + description: The train station collection location + title: train station collection location + examples: + - value: forest hills + keywords: + - location + - train + slot_uri: MIXS:0000838 + range: TrainStatLocEnum + train_stop_loc: + description: The train stop collection location + title: train stop collection location + examples: + - value: end + keywords: + - location + - stop + - train + slot_uri: MIXS:0000839 + range: TrainStopLocEnum + travel_out_six_month: + annotations: + Expected_value: country name + description: Specification of the countries travelled in the last six months; can include multiple travels + title: travel outside the country in last six months + keywords: + - months + slot_uri: MIXS:0000268 + range: string + multivalued: true + trna_ext_software: + description: Tools used for tRNA identification + title: tRNA extraction software + examples: + - value: infernal;v2;default parameters + in_subset: + - sequencing + keywords: + - software + slot_uri: MIXS:0000068 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + trnas: + annotations: + Expected_value: value from 0-21 + description: The total number of tRNAs identified from the SAG or MAG + title: number of standard tRNAs extracted + examples: + - value: '18' + in_subset: + - sequencing + keywords: + - number + string_serialization: '{integer}' + slot_uri: MIXS:0000067 + trophic_level: + description: Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) + title: trophic level + examples: + - value: heterotroph + in_subset: + - nucleic acid sequence source + keywords: + - level + slot_uri: MIXS:0000032 + range: TrophicLevelEnum + turbidity: + description: Measure of the amount of cloudiness or haziness in water caused by individual particles + title: turbidity + examples: + - value: 0.3 nephelometric turbidity units + slot_uri: MIXS:0000191 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tvdss_of_hcr_press: + annotations: + Preferred_unit: meter + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m) + title: depth (TVDSS) of hydrocarbon resource pressure + keywords: + - depth + - hydrocarbon + - pressure + - resource + slot_uri: MIXS:0000397 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tvdss_of_hcr_temp: + annotations: + Preferred_unit: meter + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m) + title: depth (TVDSS) of hydrocarbon resource temperature + keywords: + - depth + - hydrocarbon + - resource + - temperature + slot_uri: MIXS:0000394 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + twin_sibling: + description: Specification of twin sibling presence + title: twin sibling presence + examples: + - value: 'yes' + keywords: + - presence + slot_uri: MIXS:0000326 + range: boolean + typ_occup_density: + description: Customary or normal density of occupants + title: typical occupant density + examples: + - value: '25' + keywords: + - density + slot_uri: MIXS:0000771 + range: float + required: true + type_of_symbiosis: + description: Type of biological interaction established between the symbiotic host organism being sampled and its respective host + title: type of symbiosis + examples: + - value: parasitic + keywords: + - symbiosis + - type + slot_uri: MIXS:0001307 + range: TypeOfSymbiosisEnum + recommended: true + urine_collect_meth: + description: Specification of urine collection method + title: urine/collection method + examples: + - value: catheter + keywords: + - method + slot_uri: MIXS:0000899 + range: UrineCollectMethEnum + urobiom_sex: + annotations: + Expected_value: sex of the symbiotic organism (host of the samples); enumeration + description: Physical sex of the host + title: host sex + keywords: + - host + - host. + slot_uri: MIXS:0000862 + range: UrobiomSexEnum + urogenit_disord: + description: History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18) + title: urogenital disorder + keywords: + - disorder + slot_uri: MIXS:0000289 + range: string + multivalued: true + urogenit_tract_disor: + description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18) + title: urine/urogenital tract disorder + keywords: + - disorder + slot_uri: MIXS:0000278 + range: string + multivalued: true + ventilation_rate: + annotations: + Preferred_unit: cubic meter per minute, liters per second + description: Ventilation rate of the system in the sampled premises + title: ventilation rate + examples: + - value: 750 cubic meter per minute + keywords: + - rate + slot_uri: MIXS:0000114 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ventilation_type: + annotations: + Expected_value: ventilation type name + description: Ventilation system used in the sampled premises + title: ventilation type + examples: + - value: Operable windows + keywords: + - type + slot_uri: MIXS:0000756 + range: string + multivalued: true + vfa: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of Volatile Fatty Acids in the sample + title: volatile fatty acids + slot_uri: MIXS:0000152 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + vfa_fw: + annotations: + Preferred_unit: milligram per liter + description: Original volatile fatty acid concentration in the hydrocarbon resource + title: vfa in formation water + keywords: + - water + slot_uri: MIXS:0000408 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + vir_ident_software: + annotations: + Expected_value: software name, version and relevant parameters + description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used + title: viral identification software + examples: + - value: VirSorter; 1.0.4; Virome database, category 2 + in_subset: + - sequencing + keywords: + - identifier + - software + string_serialization: '{software};{version};{parameters}' + slot_uri: MIXS:0000081 + virus_enrich_appr: + description: List of approaches used to enrich the sample for viruses, if any + title: virus enrichment approach + examples: + - value: filtration + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + - value: FeCl Precipitation + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + - value: ultracentrifugation + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + - value: DNAse + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + in_subset: + - nucleic acid sequence source + keywords: + - enrichment + slot_uri: MIXS:0000036 + range: VirusEnrichApprEnum + vis_media: + annotations: + Expected_value: enumeration + description: The building visual media + title: visual media + examples: + - value: 3D scans + string_serialization: '[photos|videos|commonly of the building|site context (adjacent buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]' + slot_uri: MIXS:0000840 + viscosity: + annotations: + Expected_value: measurement value;measurement value + Preferred_unit: cP at degree Celsius + description: A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 C) + title: viscosity + string_serialization: '{float} {unit};{float} {unit}' + slot_uri: MIXS:0000126 + volatile_org_comp: + annotations: + Expected_value: volatile organic compound name;measurement value + Preferred_unit: microgram per cubic meter, parts per million, nanogram per liter + description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound + title: volatile organic compounds + examples: + - value: formaldehyde;500 nanogram per liter + keywords: + - organic + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000115 + multivalued: true + wall_area: + annotations: + Preferred_unit: square meter + description: The total area of the sampled room's walls + title: wall area + keywords: + - area + - wall + slot_uri: MIXS:0000198 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + wall_const_type: + description: The building class of the wall defined by the composition of the building elements and fire-resistance rating + title: wall construction type + examples: + - value: fire resistive + keywords: + - type + - wall + slot_uri: MIXS:0000841 + range: WallConstTypeEnum + wall_finish_mat: + description: The material utilized to finish the outer most layer of the wall + title: wall finish material + examples: + - value: wood + keywords: + - material + - wall + slot_uri: MIXS:0000842 + range: WallFinishMatEnum + wall_height: + annotations: + Preferred_unit: centimeter + description: The average height of the walls in the sampled room + title: wall height + keywords: + - height + - wall + slot_uri: MIXS:0000221 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + wall_loc: + description: The relative location of the wall within the room + title: wall location + examples: + - value: north + keywords: + - location + - wall + slot_uri: MIXS:0000843 + range: CompassDirections8Enum + wall_surf_treatment: + description: The surface treatment of interior wall + title: wall surface treatment + examples: + - value: paneling + keywords: + - surface + - treatment + - wall + slot_uri: MIXS:0000845 + range: WallSurfTreatmentEnum + wall_texture: + description: The feel, appearance, or consistency of a wall surface + title: wall texture + examples: + - value: popcorn + keywords: + - texture + - wall + slot_uri: MIXS:0000846 + range: CeilingWallTextureEnum + wall_thermal_mass: + annotations: + Preferred_unit: joule per degree Celsius + description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint + title: wall thermal mass + keywords: + - mass + - wall + slot_uri: MIXS:0000222 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + wall_water_mold: + description: Signs of the presence of mold or mildew on a wall + title: wall signs of water/mold + examples: + - value: no presence of mold visible + keywords: + - wall + slot_uri: MIXS:0000844 + range: MoldVisibilityEnum + wastewater_type: + annotations: + Expected_value: wastewater type name + description: The origin of wastewater such as human waste, rainfall, storm drains, etc + title: wastewater type + keywords: + - type + slot_uri: MIXS:0000353 + range: string + water_cont_soil_meth: + description: Reference or method used in determining the water content of soil + title: water content method + keywords: + - content + - method + - water + slot_uri: MIXS:0000323 + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + water_content: + annotations: + Preferred_unit: gram per gram or cubic centimeter per cubic centimeter + description: Water content measurement + title: water content + keywords: + - content + - water + slot_uri: MIXS:0000185 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_current: + annotations: + Preferred_unit: cubic meter per second, knots + description: Measurement of magnitude and direction of flow within a fluid + title: water current + examples: + - value: 10 cubic meter per second + keywords: + - water + slot_uri: MIXS:0000203 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_cut: + annotations: + Preferred_unit: percent + description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + title: water cut + comments: + - percent or float? + examples: + - value: 45% + keywords: + - water + slot_uri: MIXS:0000454 + range: string + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_feat_size: + annotations: + Preferred_unit: square meter + description: The size of the water feature + title: water feature size + keywords: + - feature + - size + - water + slot_uri: MIXS:0000223 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_feat_type: + description: The type of water feature present within the building being sampled + title: water feature type + examples: + - value: stream + keywords: + - feature + - type + - water + slot_uri: MIXS:0000847 + range: WaterFeatTypeEnum + water_frequency: + annotations: + Expected_value: rate + Preferred_unit: per day, per week, per month + description: Number of water delivery events within a given period of time + title: water delivery frequency + examples: + - value: 2 per day + keywords: + - delivery + - frequency + - water + string_serialization: '{float}{unit}' + slot_uri: MIXS:0001174 + water_pH: + title: water pH + examples: + - value: '7.2' + keywords: + - ph + - water + slot_uri: MIXS:0001175 + range: float + water_prod_rate: + annotations: + Preferred_unit: cubic meter per day + description: Water production rates per well (e.g. 987 m3 / day) + title: water production rate + keywords: + - production + - rate + - water + slot_uri: MIXS:0000453 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_source_adjac: + annotations: + Expected_value: ENVO_01001110 or ENVO_00000070 + description: Description of the environmental features that are adjacent to the farm water source. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes + title: environmental feature adjacent water source + examples: + - value: feedlot [ENVO:01000627] + keywords: + - adjacent + - environmental + - feature + - source + - water + slot_uri: MIXS:0001122 + range: string + multivalued: true + water_source_shared: + annotations: + Expected_value: enumeration + description: Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes + title: water source shared + examples: + - value: no sharing + keywords: + - source + - water + string_serialization: '[multiple users, agricutural|multiple users, other|no sharing]' + slot_uri: MIXS:0001176 + multivalued: true + water_temp_regm: + annotations: + Preferred_unit: degree Celsius + description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + title: water temperature regimen + examples: + - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + - temperature + - water + slot_uri: MIXS:0000590 + range: string + multivalued: true + watering_regm: + annotations: + Preferred_unit: milliliter, liter + description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens + title: watering regimen + examples: + - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + keywords: + - regimen + - water + slot_uri: MIXS:0000591 + range: string + multivalued: true + weekday: + description: The day of the week when sampling occurred + title: weekday + examples: + - value: Sunday + slot_uri: MIXS:0000848 + range: WeekdayEnum + weight_loss_3_month: + annotations: + Expected_value: weight loss specification;measurement value + Preferred_unit: kilogram, gram + description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss + title: weight loss in last three months + examples: + - value: yes;5 kilogram + keywords: + - months + - weight + string_serialization: '{boolean};{float} {unit}' + slot_uri: MIXS:0000295 + wga_amp_appr: + description: Method used to amplify genomic DNA in preparation for sequencing + title: WGA amplification approach + examples: + - value: mda based + in_subset: + - sequencing + slot_uri: MIXS:0000055 + range: WgaAmpApprEnum + wga_amp_kit: + annotations: + Expected_value: kit name + description: Kit used to amplify genomic DNA in preparation for sequencing + title: WGA amplification kit + examples: + - value: qiagen repli-g + in_subset: + - sequencing + keywords: + - kit + slot_uri: MIXS:0000006 + range: string + win: + description: 'A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' + title: well identification number + keywords: + - identifier + - number + slot_uri: MIXS:0000297 + range: string + recommended: true + wind_direction: + annotations: + Preferred_unit: degrees or cardinal direction + description: Wind direction is the direction from which a wind originates + title: wind direction + keywords: + - direction + - wind + slot_uri: MIXS:0000757 + range: string + wind_speed: + description: speed of wind measured at the time of sampling + title: wind speed + keywords: + - speed + - wind + slot_uri: MIXS:0000118 + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + window_cond: + description: The physical condition of the window at the time of sampling + title: window condition + examples: + - value: rupture + keywords: + - condition + - window + slot_uri: MIXS:0000849 + range: DamagedRupturedEnum + window_cover: + description: The type of window covering + title: window covering + examples: + - value: curtains + keywords: + - window + slot_uri: MIXS:0000850 + range: WindowCoverEnum + window_horiz_pos: + description: The horizontal position of the window on the wall + title: window horizontal position + examples: + - value: middle + keywords: + - window + slot_uri: MIXS:0000851 + range: WindowHorizPosEnum + window_loc: + description: The relative location of the window within the room + title: window location + examples: + - value: west + keywords: + - location + - window + slot_uri: MIXS:0000852 + range: CompassDirections8Enum + window_mat: + description: The type of material used to finish a window + title: window material + examples: + - value: wood + keywords: + - material + - window + slot_uri: MIXS:0000853 + range: WindowMatEnum + window_open_freq: + description: The number of times windows are opened per week + title: window open frequency + keywords: + - frequency + - window + slot_uri: MIXS:0000246 + range: integer + window_size: + annotations: + Expected_value: measurement value + Preferred_unit: inch, meter + description: The window's length and width + title: window area/size + keywords: + - window + string_serialization: '{float} {unit} x {float} {unit}' + slot_uri: MIXS:0000224 + window_status: + description: Defines whether the windows were open or closed during environmental testing + title: window status + examples: + - value: open + keywords: + - status + - window + slot_uri: MIXS:0000855 + range: WindowStatusEnum + window_type: + description: The type of windows + title: window type + examples: + - value: fixed window + keywords: + - type + - window + slot_uri: MIXS:0000856 + range: WindowTypeEnum + window_vert_pos: + description: The vertical position of the window on the wall + title: window vertical position + examples: + - value: middle + keywords: + - window + slot_uri: MIXS:0000857 + range: WindowVertPosEnum + window_water_mold: + description: Signs of the presence of mold or mildew on the window + title: window signs of water/mold + examples: + - value: no presence of mold visible + keywords: + - window + slot_uri: MIXS:0000854 + range: MoldVisibilityEnum + x16s_recover: + description: Can a 16S gene be recovered from the submitted SAG or MAG? + title: 16S recovered + examples: + - value: 'yes' + in_subset: + - sequencing + keywords: + - recover + slot_uri: MIXS:0000065 + range: boolean + x16s_recover_software: + description: Tools used for 16S rRNA gene extraction + title: 16S recovery software + examples: + - value: rambl;v2;default parameters + in_subset: + - sequencing + keywords: + - recover + - software + slot_uri: MIXS:0000066 + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + xylene: + annotations: + Preferred_unit: milligram per liter, parts per million + description: Concentration of xylene in the sample + title: xylene + slot_uri: MIXS:0000156 + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *.*$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true +classes: + MigsBa: + description: 'Minimal Information about a Genome Sequence: cultured bacteria/archaea' + title: MIGS bacteria + aliases: + - migs_ba + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - extrachrom_elements + - estimated_size + - samp_vol_we_dna_ext + - pathogenicity + - lib_reads_seqd + - rel_to_oxygen + - encoded_traits + - samp_collect_device + - number_contig + - biotic_relationship + - num_replicons + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - adapters + - assembly_software + - tax_ident + - annot + - trophic_level + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + annot: + recommended: true + assembly_name: + recommended: true + assembly_qual: + required: true + assembly_software: + required: true + biotic_relationship: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + extrachrom_elements: + recommended: true + host_disease_stat: + examples: + - value: rabies [DOID:11260] + recommended: true + isol_growth_condt: + required: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + num_replicons: + required: true + number_contig: + required: true + pathogenicity: + recommended: true + ref_biomaterial: + required: true + rel_to_oxygen: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: swabbing + sop: + recommended: true + source_mat_id: + recommended: true + specific_host: + recommended: true + subspecf_gen_lin: + recommended: true + tax_ident: + recommended: true + temp: + recommended: true + trophic_level: + recommended: true + class_uri: MIXS:0010003 + MigsEu: + description: 'Minimal Information about a Genome Sequence: eukaryote' + title: MIGS eukaryote + aliases: + - migs_eu + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - estimated_size + - extrachrom_elements + - source_mat_id + - samp_vol_we_dna_ext + - ploidy + - pathogenicity + - lib_reads_seqd + - propagation + - samp_collect_device + - number_contig + - biotic_relationship + - num_replicons + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - adapters + - assembly_software + - tax_ident + - annot + - trophic_level + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + annot: + recommended: true + assembly_name: + recommended: true + assembly_qual: + required: true + assembly_software: + required: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + host_disease_stat: + examples: + - value: rabies [DOID:11260] + isol_growth_condt: + required: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + number_contig: + required: true + pathogenicity: + recommended: true + propagation: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: swabbing + sop: + recommended: true + source_mat_id: + recommended: true + subspecf_gen_lin: + recommended: true + tax_ident: + recommended: true + temp: + recommended: true + trophic_level: + recommended: true + class_uri: MIXS:0010002 + MigsOrg: + description: 'Minimal Information about a Genome Sequence: organelle' + title: MIGS org + aliases: + - migs_org + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - extrachrom_elements + - estimated_size + - samp_vol_we_dna_ext + - lib_reads_seqd + - samp_collect_device + - number_contig + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - tax_ident + - annot + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + annot: + recommended: true + assembly_name: + recommended: true + assembly_software: + required: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + extrachrom_elements: + recommended: true + isol_growth_condt: + required: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: swabbing + sop: + recommended: true + source_mat_id: + recommended: true + subspecf_gen_lin: + recommended: true + tax_ident: + recommended: true + temp: + recommended: true + class_uri: MIXS:0010006 + MigsPl: + description: 'Minimal Information about a Genome Sequence: plasmid' + title: MIGS pl + aliases: + - migs_pl + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - estimated_size + - samp_vol_we_dna_ext + - lib_reads_seqd + - encoded_traits + - propagation + - samp_collect_device + - number_contig + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - adapters + - assembly_software + - tax_ident + - annot + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + annot: + recommended: true + assembly_name: + recommended: true + assembly_software: + required: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + encoded_traits: + recommended: true + isol_growth_condt: + required: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + propagation: + required: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: swabbing + sop: + recommended: true + source_mat_id: + recommended: true + specific_host: + recommended: true + subspecf_gen_lin: + recommended: true + tax_ident: + recommended: true + temp: + recommended: true + class_uri: MIXS:0010004 + MigsVi: + description: 'Minimal Information about a Genome Sequence: virus' + title: MIGS virus + aliases: + - migs_vi + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - estimated_size + - samp_vol_we_dna_ext + - pathogenicity + - lib_reads_seqd + - encoded_traits + - propagation + - samp_collect_device + - number_contig + - biotic_relationship + - num_replicons + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - virus_enrich_appr + - adapters + - assembly_software + - tax_ident + - annot + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + annot: + recommended: true + assembly_name: + recommended: true + assembly_software: + required: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + encoded_traits: + recommended: true + host_disease_stat: + examples: + - value: rabies [DOID:11260] + recommended: true + host_spec_range: + recommended: true + isol_growth_condt: + required: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + num_replicons: + recommended: true + pathogenicity: + recommended: true + propagation: + required: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: swabbing + sop: + recommended: true + source_mat_id: + recommended: true + specific_host: + recommended: true + subspecf_gen_lin: + recommended: true + tax_ident: + recommended: true + temp: + recommended: true + virus_enrich_appr: + recommended: true + class_uri: MIXS:0010005 + Mimag: + description: Minimum Information About a Metagenome-Assembled Genome + title: MIMAG + aliases: + - mimag + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - contam_screen_input + - mid + - assembly_name + - temp + - compl_score + - trnas + - mag_cov_software + - nucl_acid_ext + - samp_size + - alt + - bin_param + - bin_software + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - reassembly_bin + - decontam_software + - samp_collect_device + - number_contig + - trna_ext_software + - lib_layout + - contam_screen_param + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - tax_ident + - contam_score + - annot + - x16s_recover_software + - x16s_recover + - pos_cont_type + - feat_pred + - compl_software + - env_local_scale + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - compl_appr + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + assembly_name: + recommended: true + assembly_qual: + required: true + assembly_software: + required: true + bin_param: + required: true + bin_software: + required: true + compl_score: + required: true + compl_software: + required: true + contam_score: + required: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + experimental_factor: + recommended: true + lib_layout: + recommended: true + lib_reads_seqd: + recommended: true + lib_screen: + recommended: true + lib_size: + recommended: true + lib_vector: + recommended: true + mid: + recommended: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + examples: + - value: swabbing + recommended: true + samp_mat_process: + recommended: true + samp_size: + recommended: true + sop: + recommended: true + source_mat_id: + recommended: true + tax_ident: + required: true + temp: + recommended: true + class_uri: MIXS:0010011 + MimarksC: + description: 'Minimal Information about a Marker Sequence: specimen' + title: MIMARKS specimen + comments: + - for marker gene sequences from cultured or voucher-identifiable specimens + aliases: + - mimarks_c + - MIMARKS-SU + - MIMARKS-specimen + is_a: Checklist + mixin: true + slots: + - samp_name + - pcr_primers + - nucl_acid_amp + - target_subfragment + - temp + - pcr_cond + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - extrachrom_elements + - samp_vol_we_dna_ext + - rel_to_oxygen + - samp_collect_device + - biotic_relationship + - seq_quality_check + - project_name + - neg_cont_type + - chimera_check + - trophic_level + - pos_cont_type + - subspecf_gen_lin + - env_local_scale + - samp_mat_process + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - experimental_factor + - target_gene + - associated_resource + - sop + slot_usage: + alt: + recommended: true + biotic_relationship: + recommended: true + chimera_check: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + isol_growth_condt: + required: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + pcr_cond: + recommended: true + pcr_primers: + recommended: true + rel_to_oxygen: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: swabbing + samp_mat_process: + recommended: true + seq_quality_check: + recommended: true + sop: + recommended: true + source_mat_id: + recommended: true + subspecf_gen_lin: + recommended: true + target_gene: + required: true + target_subfragment: + recommended: true + temp: + recommended: true + trophic_level: + recommended: true + class_uri: MIXS:0010009 + MimarksS: + description: 'Minimal Information about a Marker Sequence: survey' + title: MIMARKS survey + comments: + - for marker gene sequences obtained directly from the environment + aliases: + - mimarks_s + - MIMARKS-SP + - MIMARKS-survey + is_a: Checklist + mixin: true + slots: + - samp_name + - pcr_primers + - size_frac + - lib_screen + - nucl_acid_amp + - lib_size + - target_subfragment + - mid + - temp + - nucl_acid_ext + - samp_size + - alt + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - samp_collect_device + - seq_quality_check + - lib_layout + - env_broad_scale + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - chimera_check + - pos_cont_type + - env_local_scale + - samp_mat_process + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - pcr_cond + - experimental_factor + - target_gene + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + assembly_software: + recommended: true + chimera_check: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + experimental_factor: + recommended: true + lib_layout: + recommended: true + lib_reads_seqd: + recommended: true + lib_screen: + recommended: true + lib_size: + recommended: true + lib_vector: + recommended: true + mid: + recommended: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + pcr_cond: + recommended: true + pcr_primers: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + examples: + - value: swabbing + recommended: true + samp_mat_process: + recommended: true + samp_size: + recommended: true + seq_quality_check: + recommended: true + sop: + recommended: true + source_mat_id: + recommended: true + target_gene: + required: true + target_subfragment: + recommended: true + temp: + recommended: true + class_uri: MIXS:0010008 + Mims: + description: Metagenome or Environmental + title: MIMS + aliases: + - mims + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - mid + - assembly_name + - temp + - nucl_acid_ext + - samp_size + - alt + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - samp_collect_device + - number_contig + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - annot + - pos_cont_type + - feat_pred + - env_local_scale + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + annot: + recommended: true + assembly_name: + recommended: true + assembly_qual: + recommended: true + assembly_software: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + experimental_factor: + recommended: true + lib_layout: + recommended: true + lib_reads_seqd: + recommended: true + lib_screen: + recommended: true + lib_size: + recommended: true + lib_vector: + recommended: true + mid: + recommended: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + number_contig: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + examples: + - value: swabbing + recommended: true + samp_mat_process: + recommended: true + samp_size: + recommended: true + sop: + recommended: true + source_mat_id: + recommended: true + temp: + recommended: true + class_uri: MIXS:0010007 + Misag: + description: Minimum Information About a Single Amplified Genome + title: Minimum Information About a Single Amplified Genome + aliases: + - misag + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - contam_screen_input + - mid + - assembly_name + - temp + - compl_score + - trnas + - nucl_acid_ext + - samp_size + - alt + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - wga_amp_kit + - decontam_software + - samp_collect_device + - number_contig + - trna_ext_software + - sc_lysis_method + - lib_layout + - contam_screen_param + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - tax_ident + - contam_score + - annot + - x16s_recover_software + - x16s_recover + - pos_cont_type + - feat_pred + - compl_software + - env_local_scale + - sort_tech + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - wga_amp_appr + - compl_appr + - env_medium + - samp_taxon_id + - geo_loc_name + - sc_lysis_approach + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + assembly_name: + recommended: true + assembly_qual: + required: true + assembly_software: + required: true + compl_score: + required: true + compl_software: + required: true + contam_score: + required: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + experimental_factor: + recommended: true + lib_layout: + recommended: true + lib_reads_seqd: + recommended: true + lib_screen: + recommended: true + lib_size: + recommended: true + lib_vector: + recommended: true + mid: + recommended: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + examples: + - value: swabbing + recommended: true + samp_mat_process: + recommended: true + samp_size: + recommended: true + sc_lysis_approach: + required: true + sop: + recommended: true + sort_tech: + required: true + source_mat_id: + recommended: true + tax_ident: + required: true + temp: + recommended: true + wga_amp_appr: + required: true + class_uri: MIXS:0010010 + Miuvig: + description: Minimum Information About an Uncultivated Virus Genome + title: Minimum Information About an Uncultivated Virus Genome + aliases: + - miuvig + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - source_uvig + - ref_db + - nucl_acid_amp + - lib_size + - mid + - assembly_name + - temp + - compl_score + - trnas + - nucl_acid_ext + - samp_size + - alt + - estimated_size + - source_mat_id + - samp_vol_we_dna_ext + - pathogenicity + - lib_reads_seqd + - samp_collect_device + - number_contig + - biotic_relationship + - trna_ext_software + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - virus_enrich_appr + - adapters + - assembly_software + - tax_ident + - annot + - pos_cont_type + - feat_pred + - compl_software + - env_local_scale + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - compl_appr + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - sort_tech + - sc_lysis_approach + - sc_lysis_method + - wga_amp_appr + - wga_amp_kit + - bin_param + - bin_software + - reassembly_bin + - mag_cov_software + - vir_ident_software + - pred_genome_type + - pred_genome_struc + - detec_type + - otu_class_appr + - otu_seq_comp_appr + - otu_db + - host_pred_appr + - host_pred_est_acc + - associated_resource + - sop + slot_usage: + adapters: + recommended: true + alt: + recommended: true + assembly_name: + recommended: true + assembly_qual: + required: true + assembly_software: + required: true + bin_param: + recommended: true + bin_software: + recommended: true + compl_appr: + recommended: true + compl_score: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + detec_type: + required: true + elev: + recommended: true + experimental_factor: + recommended: true + feat_pred: + recommended: true + host_disease_stat: + examples: + - value: rabies [DOID:11260] + recommended: true + host_pred_appr: + recommended: true + host_pred_est_acc: + recommended: true + lib_layout: + recommended: true + lib_reads_seqd: + recommended: true + lib_screen: + recommended: true + lib_size: + recommended: true + lib_vector: + recommended: true + mid: + recommended: true + nucl_acid_amp: + recommended: true + nucl_acid_ext: + recommended: true + number_contig: + required: true + otu_class_appr: + recommended: true + otu_db: + recommended: true + otu_seq_comp_appr: + recommended: true + pred_genome_struc: + required: true + pred_genome_type: + required: true + reassembly_bin: + recommended: true + ref_db: + recommended: true + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + examples: + - value: swabbing + recommended: true + samp_mat_process: + recommended: true + samp_size: + recommended: true + sc_lysis_approach: + recommended: true + sc_lysis_method: + recommended: true + sim_search_meth: + recommended: true + size_frac: + recommended: true + sop: + recommended: true + sort_tech: + recommended: true + source_mat_id: + recommended: true + source_uvig: + required: true + tax_class: + recommended: true + temp: + recommended: true + vir_ident_software: + required: true + virus_enrich_appr: + required: true + wga_amp_appr: + recommended: true + wga_amp_kit: + recommended: true + class_uri: MIXS:0010012 + Agriculture: + annotations: + use_cases: + tag: use_cases + value: Agricultural Microbiomes Research Coordination Network, model cropping and plant systems focused on agricultural plant and soil microbe; microbiome studies in agricultural sites; long-term ecological research in croplands; eDNA in manure samples; describing agricultural microbiome studies + description: A collection of terms appropriate when sequencing samples obtained in an agricultural environment. Suitable to capture metadata appropriate to enhance crop productivity and agroecosystem health with the aim to facilitate research of agricultural microbiomes and their relationships to plant productivity and sustainable crop production from diverse crop management contexts. + title: agriculture + aliases: + - MIxS-Ag (agriculture) + is_a: Extension + slots: + - plant_growth_med + - photosynt_activ + - photosynt_activ_meth + - samp_collect_method + - enrichment_protocol + - library_prep_kit + - sequencing_location + - soil_temp + - soil_pH + - soil_conductivity + - rel_location + - soil_cover + - porosity + - soil_texture + - soil_texture_meth + - host_symbiont + - host_disease_stat + - pres_animal_insect + - plant_water_method + - anim_water_method + - farm_water_source + - water_source_shared + - water_pH + - elev + - season + - solar_irradiance + - crop_yield + - season_humidity + - humidity + - adjacent_environment + - chem_administration + - food_prod + - lot_number + - fertilizer_admin + - samp_store_temp + - food_trav_mode + - food_trav_vehic + - farm_equip_san + - farm_equip + - farm_equip_shared + - food_harvest_proc + - plant_struc + - host_dry_mass + - ances_data + - genetic_mod + - food_product_type + - food_source + - spikein_strain + - organism_count + - size_frac_low + - size_frac_up + - cult_isol_date + - samp_pooling + - root_med_macronutr + - root_med_carbon + - root_med_ph + - depth + - specific_host + - pathogenicity + - biotic_relationship + - water_temp_regm + - watering_regm + - standing_water_regm + - gaseous_environment + - fungicide_regm + - climate_environment + - herbicide_regm + - non_min_nutr_regm + - pesticide_regm + - ph_regm + - salt_regm + - season_environment + - temp + - perturbation + - isol_growth_condt + - samp_store_dur + - samp_store_loc + - samp_collect_device + - samp_mat_process + - host_age + - host_common_name + - host_genotype + - host_height + - host_subspecf_genlin + - host_length + - host_life_stage + - host_phenotype + - host_taxid + - host_tot_mass + - host_spec_range + - trophic_level + - plant_product + - samp_size + - oxy_stat_samp + - seq_meth + - samp_vol_we_dna_ext + - pcr_primers + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - target_gene + - target_subfragment + - mid + - adapters + - pcr_cond + - seq_quality_check + - chimera_check + - assembly_name + - assembly_qual + - assembly_software + - annot + - associated_resource + - sop + - source_mat_id + - fao_class + - local_class + - local_class_meth + - soil_type + - soil_type_meth + - soil_horizon + - horizon_meth + - link_class_info + - previous_land_use + - prev_land_use_meth + - crop_rotation + - agrochem_addition + - tillage + - fire + - flooding + - extreme_event + - link_climate_info + - annual_temp + - season_temp + - annual_precpt + - season_precpt + - cur_land_use + - slope_gradient + - slope_aspect + - profile_position + - drainage_class + - store_cond + - ph_meth + - cur_vegetation + - cur_vegetation_meth + - tot_org_carb + - tot_org_c_meth + - tot_nitro_content + - tot_nitro_cont_meth + - microbial_biomass + - micro_biomass_meth + - heavy_metals_meth + - tot_carb + - tot_phosphate + - sieving + - pool_dna_extracts + - misc_param + slot_usage: + adapters: + required: true + annot: + recommended: true + assembly_name: + required: true + biotic_relationship: + recommended: true + chem_administration: + required: true + chimera_check: + required: true + climate_environment: + string_serialization: '{text};{period};{interval};{period}' + recommended: true + crop_rotation: + string_serialization: '{boolean};Rn/{timestamp}/{period}' + recommended: true + cur_vegetation: + recommended: true + cur_vegetation_meth: + recommended: true + depth: + examples: + - value: 5 cm + recommended: true + drainage_class: + recommended: true + enrichment_protocol: + recommended: true + extreme_event: + recommended: true + fao_class: + recommended: true + fire: + recommended: true + flooding: + recommended: true + food_product_type: + examples: + - value: delicatessen salad; FOODON:03316276 + food_source: + examples: + - value: red swamp crayfish; FOODON:03412231 + required: true + fungicide_regm: + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + gaseous_environment: + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + heavy_metals_meth: + string_serialization: '{PMID|DOI|URL}' + recommended: true + herbicide_regm: + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + horizon_meth: + recommended: true + host_age: + required: true + host_common_name: + required: true + host_disease_stat: + examples: + - value: downy mildew + recommended: true + host_genotype: + required: true + host_height: + required: true + host_length: + required: true + host_life_stage: + required: true + host_phenotype: + required: true + host_spec_range: + required: true + host_symbiont: + examples: + - value: Paragordius varius + host_taxid: + examples: + - value: '9606' + string_serialization: '{integer}' + required: true + host_tot_mass: + required: true + humidity: + examples: + - value: 30% relative humidity + recommended: true + lib_layout: + recommended: true + lib_reads_seqd: + required: true + lib_screen: + required: true + lib_vector: + required: true + library_prep_kit: + examples: + - value: llumina DNA Prep, (M) Tagmentation + local_class: + recommended: true + local_class_meth: + recommended: true + micro_biomass_meth: + required: true + microbial_biomass: + required: true + mid: + required: true + non_min_nutr_regm: + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + nucl_acid_amp: + required: true + nucl_acid_ext: + required: true + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + recommended: true + oxy_stat_samp: + recommended: true + pathogenicity: + required: true + pcr_cond: + required: true + pcr_primers: + required: true + perturbation: + recommended: true + pesticide_regm: + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + ph_meth: + recommended: true + ph_regm: + string_serialization: '{float};{period};{interval};{period}' + recommended: true + plant_growth_med: + examples: + - value: hydroponic plant culture media [EO:0007067] + plant_product: + recommended: true + plant_struc: + recommended: true + pool_dna_extracts: + string_serialization: '{boolean};{float} {unit}' + required: true + prev_land_use_meth: + recommended: true + previous_land_use: + recommended: true + profile_position: + recommended: true + rel_location: + recommended: true + salt_regm: + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + samp_collect_device: + examples: + - value: biopsy, niskin bottle, push core + required: true + samp_collect_method: + examples: + - value: environmental swab sampling + samp_mat_process: + required: true + samp_pooling: + recommended: true + samp_size: + required: true + samp_store_dur: + required: true + samp_store_loc: + required: true + samp_vol_we_dna_ext: + required: true + season_environment: + string_serialization: '{text};{period};{interval};{period}' + recommended: true + sieving: + required: true + slope_aspect: + recommended: true + slope_gradient: + recommended: true + soil_conductivity: + description: Conductivity of some soil. + soil_cover: + recommended: true + soil_horizon: + recommended: true + soil_pH: + description: pH of some soil. + soil_type: + required: true + soil_type_meth: + required: true + specific_host: + required: true + standing_water_regm: + string_serialization: '{text};{period};{interval};{period}' + recommended: true + store_cond: + required: true + target_gene: + required: true + target_subfragment: + required: true + temp: + required: true + tillage: + recommended: true + tot_carb: + recommended: true + tot_nitro_cont_meth: + recommended: true + tot_nitro_content: + recommended: true + tot_org_c_meth: + recommended: true + tot_org_carb: + recommended: true + tot_phosphate: + recommended: true + trophic_level: + recommended: true + water_pH: + description: The pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid. + water_temp_regm: + string_serialization: '{float} {unit};{period};{interval};{period}' + recommended: true + watering_regm: + string_serialization: '{float} {unit};{period};{interval};{period}' + recommended: true + class_uri: MIXS:0016018 + Air: + annotations: + use_cases: + tag: use_cases + value: bioaerosol samples, pathogen load in urban air, aerosols + description: A collection of terms appropriate when collecting and sequencing samples obtained from a gaseous environment. + title: air + aliases: + - MIxS-air + is_a: Extension + slots: + - samp_name + - project_name + - alt + - elev + - barometric_press + - carb_dioxide + - carb_monoxide + - chem_administration + - humidity + - methane + - organism_count + - oxygen + - oxy_stat_samp + - perturbation + - pollutants + - air_PM_concen + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - solar_irradiance + - temp + - ventilation_rate + - ventilation_type + - volatile_org_comp + - wind_direction + - wind_speed + - misc_param + slot_usage: + alt: + required: true + elev: + recommended: true + humidity: + examples: + - value: 25 gram per cubic meter + methane: + examples: + - value: 1800 parts per billion + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + wind_direction: + examples: + - value: Northwest + wind_speed: + examples: + - value: 21 kilometer per hour + class_uri: MIXS:0016000 + BuiltEnvironment: + annotations: + use_cases: + tag: use_cases + value: microbiology studies of the built environment, NASA space station sampling, MetaSUB transit system sampling, home, hospitals, office buildings + description: A collection of terms appropriate when collecting samples and sequencing samples obtained in the built-up environment, which includes terms for surface material, humidity, temperature, moisture and occupancy type along with specific metadata terms describing the indoor air, building and sample properties. + title: built environment + aliases: + - MIxS-BE (built environment) + is_a: Extension + slots: + - samp_name + - project_name + - surf_material + - surf_air_cont + - rel_air_humidity + - abs_air_humidity + - surf_humidity + - air_temp + - surf_temp + - surf_moisture_ph + - build_occup_type + - surf_moisture + - dew_point + - carb_dioxide + - ventilation_type + - organism_count + - indoor_space + - indoor_surf + - filter_type + - heat_cool_type + - substructure_type + - building_setting + - light_type + - samp_sort_meth + - space_typ_state + - typ_occup_density + - occup_samp + - occup_density_samp + - address + - adj_room + - aero_struc + - amount_light + - arch_struc + - avg_occup + - avg_dew_point + - avg_temp + - bathroom_count + - bedroom_count + - built_struc_age + - built_struc_set + - built_struc_type + - ceil_area + - ceil_cond + - ceil_finish_mat + - ceil_water_mold + - ceil_struc + - ceil_texture + - ceil_thermal_mass + - ceil_type + - cool_syst_id + - date_last_rain + - build_docs + - door_size + - door_cond + - door_direct + - door_loc + - door_mat + - door_move + - door_water_mold + - door_type + - door_comp_type + - door_type_metal + - door_type_wood + - drawings + - elevator + - escalator + - exp_duct + - exp_pipe + - ext_door + - fireplace_type + - floor_age + - floor_area + - floor_cond + - floor_count + - floor_finish_mat + - floor_water_mold + - floor_struc + - floor_thermal_mass + - freq_clean + - freq_cook + - furniture + - gender_restroom + - hall_count + - handidness + - heat_deliv_loc + - heat_sys_deliv_meth + - heat_system_id + - height_carper_fiber + - inside_lux + - int_wall_cond + - last_clean + - max_occup + - mech_struc + - number_plants + - number_pets + - number_resident + - occup_document + - ext_wall_orient + - ext_window_orient + - rel_humidity_out + - pres_animal_insect + - quad_pos + - rel_samp_loc + - room_air_exch_rate + - room_architec_elem + - room_condt + - room_count + - room_dim + - room_door_dist + - room_loc + - room_moist_dam_hist + - room_net_area + - room_occup + - room_samp_pos + - room_type + - room_vol + - room_window_count + - room_connected + - room_hallway + - room_door_share + - room_wall_share + - samp_weather + - samp_floor + - samp_room_id + - samp_time_out + - season + - season_use + - shading_device_cond + - shading_device_loc + - shading_device_mat + - shad_dev_water_mold + - shading_device_type + - specific_humidity + - specific + - temp_out + - train_line + - train_stat_loc + - train_stop_loc + - vis_media + - wall_area + - wall_const_type + - wall_finish_mat + - wall_height + - wall_loc + - wall_water_mold + - wall_surf_treatment + - wall_texture + - wall_thermal_mass + - water_feat_size + - water_feat_type + - weekday + - window_size + - window_cond + - window_cover + - window_horiz_pos + - window_loc + - window_mat + - window_open_freq + - window_water_mold + - window_status + - window_type + - window_vert_pos + slot_usage: + air_temp: + examples: + - value: 20 degree Celsius + required: true + avg_occup: + examples: + - value: '2' + carb_dioxide: + required: true + freq_clean: + string_serialization: '[ Daily| Weekly| Monthly| Quarterly | Annually| other]' + indoor_surf: + required: true + recommended: true + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + required: true + surf_material: + required: true + recommended: true + ventilation_type: + required: true + class_uri: MIXS:0016001 + FoodAnimalAndAnimalFeed: + annotations: + use_cases: + tag: use_cases + value: Microbiome of farm animals, their feed, and pet food. + description: A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from farm animals and their feed. + title: food-animal and animal feed + comments: + - This extension is intended to work alongside the other food extensions (farm environment, food production facility, and human foods) for capturing contextual data across the food supply-chain environment. + aliases: + - MIxS-Food (animal and animal feed) + is_a: Extension + slots: + - samp_name + - project_name + - lat_lon + - geo_loc_name + - collection_date + - seq_meth + - samp_size + - samp_collect_device + - experimental_factor + - nucl_acid_ext + - organism_count + - spikein_count + - samp_store_temp + - samp_store_dur + - samp_vol_we_dna_ext + - pool_dna_extracts + - temp + - samp_store_loc + - samp_transport_cont + - perturbation + - coll_site_geo_feat + - food_origin + - food_prod + - food_product_type + - food_source + - IFSAC_category + - intended_consumer + - samp_purpose + - animal_am + - animal_am_dur + - animal_am_freq + - animal_am_route + - animal_am_use + - animal_body_cond + - animal_diet + - animal_feed_equip + - animal_group_size + - animal_housing + - animal_sex + - bacterial_density + - cons_food_stor_dur + - cons_food_stor_temp + - cons_purch_date + - cons_qty_purchased + - cult_isol_date + - cult_result + - cult_result_org + - cult_target + - enrichment_protocol + - food_additive + - food_contact_surf + - food_contain_wrap + - food_cooking_proc + - food_dis_point + - food_dis_point_city + - food_ingredient + - food_pack_capacity + - food_pack_integrity + - food_pack_medium + - food_preserv_proc + - food_prior_contact + - food_prod_synonym + - food_product_qual + - food_quality_date + - food_source_age + - food_trace_list + - food_trav_mode + - food_trav_vehic + - food_treat_proc + - HACCP_term + - library_prep_kit + - lot_number + - microb_cult_med + - part_plant_animal + - repository_name + - samp_collect_method + - samp_pooling + - samp_rep_biol + - samp_rep_tech + - samp_source_mat_cat + - samp_stor_device + - samp_stor_media + - samp_transport_dur + - samp_transport_temp + - sequencing_kit + - sequencing_location + - serovar_or_serotype + - spikein_AMR + - spikein_antibiotic + - spikein_growth_med + - spikein_metal + - spikein_org + - spikein_serovar + - spikein_strain + - study_design + - study_inc_dur + - study_inc_temp + - study_timecourse + - study_tmnt + - timepoint + - misc_param + slot_usage: + food_origin: + required: true + food_pack_medium: + examples: + - value: packed in fruit juice [FOODON:03480039] + food_prod: + required: true + food_product_type: + examples: + - value: shrimp (peeled, deep-frozen) [FOODON:03317171] + required: true + food_source: + examples: + - value: giant tiger prawn [FOODON:03412612] + intended_consumer: + required: true + library_prep_kit: + examples: + - value: Illumina DNA Prep + organism_count: + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + pool_dna_extracts: + string_serialization: '{boolean},{integer}' + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: environmental swab sampling + samp_purpose: + required: true + class_uri: MIXS:0016019 + FoodFarmEnvironment: + annotations: + use_cases: + tag: use_cases + value: Microbiome of farm and field crops as well as environmental samples including irrigation, soil amendments, and farm equipment. + description: A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from the farm environment, including soil, manure, and food harvesting equipment. + title: food-farm environment + comments: + - This extension is intended to work alongside the other food extensions (animals and animal feed, food production facility, and human foods) for capturing contextual data across the food supply-chain environment. + aliases: + - MIxS-Food (farm environment) + is_a: Extension + slots: + - samp_name + - project_name + - lat_lon + - geo_loc_name + - collection_date + - seq_meth + - samp_size + - samp_collect_device + - nucl_acid_ext + - humidity + - organism_count + - spikein_count + - samp_store_temp + - solar_irradiance + - ventilation_rate + - samp_store_dur + - wind_speed + - salinity + - samp_vol_we_dna_ext + - previous_land_use + - crop_rotation + - soil_type_meth + - tot_org_c_meth + - tot_nitro_cont_meth + - host_age + - host_dry_mass + - host_height + - host_length + - host_tot_mass + - root_med_carbon + - root_med_macronutr + - root_med_micronutr + - depth + - season_temp + - season_precpt + - tot_org_carb + - tot_nitro_content + - conduc + - turbidity + - size_frac_low + - size_frac_up + - temp + - ventilation_type + - wind_direction + - genetic_mod + - host_phenotype + - ph + - ances_data + - biotic_regm + - chem_administration + - growth_habit + - host_disease_stat + - host_genotype + - host_taxid + - mechanical_damage + - perturbation + - root_cond + - root_med_ph + - tillage + - ph_meth + - growth_medium + - season + - food_product_type + - samp_type + - farm_water_source + - plant_water_method + - air_PM_concen + - animal_feed_equip + - animal_intrusion + - anim_water_method + - crop_yield + - cult_result + - cult_result_org + - cult_target + - plant_part_maturity + - adjacent_environment + - water_source_adjac + - farm_equip_shared + - farm_equip_san + - farm_equip_san_freq + - farm_equip + - fertilizer_admin + - fertilizer_date + - animal_group_size + - animal_diet + - food_contact_surf + - food_contain_wrap + - food_harvest_proc + - food_pack_medium + - food_preserv_proc + - food_prod_char + - prod_label_claims + - food_trav_mode + - food_trav_vehic + - food_source + - food_treat_proc + - extr_weather_event + - date_extr_weath + - host_subspecf_genlin + - intended_consumer + - library_prep_kit + - air_flow_impede + - lot_number + - season_humidity + - part_plant_animal + - plant_growth_med + - plant_reprod_crop + - samp_purpose + - repository_name + - samp_pooling + - samp_source_mat_cat + - sequencing_kit + - sequencing_location + - serovar_or_serotype + - soil_conductivity + - soil_cover + - soil_pH + - rel_location + - soil_porosity + - soil_temp + - soil_texture_class + - soil_texture_meth + - soil_type + - spikein_org + - spikein_serovar + - spikein_growth_med + - spikein_strain + - spikein_antibiotic + - spikein_metal + - timepoint + - water_frequency + - water_pH + - water_source_shared + - enrichment_protocol + - food_quality_date + - IFSAC_category + - animal_housing + - cult_isol_date + - food_clean_proc + - misc_param + slot_usage: + biotic_regm: + required: true + chem_administration: + required: true + crop_rotation: + string_serialization: '{boolean};{Rn/start_time/end_time/duration}' + depth: + examples: + - value: 10 meter + required: true + food_pack_medium: + examples: + - value: vacuum-packed [FOODON:03480027] + food_product_type: + examples: + - value: shrimp (peeled, deep-frozen) [FOODON:03317171] + required: true + food_source: + examples: + - value: giant tiger prawn [FOODON:03412612] + host_age: + examples: + - value: 10 days + host_disease_stat: + examples: + - value: downy mildew + recommended: true + host_genotype: + examples: + - value: Ts + host_height: + examples: + - value: 1 meter + host_phenotype: + examples: + - value: seed pod; green [PATO:0000320] + host_taxid: + examples: + - value: '4530' + string_serialization: '{NCBI taxid}' + host_tot_mass: + examples: + - value: 2500 gram + humidity: + examples: + - value: 30% relative humidity + library_prep_kit: + examples: + - value: Illumina DNA Prep + organism_count: + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + plant_growth_med: + examples: + - value: soil + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + soil_conductivity: + description: Conductivity of soil at time of sampling. + soil_pH: + description: The pH of soil at time of sampling. + soil_type: + string_serialization: '{termLabel} [{termID}]' + water_pH: + description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid. + wind_direction: + examples: + - value: 0 degrees; Northwest + wind_speed: + examples: + - value: 1.6 kilometers per hour + class_uri: MIXS:0016020 + FoodFoodProductionFacility: + annotations: + use_cases: + tag: use_cases + value: Microbiome of food production facilities/factories + description: A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from food production facilities. + title: food-food production facility + comments: + - This extension is intended to work alongside the other food extensions (animals and animal feed, farm environment, and human foods) for capturing contextual data across the food supply-chain environment. + aliases: + - MIxS-Food(food production facility) + is_a: Extension + slots: + - samp_name + - project_name + - lat_lon + - geo_loc_name + - collection_date + - seq_meth + - samp_size + - samp_collect_device + - experimental_factor + - nucl_acid_ext + - organism_count + - samp_store_temp + - samp_store_dur + - air_temp + - room_dim + - freq_clean + - samp_room_id + - samp_vol_we_dna_ext + - pool_dna_extracts + - samp_store_loc + - surf_material + - indoor_surf + - avg_occup + - samp_floor + - genetic_mod + - coll_site_geo_feat + - samp_source_mat_cat + - samp_type + - samp_stor_media + - samp_stor_device + - food_product_type + - IFSAC_category + - food_product_qual + - food_contact_surf + - facility_type + - food_trav_mode + - food_trav_vehic + - samp_transport_dur + - samp_transport_temp + - samp_collect_method + - num_samp_collect + - lot_number + - hygienic_area + - env_monitoring_zone + - area_samp_size + - samp_surf_moisture + - samp_loc_condition + - biocide_used + - ster_meth_samp_room + - enrichment_protocol + - cult_target + - microb_cult_med + - timepoint + - bacterial_density + - cult_isol_date + - cult_result + - cult_result_org + - subspecf_gen_lin + - samp_pooling + - samp_purpose + - samp_rep_tech + - samp_rep_biol + - samp_transport_cont + - study_design + - nucl_acid_ext_kit + - library_prep_kit + - sequencing_kit + - sequencing_location + - study_inc_temp + - study_inc_dur + - study_timecourse + - study_tmnt + - food_source + - food_dis_point + - food_dis_point_city + - food_origin + - food_prod_synonym + - food_additive + - food_trace_list + - part_plant_animal + - food_ingredient + - spec_intended_cons + - HACCP_term + - dietary_claim_use + - food_allergen_label + - food_prod_char + - prod_label_claims + - food_name_status + - food_preserv_proc + - food_cooking_proc + - food_treat_proc + - food_contain_wrap + - food_pack_capacity + - food_pack_medium + - food_prior_contact + - food_prod + - food_quality_date + - repository_name + - intended_consumer + - food_pack_integrity + - misc_param + slot_usage: + air_temp: + examples: + - value: 4 degree Celsius + avg_occup: + examples: + - value: '6' + food_contact_surf: + required: true + food_pack_medium: + examples: + - value: vacuum-packed [FOODON:03480027] + food_product_qual: + required: true + food_product_type: + examples: + - value: shrimp (peeled, deep-frozen) [FOODON:03317171] + required: true + food_source: + examples: + - value: giant tiger prawn [FOODON:03412612] + library_prep_kit: + examples: + - value: Illumina DNA Prep + organism_count: + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + pool_dna_extracts: + string_serialization: '{boolean},{integer}' + samp_collect_device: + examples: + - value: biopsy, niskin bottle, push core + samp_collect_method: + examples: + - value: environmental swab sampling + samp_source_mat_cat: + required: true + samp_stor_device: + required: true + samp_stor_media: + required: true + class_uri: MIXS:0016021 + FoodHumanFoods: + annotations: + use_cases: + tag: use_cases + value: Microbiome of foods intended for human consumption. + description: A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from human food products. + title: food-human foods + comments: + - This extension is intended to work alongside the other food extensions (animals and animal feed, farm environment, and food production facilities) for capturing contextual data across the food supply-chain environment. + aliases: + - MIxS-Food (human foods) + is_a: Extension + slots: + - samp_name + - project_name + - lat_lon + - geo_loc_name + - collection_date + - seq_meth + - samp_size + - samp_collect_device + - experimental_factor + - nucl_acid_ext + - organism_count + - spikein_count + - samp_store_temp + - samp_store_dur + - samp_vol_we_dna_ext + - pool_dna_extracts + - temp + - samp_store_loc + - genetic_mod + - perturbation + - coll_site_geo_feat + - food_product_type + - IFSAC_category + - ferm_chem_add + - ferm_chem_add_perc + - ferm_headspace_oxy + - ferm_medium + - ferm_pH + - ferm_rel_humidity + - ferm_temp + - ferm_time + - ferm_vessel + - bacterial_density + - cons_food_stor_dur + - cons_food_stor_temp + - cons_purch_date + - cons_qty_purchased + - cult_isol_date + - cult_result + - cult_result_org + - cult_target + - dietary_claim_use + - enrichment_protocol + - food_additive + - food_allergen_label + - food_contact_surf + - food_contain_wrap + - food_cooking_proc + - food_dis_point + - food_ingredient + - food_name_status + - food_origin + - food_pack_capacity + - food_pack_integrity + - food_pack_medium + - food_preserv_proc + - food_prior_contact + - food_prod + - food_prod_synonym + - food_product_qual + - food_quality_date + - food_source + - food_trace_list + - food_trav_mode + - food_trav_vehic + - food_treat_proc + - HACCP_term + - intended_consumer + - library_prep_kit + - lot_number + - microb_cult_med + - microb_start + - microb_start_count + - microb_start_inoc + - microb_start_prep + - microb_start_source + - microb_start_taxID + - nucl_acid_ext_kit + - num_samp_collect + - part_plant_animal + - repository_name + - samp_collect_method + - samp_pooling + - samp_rep_biol + - samp_rep_tech + - samp_source_mat_cat + - samp_stor_device + - samp_stor_media + - samp_transport_cont + - samp_transport_dur + - samp_transport_temp + - samp_purpose + - sequencing_kit + - sequencing_location + - serovar_or_serotype + - spikein_AMR + - spikein_antibiotic + - spikein_growth_med + - spikein_metal + - spikein_org + - spikein_serovar + - spikein_strain + - study_design + - study_inc_dur + - study_inc_temp + - study_timecourse + - study_tmnt + - timepoint + - misc_param + slot_usage: + food_pack_medium: + examples: + - value: vacuum-packed[FOODON:03480027] + food_product_type: + examples: + - value: shrimp (peeled, deep-frozen) [FOODON:03317171] + required: true + food_source: + examples: + - value: giant tiger prawn [FOODON:03412612] + library_prep_kit: + examples: + - value: Illumina DNA Prep + organism_count: + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + pool_dna_extracts: + string_serialization: '{boolean},{integer}' + samp_collect_device: + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + samp_collect_method: + examples: + - value: environmental swab sampling + class_uri: MIXS:0016022 + HostAssociated: + annotations: + use_cases: + tag: use_cases + value: elephant fecal matter or cat oral cavity + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from a non-human host, to examine the host-associated microbiome or genome. + title: host-associated + comments: + - This is a very broad package, intended to capture many kinds of sequences derived from the bodies of or derived from an organism. Where possible, please use a more specific package. For example, consider using food-animal and animal feed extension for sampling of farm animals reared for consumption. For human stool microbiomes, consider MIxS-human-gut. Incidental associations of environmental material with an organism may also be better served by other packages. For example, nucleic acids derived from soil that was sampled from the hoof of a cow may be better described by terms from the soil extension; however, soil embedded in a wound on a cow’s leg would be best described by terms in this extension + aliases: + - MIxS-host-associated + is_a: Extension + slots: + - samp_name + - project_name + - alt + - depth + - elev + - ances_data + - biol_stat + - genetic_mod + - host_common_name + - samp_capt_status + - samp_dis_stage + - host_taxid + - host_subject_id + - host_age + - host_life_stage + - host_sex + - host_disease_stat + - chem_administration + - host_body_habitat + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_length + - host_diet + - host_last_meal + - host_growth_cond + - host_substrate + - host_fam_rel + - host_subspecf_genlin + - host_genotype + - host_phenotype + - host_body_temp + - host_dry_mass + - blood_press_diast + - blood_press_syst + - host_color + - host_shape + - gravidity + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - host_symbiont + - misc_param + slot_usage: + alt: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + host_age: + examples: + - value: 10 days + host_body_habitat: + examples: + - value: nasopharynx + host_body_site: + examples: + - value: gill [UBERON:0002535] + host_body_temp: + examples: + - value: 15 degree Celsius + host_common_name: + examples: + - value: human + host_diet: + examples: + - value: herbivore + host_disease_stat: + examples: + - value: rabies [DOID:11260] + host_fam_rel: + examples: + - value: offspring;Mussel25 + host_genotype: + examples: + - value: C57BL/6 + host_height: + examples: + - value: 0.1 meter + host_last_meal: + examples: + - value: corn feed;P2H + host_life_stage: + examples: + - value: adult + host_phenotype: + examples: + - value: elongated [PATO:0001154] + host_subject_id: + examples: + - value: MPI123 + host_symbiont: + examples: + - value: flukeworms + host_taxid: + examples: + - value: '7955' + string_serialization: '{NCBI taxid}' + host_tot_mass: + examples: + - value: 2500 gram + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016002 + HumanAssociated: + annotations: + use_cases: + tag: use_cases + value: blood samples or biopsy samples. + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their human-associated microbiome or genome, that does not have a specific extension (e.g., skin, gut, vaginal). + title: human-associated + comments: + - For stool samples use MIxS-human-gut extension. + aliases: + - MIxS-human-associated + is_a: Extension + slots: + - samp_name + - project_name + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - smoker + - host_hiv_stat + - drug_usage + - host_body_mass_index + - diet_last_six_month + - weight_loss_3_month + - ethnicity + - host_occupation + - pet_farm_animal + - travel_out_six_month + - twin_sibling + - medic_hist_perform + - study_complt_stat + - pulmonary_disord + - nose_throat_disord + - blood_blood_disord + - host_pulse + - gestation_state + - maternal_health_stat + - foetal_health_stat + - amniotic_fluid_color + - kidney_disord + - urogenit_tract_disor + - urine_collect_meth + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - host_symbiont + - samp_store_loc + - misc_param + slot_usage: + host_age: + examples: + - value: 30 years + host_body_site: + examples: + - value: Lung parenchyma [fma27360] + host_body_temp: + examples: + - value: 36.5 degree Celsius + host_diet: + examples: + - value: high-fat + host_disease_stat: + examples: + - value: measles [DOID:8622] + host_fam_rel: + examples: + - value: mother;ID298 + host_genotype: + examples: + - value: ST1 + host_height: + examples: + - value: 1.75 meter + host_last_meal: + examples: + - value: french fries;P5H30M + host_phenotype: + examples: + - value: Tinnitus [HP:0000360] + host_subject_id: + examples: + - value: MPI123 + host_symbiont: + examples: + - value: flukeworms + host_tot_mass: + examples: + - value: 65 kilogram + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016003 + HumanGut: + annotations: + use_cases: + tag: use_cases + value: human stool or fecal samples, or samples collected directly from the gut. + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome. + title: human-gut + aliases: + - MIxS-human-gut + is_a: Extension + slots: + - samp_name + - project_name + - gastrointest_disord + - liver_disord + - special_diet + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_store_temp + - samp_vol_we_dna_ext + - samp_store_dur + - host_symbiont + - samp_store_loc + - misc_param + slot_usage: + host_age: + examples: + - value: 30 years + host_body_site: + examples: + - value: Wall of gut [fma45653] + host_body_temp: + examples: + - value: 36.5 degree Celsius + host_diet: + examples: + - value: high-fat + host_disease_stat: + examples: + - value: measles [DOID:8622] + host_fam_rel: + examples: + - value: mother;ID298 + host_genotype: + examples: + - value: ST1 + host_height: + examples: + - value: 1.75 meter + host_last_meal: + examples: + - value: french fries;P5H30M + host_phenotype: + examples: + - value: Tinnitus [HP:0000360] + host_subject_id: + examples: + - value: MPI123 + host_symbiont: + examples: + - value: flukeworms + host_tot_mass: + examples: + - value: 65 kilogram + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016004 + HumanOral: + annotations: + use_cases: + tag: use_cases + value: mouth swab sampling, dental microbiome samples, microbiome of oral swabs, nasal, mouth, throat, teeth, tongue microbiome studies + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their oral-associated microbiome. + title: human-oral + aliases: + - MIxS-human-oral + is_a: Extension + slots: + - samp_name + - project_name + - nose_mouth_teeth_throat_disord + - time_last_toothbrush + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - host_symbiont + - samp_store_loc + - misc_param + slot_usage: + host_age: + examples: + - value: 30 years + host_body_site: + examples: + - value: Epithelium of tongue [fma284658] + host_body_temp: + examples: + - value: 36.5 degree Celsius + host_diet: + examples: + - value: high-fat + host_disease_stat: + examples: + - value: measles [DOID:8622] + host_fam_rel: + examples: + - value: mother;ID298 + host_genotype: + examples: + - value: ST1 + host_height: + examples: + - value: 1.75 meter + host_last_meal: + examples: + - value: french fries;P5H30M + host_phenotype: + examples: + - value: Tinnitus [HP:0000360] + host_subject_id: + examples: + - value: MPI123 + host_symbiont: + examples: + - value: flukeworms + host_tot_mass: + examples: + - value: 65 kilogram + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016005 + HumanSkin: + annotations: + use_cases: + tag: use_cases + value: swab samples taken on a person’s skin surface. + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their skin-associated microbiome. + title: human-skin + aliases: + - MIxS-human-skin + is_a: Extension + slots: + - samp_name + - project_name + - dermatology_disord + - time_since_last_wash + - dominant_hand + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - host_symbiont + - misc_param + slot_usage: + host_age: + examples: + - value: 30 years + host_body_site: + examples: + - value: Skin of palm of left hand [fma38303] + host_body_temp: + examples: + - value: 36.5 degree Celsius + host_diet: + examples: + - value: high-fat + host_disease_stat: + examples: + - value: measles [DOID:8622] + host_fam_rel: + examples: + - value: mother;ID298 + host_genotype: + examples: + - value: ST1 + host_height: + examples: + - value: 1.75 meter + host_last_meal: + examples: + - value: french fries;P5H30M + host_phenotype: + examples: + - value: Tinnitus [HP:0000360] + host_subject_id: + examples: + - value: MPI123 + host_symbiont: + examples: + - value: flukeworms + host_tot_mass: + examples: + - value: 65 kilogram + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016006 + HumanVaginal: + annotations: + use_cases: + tag: use_cases + value: vaginal swabbing + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their vaginal-associated microbiome. + title: human-vaginal + aliases: + - MIxS-human-vaginal + is_a: Extension + slots: + - samp_name + - project_name + - menarche + - sexual_act + - pregnancy + - douche + - birth_control + - menopause + - hrt + - hysterectomy + - gynecologic_disord + - urogenit_disord + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_loc + - samp_store_dur + - host_symbiont + - misc_param + slot_usage: + host_age: + examples: + - value: 30 years + host_body_site: + examples: + - value: Ectocervix [fma86484] + host_body_temp: + examples: + - value: 36.5 degree Celsius + host_diet: + examples: + - value: high-fat + host_disease_stat: + examples: + - value: measles [DOID:8622] + host_fam_rel: + examples: + - value: mother;ID298 + host_genotype: + examples: + - value: ST1 + host_height: + examples: + - value: 1.75 meter + host_last_meal: + examples: + - value: french fries;P5H30M + host_phenotype: + examples: + - value: Tinnitus [HP:0000360] + host_subject_id: + examples: + - value: MPI123 + host_symbiont: + examples: + - value: flukeworms + host_tot_mass: + examples: + - value: 65 kilogram + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016007 + HydrocarbonResourcesCores: + annotations: + use_cases: + tag: use_cases + value: The microbial characterization of hydrocarbon occurrences, defined as the natural and artificial environmental features that are rich in hydrocarbons, from hydrocarbon rich formations, such as reservoir cores. + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from environments pertaining to hydrocarbon resources, specifically core samples. + title: hydrocarbon resources-cores + aliases: + - MIxS-HCR (hydrocarbon resources-cores) + is_a: Extension + slots: + - samp_name + - project_name + - hcr + - hc_produced + - basin + - field + - reservoir + - hcr_temp + - tvdss_of_hcr_temp + - hcr_pressure + - tvdss_of_hcr_press + - permeability + - porosity + - lithology + - depos_env + - hcr_geol_age + - owc_tvdss + - hcr_fw_salinity + - sulfate_fw + - vfa_fw + - sr_kerog_type + - sr_lithology + - sr_dep_env + - sr_geol_age + - samp_well_name + - win + - samp_type + - samp_subtype + - temp + - pressure + - samp_tvdss + - samp_md + - elev + - oxy_stat_samp + - samp_transport_cond + - samp_store_temp + - samp_store_dur + - samp_store_loc + - samp_vol_we_dna_ext + - organism_count + - org_count_qpcr_info + - ph + - salinity + - alkalinity + - alkalinity_method + - sulfate + - sulfide + - tot_sulfur + - nitrate + - nitrite + - ammonium + - tot_nitro + - diss_iron + - sodium + - chloride + - potassium + - magnesium + - calcium + - tot_iron + - diss_org_carb + - diss_inorg_carb + - diss_inorg_phosp + - tot_phosp + - suspend_solids + - density + - diss_carb_dioxide + - diss_oxygen_fluid + - vfa + - benzene + - toluene + - ethylbenzene + - xylene + - api + - tan + - viscosity + - pour_point + - saturates_pc + - aromatics_pc + - resins_pc + - asphaltenes_pc + - misc_param + - additional_info + slot_usage: + ammonium: + recommended: true + depos_env: + examples: + - value: Continental - Alluvial + diss_inorg_phosp: + recommended: true + hcr_temp: + required: true + nitrate: + recommended: true + nitrite: + recommended: true + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + recommended: true + ph: + recommended: true + samp_vol_we_dna_ext: + recommended: true + sulfate: + recommended: true + sulfate_fw: + required: true + sulfide: + recommended: true + temp: + required: true + vfa_fw: + required: true + class_uri: MIXS:0016015 + HydrocarbonResourcesFluidsSwabs: + annotations: + use_cases: + tag: use_cases + value: The microbial characterization of hydrocarbon occurrences, defined as the natural and artificial environmental features that are rich in hydrocarbons, from hydrocarbon resource fluids. + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from environments pertaining to hydrocarbon resources, specifically run-off liquids samples and swabs. + title: hydrocarbon resources-fluids/swabs + aliases: + - MIxS-HCR (hydrocarbon resources-fluids/swabs) + is_a: Extension + slots: + - samp_name + - project_name + - hcr + - hc_produced + - basin + - field + - reservoir + - hcr_temp + - tvdss_of_hcr_temp + - hcr_pressure + - tvdss_of_hcr_press + - lithology + - depos_env + - hcr_geol_age + - hcr_fw_salinity + - sulfate_fw + - vfa_fw + - prod_start_date + - prod_rate + - water_prod_rate + - water_cut + - iwf + - add_recov_method + - iw_bt_date_well + - biocide + - biocide_admin_method + - chem_treatment + - chem_treat_method + - samp_loc_corr_rate + - samp_well_name + - win + - samp_type + - samp_subtype + - samp_collect_point + - temp + - pressure + - oxy_stat_samp + - samp_preserv + - samp_transport_cond + - samp_store_temp + - samp_store_dur + - samp_store_loc + - samp_vol_we_dna_ext + - organism_count + - org_count_qpcr_info + - ph + - salinity + - alkalinity + - alkalinity_method + - sulfate + - sulfide + - tot_sulfur + - nitrate + - nitrite + - ammonium + - tot_nitro + - diss_iron + - sodium + - chloride + - potassium + - magnesium + - calcium + - tot_iron + - diss_org_carb + - diss_inorg_carb + - diss_inorg_phosp + - tot_phosp + - suspend_solids + - density + - diss_carb_dioxide + - diss_oxygen_fluid + - vfa + - benzene + - toluene + - ethylbenzene + - xylene + - api + - tan + - viscosity + - pour_point + - saturates_pc + - aromatics_pc + - resins_pc + - asphaltenes_pc + - misc_param + - additional_info + slot_usage: + ammonium: + recommended: true + depos_env: + examples: + - value: Marine - Reef + diss_inorg_phosp: + recommended: true + hcr_temp: + recommended: true + nitrate: + required: true + nitrite: + recommended: true + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + recommended: true + ph: + recommended: true + samp_vol_we_dna_ext: + recommended: true + sulfate: + required: true + sulfate_fw: + recommended: true + sulfide: + required: true + temp: + required: true + vfa_fw: + recommended: true + class_uri: MIXS:0016016 + MicrobialMatBiofilm: + annotations: + use_cases: + tag: use_cases + value: samples from microbial mats at cold seeps + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from biofilm environments including microbial mats. + title: microbial mat/biofilm + aliases: + - MIxS-microbial mat/biofilm + is_a: Extension + slots: + - samp_name + - project_name + - depth + - elev + - alkalinity + - alkyl_diethers + - aminopept_act + - ammonium + - bacteria_carb_prod + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - glucosidase_act + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - methane + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - part_org_carb + - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - potassium + - pressure + - redox_potential + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - sodium + - sulfate + - sulfide + - temp + - tot_carb + - tot_nitro_content + - tot_org_carb + - turbidity + - water_content + slot_usage: + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + methane: + examples: + - value: 0.15 micromole per liter + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + water_content: + string_serialization: '{float} {unit}' + class_uri: MIXS:0016008 + MiscellaneousNaturalOrArtificialEnvironment: + description: A collection of generic terms appropriate when collecting and sequencing samples obtained from environments, where there is no specific extension already available. + title: miscellaneous natural or artificial environment + aliases: + - MIxS-miscellaneous natural or artificial environment + is_a: Extension + slots: + - samp_name + - project_name + - alt + - depth + - elev + - alkalinity + - ammonium + - biomass + - bromide + - calcium + - chem_administration + - chloride + - chlorophyll + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_nitro + - diss_oxygen + - misc_param + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - perturbation + - phosphate + - phosplipid_fatt_acid + - potassium + - pressure + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - sodium + - sulfate + - sulfide + - temp + - water_current + slot_usage: + alt: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016009 + PlantAssociated: + annotations: + use_cases: + tag: use_cases + value: plant surface swabs, root soil or rhizosphere, cultivated plants, plant phenotyping + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from a plant to examine it’s plant-associated microbiome. + title: plant-associated + aliases: + - MIxS-plant-associated + is_a: Extension + slots: + - samp_name + - project_name + - depth + - elev + - air_temp_regm + - ances_data + - antibiotic_regm + - biol_stat + - biotic_regm + - chem_administration + - chem_mutagen + - climate_environment + - cult_root_med + - fertilizer_regm + - fungicide_regm + - gaseous_environment + - genetic_mod + - gravity + - growth_facil + - growth_habit + - growth_hormone_regm + - herbicide_regm + - host_age + - host_common_name + - host_disease_stat + - host_dry_mass + - host_genotype + - host_height + - host_subspecf_genlin + - host_length + - host_life_stage + - host_phenotype + - host_taxid + - host_tot_mass + - host_wet_mass + - humidity_regm + - light_regm + - mechanical_damage + - mineral_nutr_regm + - misc_param + - non_min_nutr_regm + - organism_count + - oxy_stat_samp + - ph_regm + - perturbation + - pesticide_regm + - plant_growth_med + - plant_product + - plant_sex + - plant_struc + - radiation_regm + - rainfall_regm + - root_cond + - root_med_carbon + - root_med_macronutr + - root_med_micronutr + - root_med_suppl + - root_med_ph + - root_med_regl + - root_med_solid + - salt_regm + - samp_capt_status + - samp_dis_stage + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - season_environment + - standing_water_regm + - temp + - tiss_cult_growth_med + - water_temp_regm + - watering_regm + - host_symbiont + slot_usage: + climate_environment: + string_serialization: '{text};{Rn/start_time/end_time/duration}' + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + fungicide_regm: + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + gaseous_environment: + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + herbicide_regm: + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + host_age: + examples: + - value: 10 days + host_common_name: + examples: + - value: rice + host_disease_stat: + examples: + - value: downy mildew + host_genotype: + examples: + - value: Ts + host_height: + examples: + - value: 1 meter + host_life_stage: + examples: + - value: adult + host_phenotype: + examples: + - value: seed pod; green [PATO:0000320] + host_symbiont: + examples: + - value: flukeworms + host_taxid: + examples: + - value: '4530' + string_serialization: '{NCBI taxid}' + host_tot_mass: + examples: + - value: 2500 gram + non_min_nutr_regm: + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + pesticide_regm: + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + ph_regm: + string_serialization: '{float};{Rn/start_time/end_time/duration}' + plant_growth_med: + examples: + - value: hydroponic plant culture media [EO:0007067] + salt_regm: + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + season_environment: + string_serialization: '{text};{Rn/start_time/end_time/duration}' + standing_water_regm: + string_serialization: '{text};{Rn/start_time/end_time/duration}' + water_temp_regm: + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + watering_regm: + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + class_uri: MIXS:0016010 + Sediment: + annotations: + use_cases: + tag: use_cases + value: river bed or sea floor. + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from the sedimentary area of aquatic environments. + title: sediment + comments: + - Sedimentary layers in terrestrial environments will probably be better served by the soil extension. + aliases: + - MIxS-sediment + is_a: Extension + slots: + - samp_name + - project_name + - depth + - elev + - alkalinity + - alkyl_diethers + - aminopept_act + - ammonium + - bacteria_carb_prod + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - glucosidase_act + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - methane + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - particle_class + - part_org_carb + - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - porosity + - potassium + - pressure + - redox_potential + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - sediment_type + - silicate + - sodium + - sulfate + - sulfide + - temp + - tidal_stage + - tot_carb + - tot_depth_water_col + - tot_nitro_content + - tot_org_carb + - turbidity + - water_content + slot_usage: + depth: + examples: + - value: 10 meter + required: true + elev: + recommended: true + methane: + examples: + - value: 0.15 micromole per liter + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + water_content: + string_serialization: '{float} {unit}' + class_uri: MIXS:0016011 + Soil: + annotations: + use_cases: + tag: use_cases + value: soil collection, island microbiome sampling, farm land or forest floor. + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium. + title: soil + see_also: + - https://www.fao.org/agriculture/crops/thematic-sitemap/theme/spi/soil-biodiversity/research-into-soil-biodiversity/the-terragenome-project/en/ + aliases: + - MIxS-soil + is_a: Extension + slots: + - samp_name + - project_name + - depth + - elev + - cur_land_use + - cur_vegetation + - cur_vegetation_meth + - previous_land_use + - prev_land_use_meth + - crop_rotation + - agrochem_addition + - tillage + - fire + - flooding + - extreme_event + - soil_horizon + - horizon_meth + - sieving + - water_content + - water_cont_soil_meth + - samp_vol_we_dna_ext + - pool_dna_extracts + - store_cond + - link_climate_info + - annual_temp + - season_temp + - annual_precpt + - season_precpt + - link_class_info + - fao_class + - local_class + - local_class_meth + - org_nitro + - temp + - soil_type + - soil_type_meth + - slope_gradient + - slope_aspect + - profile_position + - drainage_class + - soil_texture + - soil_texture_meth + - ph + - ph_meth + - org_matter + - tot_org_carb + - tot_org_c_meth + - tot_nitro_content + - tot_nitro_cont_meth + - microbial_biomass + - micro_biomass_meth + - link_addit_analys + - heavy_metals + - heavy_metals_meth + - al_sat + - al_sat_meth + - misc_param + slot_usage: + crop_rotation: + string_serialization: '{boolean};{Rn/start_time/end_time/duration}' + depth: + examples: + - value: 10 meter + required: true + elev: + required: true + heavy_metals_meth: + string_serialization: '{PMID}|{DOI}|{URL}' + pool_dna_extracts: + string_serialization: '{boolean};{integer}' + soil_type: + string_serialization: '{termLabel} [{termID}]' + water_content: + string_serialization: '{float}' + class_uri: MIXS:0016012 + SymbiontAssociated: + annotations: + use_cases: + tag: use_cases + value: the microbiome sequence of a flea sampled from a farm animal + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from an organism that lives in close association with any other organism(s). + title: symbiont-associated + aliases: + - MIxS-SA (symbiont-associated) + is_a: Extension + slots: + - samp_name + - project_name + - lat_lon + - geo_loc_name + - collection_date + - alt + - depth + - elev + - host_subject_id + - host_common_name + - host_taxid + - source_mat_id + - host_dependence + - type_of_symbiosis + - sym_life_cycle_type + - host_life_stage + - host_age + - urobiom_sex + - mode_transmission + - route_transmission + - host_body_habitat + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_length + - host_growth_cond + - host_substrate + - host_fam_rel + - host_infra_spec_name + - host_infra_spec_rank + - host_genotype + - host_phenotype + - host_dry_mass + - host_color + - host_shape + - gravidity + - host_number + - host_symbiont + - host_specificity + - symbiont_host_role + - host_cellular_loc + - association_duration + - host_of_host_coinf + - host_of_host_name + - host_of_host_env_loc + - host_of_host_env_med + - host_of_host_taxid + - host_of_host_sub_id + - host_of_host_disease + - host_of_host_fam_rel + - host_of_host_infname + - host_of_host_infrank + - host_of_host_geno + - host_of_host_pheno + - host_of_host_gravid + - host_of_host_totmass + - chem_administration + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - samp_store_sol + - misc_param + slot_usage: + alt: + recommended: true + depth: + examples: + - value: 10 meter + recommended: true + elev: + recommended: true + host_body_habitat: + examples: + - value: anterior end of a tapeworm + host_body_site: + examples: + - value: scolex [UBERON:0015119] + host_common_name: + examples: + - value: trematode + host_fam_rel: + examples: + - value: clone;P15 + host_life_stage: + examples: + - value: redia + required: true + host_phenotype: + examples: + - value: soldier + host_subject_id: + examples: + - value: P14 + host_symbiont: + examples: + - value: Paragordius varius + host_taxid: + examples: + - value: '395013' + string_serialization: '{integer}' + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016023 + WastewaterSludge: + annotations: + use_cases: + tag: use_cases + value: sewerage or industrial wastewater + description: A collection of terms appropriate when collecting samples and sequencing samples obtained from any solid, semisolid or liquid waste. + title: wastewater/sludge + aliases: + - MIxS-wastewater/sludge + is_a: Extension + slots: + - samp_name + - project_name + - depth + - alkalinity + - biochem_oxygen_dem + - chem_administration + - chem_oxygen_dem + - efficiency_percent + - emulsions + - gaseous_substances + - indust_eff_percent + - inorg_particles + - misc_param + - nitrate + - org_particles + - organism_count + - oxy_stat_samp + - ph + - perturbation + - phosphate + - pre_treatment + - primary_treatment + - reactor_type + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - secondary_treatment + - sewage_type + - sludge_retent_time + - sodium + - soluble_inorg_mat + - soluble_org_mat + - suspend_solids + - temp + - tertiary_treatment + - tot_nitro + - tot_phosphate + - wastewater_type + slot_usage: + depth: + examples: + - value: 10 meter + recommended: true + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016013 + Water: + annotations: + use_cases: + tag: use_cases + value: sea or river water, global ocean sampling day + description: A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment. + title: water + see_also: + - https://www.vliz.be/projects/assembleplus/research/ocean-sampling-day-2018.html + aliases: + - MIxS-water + is_a: Extension + slots: + - samp_name + - project_name + - depth + - elev + - alkalinity + - alkalinity_method + - alkyl_diethers + - aminopept_act + - ammonium + - atmospheric_data + - bacteria_carb_prod + - bac_prod + - bac_resp + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - conduc + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_inorg_nitro + - diss_inorg_phosp + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - down_par + - fluor + - glucosidase_act + - light_intensity + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - part_org_carb + - part_org_nitro + - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - photon_flux + - potassium + - pressure + - primary_prod + - redox_potential + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - size_frac_low + - size_frac_up + - sodium + - soluble_react_phosp + - sulfate + - sulfide + - suspend_part_matter + - temp + - tidal_stage + - tot_depth_water_col + - tot_diss_nitro + - tot_inorg_nitro + - tot_nitro + - tot_part_carb + - tot_phosp + - turbidity + - water_current + slot_usage: + depth: + examples: + - value: 10 meter + required: true + elev: + recommended: true + organism_count: + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + class_uri: MIXS:0016014 + Checklist: + description: A collection of metadata terms (slots) to minimally describe the sampling and sequencing method of a specimen used to generate a nucleotide sequence. + Extension: + description: A collection of recommended metadata terms (slots) developed by community experts, describing the specific context under which a sample was collected. + aliases: + - EnvironmentalPackage + MixsCompliantData: + description: A collection of Data that comply with some combination of a MIxS checklist and environmental extension + title: MIxS compliant data + slots: + - migs_ba_data + - agriculture_data + - migs_ba_agriculture_data + - air_data + - migs_ba_air_data + - built_environment_data + - migs_ba_built_environment_data + - food_animal_and_animal_feed_data + - migs_ba_food_animal_and_animal_feed_data + - food_farm_environment_data + - migs_ba_food_farm_environment_data + - food_food_production_facility_data + - migs_ba_food_food_production_facility_data + - food_human_foods_data + - migs_ba_food_human_foods_data + - host_associated_data + - migs_ba_host_associated_data + - human_associated_data + - migs_ba_human_associated_data + - human_gut_data + - migs_ba_human_gut_data + - human_oral_data + - migs_ba_human_oral_data + - human_skin_data + - migs_ba_human_skin_data + - human_vaginal_data + - migs_ba_human_vaginal_data + - hydrocarbon_resources_cores_data + - migs_ba_hydrocarbon_resources_cores_data + - hydrocarbon_resources_fluids_swabs_data + - migs_ba_hydrocarbon_resources_fluids_swabs_data + - microbial_mat_biofilm_data + - migs_ba_microbial_mat_biofilm_data + - miscellaneous_natural_or_artificial_environment_data + - migs_ba_miscellaneous_natural_or_artificial_environment_data + - plant_associated_data + - migs_ba_plant_associated_data + - sediment_data + - migs_ba_sediment_data + - soil_data + - migs_ba_soil_data + - symbiont_associated_data + - migs_ba_symbiont_associated_data + - wastewater_sludge_data + - migs_ba_wastewater_sludge_data + - water_data + - migs_ba_water_data + - migs_eu_data + - migs_eu_agriculture_data + - migs_eu_air_data + - migs_eu_built_environment_data + - migs_eu_food_animal_and_animal_feed_data + - migs_eu_food_farm_environment_data + - migs_eu_food_food_production_facility_data + - migs_eu_food_human_foods_data + - migs_eu_host_associated_data + - migs_eu_human_associated_data + - migs_eu_human_gut_data + - migs_eu_human_oral_data + - migs_eu_human_skin_data + - migs_eu_human_vaginal_data + - migs_eu_hydrocarbon_resources_cores_data + - migs_eu_hydrocarbon_resources_fluids_swabs_data + - migs_eu_microbial_mat_biofilm_data + - migs_eu_miscellaneous_natural_or_artificial_environment_data + - migs_eu_plant_associated_data + - migs_eu_sediment_data + - migs_eu_soil_data + - migs_eu_symbiont_associated_data + - migs_eu_wastewater_sludge_data + - migs_eu_water_data + - migs_org_data + - migs_org_agriculture_data + - migs_org_air_data + - migs_org_built_environment_data + - migs_org_food_animal_and_animal_feed_data + - migs_org_food_farm_environment_data + - migs_org_food_food_production_facility_data + - migs_org_food_human_foods_data + - migs_org_host_associated_data + - migs_org_human_associated_data + - migs_org_human_gut_data + - migs_org_human_oral_data + - migs_org_human_skin_data + - migs_org_human_vaginal_data + - migs_org_hydrocarbon_resources_cores_data + - migs_org_hydrocarbon_resources_fluids_swabs_data + - migs_org_microbial_mat_biofilm_data + - migs_org_miscellaneous_natural_or_artificial_environment_data + - migs_org_plant_associated_data + - migs_org_sediment_data + - migs_org_soil_data + - migs_org_symbiont_associated_data + - migs_org_wastewater_sludge_data + - migs_org_water_data + - migs_pl_data + - migs_pl_agriculture_data + - migs_pl_air_data + - migs_pl_built_environment_data + - migs_pl_food_animal_and_animal_feed_data + - migs_pl_food_farm_environment_data + - migs_pl_food_food_production_facility_data + - migs_pl_food_human_foods_data + - migs_pl_host_associated_data + - migs_pl_human_associated_data + - migs_pl_human_gut_data + - migs_pl_human_oral_data + - migs_pl_human_skin_data + - migs_pl_human_vaginal_data + - migs_pl_hydrocarbon_resources_cores_data + - migs_pl_hydrocarbon_resources_fluids_swabs_data + - migs_pl_microbial_mat_biofilm_data + - migs_pl_miscellaneous_natural_or_artificial_environment_data + - migs_pl_plant_associated_data + - migs_pl_sediment_data + - migs_pl_soil_data + - migs_pl_symbiont_associated_data + - migs_pl_wastewater_sludge_data + - migs_pl_water_data + - migs_vi_data + - migs_vi_agriculture_data + - migs_vi_air_data + - migs_vi_built_environment_data + - migs_vi_food_animal_and_animal_feed_data + - migs_vi_food_farm_environment_data + - migs_vi_food_food_production_facility_data + - migs_vi_food_human_foods_data + - migs_vi_host_associated_data + - migs_vi_human_associated_data + - migs_vi_human_gut_data + - migs_vi_human_oral_data + - migs_vi_human_skin_data + - migs_vi_human_vaginal_data + - migs_vi_hydrocarbon_resources_cores_data + - migs_vi_hydrocarbon_resources_fluids_swabs_data + - migs_vi_microbial_mat_biofilm_data + - migs_vi_miscellaneous_natural_or_artificial_environment_data + - migs_vi_plant_associated_data + - migs_vi_sediment_data + - migs_vi_soil_data + - migs_vi_symbiont_associated_data + - migs_vi_wastewater_sludge_data + - migs_vi_water_data + - mimag_data + - mimag_agriculture_data + - mimag_air_data + - mimag_built_environment_data + - mimag_food_animal_and_animal_feed_data + - mimag_food_farm_environment_data + - mimag_food_food_production_facility_data + - mimag_food_human_foods_data + - mimag_host_associated_data + - mimag_human_associated_data + - mimag_human_gut_data + - mimag_human_oral_data + - mimag_human_skin_data + - mimag_human_vaginal_data + - mimag_hydrocarbon_resources_cores_data + - mimag_hydrocarbon_resources_fluids_swabs_data + - mimag_microbial_mat_biofilm_data + - mimag_miscellaneous_natural_or_artificial_environment_data + - mimag_plant_associated_data + - mimag_sediment_data + - mimag_soil_data + - mimag_symbiont_associated_data + - mimag_wastewater_sludge_data + - mimag_water_data + - mimarks_c_data + - mimarks_c_agriculture_data + - mimarks_c_air_data + - mimarks_c_built_environment_data + - mimarks_c_food_animal_and_animal_feed_data + - mimarks_c_food_farm_environment_data + - mimarks_c_food_food_production_facility_data + - mimarks_c_food_human_foods_data + - mimarks_c_host_associated_data + - mimarks_c_human_associated_data + - mimarks_c_human_gut_data + - mimarks_c_human_oral_data + - mimarks_c_human_skin_data + - mimarks_c_human_vaginal_data + - mimarks_c_hydrocarbon_resources_cores_data + - mimarks_c_hydrocarbon_resources_fluids_swabs_data + - mimarks_c_microbial_mat_biofilm_data + - mimarks_c_miscellaneous_natural_or_artificial_environment_data + - mimarks_c_plant_associated_data + - mimarks_c_sediment_data + - mimarks_c_soil_data + - mimarks_c_symbiont_associated_data + - mimarks_c_wastewater_sludge_data + - mimarks_c_water_data + - mimarks_s_data + - mimarks_s_agriculture_data + - mimarks_s_air_data + - mimarks_s_built_environment_data + - mimarks_s_food_animal_and_animal_feed_data + - mimarks_s_food_farm_environment_data + - mimarks_s_food_food_production_facility_data + - mimarks_s_food_human_foods_data + - mimarks_s_host_associated_data + - mimarks_s_human_associated_data + - mimarks_s_human_gut_data + - mimarks_s_human_oral_data + - mimarks_s_human_skin_data + - mimarks_s_human_vaginal_data + - mimarks_s_hydrocarbon_resources_cores_data + - mimarks_s_hydrocarbon_resources_fluids_swabs_data + - mimarks_s_microbial_mat_biofilm_data + - mimarks_s_miscellaneous_natural_or_artificial_environment_data + - mimarks_s_plant_associated_data + - mimarks_s_sediment_data + - mimarks_s_soil_data + - mimarks_s_symbiont_associated_data + - mimarks_s_wastewater_sludge_data + - mimarks_s_water_data + - mims_data + - mims_agriculture_data + - mims_air_data + - mims_built_environment_data + - mims_food_animal_and_animal_feed_data + - mims_food_farm_environment_data + - mims_food_food_production_facility_data + - mims_food_human_foods_data + - mims_host_associated_data + - mims_human_associated_data + - mims_human_gut_data + - mims_human_oral_data + - mims_human_skin_data + - mims_human_vaginal_data + - mims_hydrocarbon_resources_cores_data + - mims_hydrocarbon_resources_fluids_swabs_data + - mims_microbial_mat_biofilm_data + - mims_miscellaneous_natural_or_artificial_environment_data + - mims_plant_associated_data + - mims_sediment_data + - mims_soil_data + - mims_symbiont_associated_data + - mims_wastewater_sludge_data + - mims_water_data + - misag_data + - misag_agriculture_data + - misag_air_data + - misag_built_environment_data + - misag_food_animal_and_animal_feed_data + - misag_food_farm_environment_data + - misag_food_food_production_facility_data + - misag_food_human_foods_data + - misag_host_associated_data + - misag_human_associated_data + - misag_human_gut_data + - misag_human_oral_data + - misag_human_skin_data + - misag_human_vaginal_data + - misag_hydrocarbon_resources_cores_data + - misag_hydrocarbon_resources_fluids_swabs_data + - misag_microbial_mat_biofilm_data + - misag_miscellaneous_natural_or_artificial_environment_data + - misag_plant_associated_data + - misag_sediment_data + - misag_soil_data + - misag_symbiont_associated_data + - misag_wastewater_sludge_data + - misag_water_data + - miuvig_data + - miuvig_agriculture_data + - miuvig_air_data + - miuvig_built_environment_data + - miuvig_food_animal_and_animal_feed_data + - miuvig_food_farm_environment_data + - miuvig_food_food_production_facility_data + - miuvig_food_human_foods_data + - miuvig_host_associated_data + - miuvig_human_associated_data + - miuvig_human_gut_data + - miuvig_human_oral_data + - miuvig_human_skin_data + - miuvig_human_vaginal_data + - miuvig_hydrocarbon_resources_cores_data + - miuvig_hydrocarbon_resources_fluids_swabs_data + - miuvig_microbial_mat_biofilm_data + - miuvig_miscellaneous_natural_or_artificial_environment_data + - miuvig_plant_associated_data + - miuvig_sediment_data + - miuvig_soil_data + - miuvig_symbiont_associated_data + - miuvig_wastewater_sludge_data + - miuvig_water_data + tree_root: true + MigsBaAgriculture: + description: MIxS Data that comply with the MigsBa checklist and the Agriculture Extension + title: MigsBa combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - MigsBa + class_uri: MIXS:0010003_0016018 + MigsBaAir: + description: MIxS Data that comply with the MigsBa checklist and the Air Extension + title: MigsBa combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - MigsBa + class_uri: MIXS:0010003_0016000 + MigsBaBuiltEnvironment: + description: MIxS Data that comply with the MigsBa checklist and the BuiltEnvironment Extension + title: MigsBa combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016001 + MigsBaFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the MigsBa checklist and the FoodAnimalAndAnimalFeed Extension + title: MigsBa combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsBa + class_uri: MIXS:0010003_0016019 + MigsBaFoodFarmEnvironment: + description: MIxS Data that comply with the MigsBa checklist and the FoodFarmEnvironment Extension + title: MigsBa combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016020 + MigsBaFoodFoodProductionFacility: + description: MIxS Data that comply with the MigsBa checklist and the FoodFoodProductionFacility Extension + title: MigsBa combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - MigsBa + class_uri: MIXS:0010003_0016021 + MigsBaFoodHumanFoods: + description: MIxS Data that comply with the MigsBa checklist and the FoodHumanFoods Extension + title: MigsBa combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - MigsBa + class_uri: MIXS:0010003_0016022 + MigsBaHostAssociated: + description: MIxS Data that comply with the MigsBa checklist and the HostAssociated Extension + title: MigsBa combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016002 + MigsBaHumanAssociated: + description: MIxS Data that comply with the MigsBa checklist and the HumanAssociated Extension + title: MigsBa combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016003 + MigsBaHumanGut: + description: MIxS Data that comply with the MigsBa checklist and the HumanGut Extension + title: MigsBa combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - MigsBa + class_uri: MIXS:0010003_0016004 + MigsBaHumanOral: + description: MIxS Data that comply with the MigsBa checklist and the HumanOral Extension + title: MigsBa combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - MigsBa + class_uri: MIXS:0010003_0016005 + MigsBaHumanSkin: + description: MIxS Data that comply with the MigsBa checklist and the HumanSkin Extension + title: MigsBa combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - MigsBa + class_uri: MIXS:0010003_0016006 + MigsBaHumanVaginal: + description: MIxS Data that comply with the MigsBa checklist and the HumanVaginal Extension + title: MigsBa combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - MigsBa + class_uri: MIXS:0010003_0016007 + MigsBaHydrocarbonResourcesCores: + description: MIxS Data that comply with the MigsBa checklist and the HydrocarbonResourcesCores Extension + title: MigsBa combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - MigsBa + class_uri: MIXS:0010003_0016015 + MigsBaHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the MigsBa checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: MigsBa combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsBa + class_uri: MIXS:0010003_0016016 + MigsBaMicrobialMatBiofilm: + description: MIxS Data that comply with the MigsBa checklist and the MicrobialMatBiofilm Extension + title: MigsBa combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - MigsBa + class_uri: MIXS:0010003_0016008 + MigsBaMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the MigsBa checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: MigsBa combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016009 + MigsBaPlantAssociated: + description: MIxS Data that comply with the MigsBa checklist and the PlantAssociated Extension + title: MigsBa combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016010 + MigsBaSediment: + description: MIxS Data that comply with the MigsBa checklist and the Sediment Extension + title: MigsBa combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016011 + MigsBaSoil: + description: MIxS Data that comply with the MigsBa checklist and the Soil Extension + title: MigsBa combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - MigsBa + class_uri: MIXS:0010003_0016012 + MigsBaSymbiontAssociated: + description: MIxS Data that comply with the MigsBa checklist and the SymbiontAssociated Extension + title: MigsBa combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016023 + MigsBaWastewaterSludge: + description: MIxS Data that comply with the MigsBa checklist and the WastewaterSludge Extension + title: MigsBa combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - MigsBa + class_uri: MIXS:0010003_0016013 + MigsBaWater: + description: MIxS Data that comply with the MigsBa checklist and the Water Extension + title: MigsBa combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - MigsBa + class_uri: MIXS:0010003_0016014 + MigsEuAgriculture: + description: MIxS Data that comply with the MigsEu checklist and the Agriculture Extension + title: MigsEu combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - MigsEu + class_uri: MIXS:0010002_0016018 + MigsEuAir: + description: MIxS Data that comply with the MigsEu checklist and the Air Extension + title: MigsEu combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - MigsEu + class_uri: MIXS:0010002_0016000 + MigsEuBuiltEnvironment: + description: MIxS Data that comply with the MigsEu checklist and the BuiltEnvironment Extension + title: MigsEu combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016001 + MigsEuFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the MigsEu checklist and the FoodAnimalAndAnimalFeed Extension + title: MigsEu combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsEu + class_uri: MIXS:0010002_0016019 + MigsEuFoodFarmEnvironment: + description: MIxS Data that comply with the MigsEu checklist and the FoodFarmEnvironment Extension + title: MigsEu combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016020 + MigsEuFoodFoodProductionFacility: + description: MIxS Data that comply with the MigsEu checklist and the FoodFoodProductionFacility Extension + title: MigsEu combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - MigsEu + class_uri: MIXS:0010002_0016021 + MigsEuFoodHumanFoods: + description: MIxS Data that comply with the MigsEu checklist and the FoodHumanFoods Extension + title: MigsEu combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - MigsEu + class_uri: MIXS:0010002_0016022 + MigsEuHostAssociated: + description: MIxS Data that comply with the MigsEu checklist and the HostAssociated Extension + title: MigsEu combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016002 + MigsEuHumanAssociated: + description: MIxS Data that comply with the MigsEu checklist and the HumanAssociated Extension + title: MigsEu combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016003 + MigsEuHumanGut: + description: MIxS Data that comply with the MigsEu checklist and the HumanGut Extension + title: MigsEu combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - MigsEu + class_uri: MIXS:0010002_0016004 + MigsEuHumanOral: + description: MIxS Data that comply with the MigsEu checklist and the HumanOral Extension + title: MigsEu combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - MigsEu + class_uri: MIXS:0010002_0016005 + MigsEuHumanSkin: + description: MIxS Data that comply with the MigsEu checklist and the HumanSkin Extension + title: MigsEu combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - MigsEu + class_uri: MIXS:0010002_0016006 + MigsEuHumanVaginal: + description: MIxS Data that comply with the MigsEu checklist and the HumanVaginal Extension + title: MigsEu combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - MigsEu + class_uri: MIXS:0010002_0016007 + MigsEuHydrocarbonResourcesCores: + description: MIxS Data that comply with the MigsEu checklist and the HydrocarbonResourcesCores Extension + title: MigsEu combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - MigsEu + class_uri: MIXS:0010002_0016015 + MigsEuHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the MigsEu checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: MigsEu combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsEu + class_uri: MIXS:0010002_0016016 + MigsEuMicrobialMatBiofilm: + description: MIxS Data that comply with the MigsEu checklist and the MicrobialMatBiofilm Extension + title: MigsEu combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - MigsEu + class_uri: MIXS:0010002_0016008 + MigsEuMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the MigsEu checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: MigsEu combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016009 + MigsEuPlantAssociated: + description: MIxS Data that comply with the MigsEu checklist and the PlantAssociated Extension + title: MigsEu combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016010 + MigsEuSediment: + description: MIxS Data that comply with the MigsEu checklist and the Sediment Extension + title: MigsEu combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016011 + MigsEuSoil: + description: MIxS Data that comply with the MigsEu checklist and the Soil Extension + title: MigsEu combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - MigsEu + class_uri: MIXS:0010002_0016012 + MigsEuSymbiontAssociated: + description: MIxS Data that comply with the MigsEu checklist and the SymbiontAssociated Extension + title: MigsEu combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016023 + MigsEuWastewaterSludge: + description: MIxS Data that comply with the MigsEu checklist and the WastewaterSludge Extension + title: MigsEu combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - MigsEu + class_uri: MIXS:0010002_0016013 + MigsEuWater: + description: MIxS Data that comply with the MigsEu checklist and the Water Extension + title: MigsEu combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - MigsEu + class_uri: MIXS:0010002_0016014 + MigsOrgAgriculture: + description: MIxS Data that comply with the MigsOrg checklist and the Agriculture Extension + title: MigsOrg combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016018 + MigsOrgAir: + description: MIxS Data that comply with the MigsOrg checklist and the Air Extension + title: MigsOrg combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016000 + MigsOrgBuiltEnvironment: + description: MIxS Data that comply with the MigsOrg checklist and the BuiltEnvironment Extension + title: MigsOrg combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016001 + MigsOrgFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the MigsOrg checklist and the FoodAnimalAndAnimalFeed Extension + title: MigsOrg combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016019 + MigsOrgFoodFarmEnvironment: + description: MIxS Data that comply with the MigsOrg checklist and the FoodFarmEnvironment Extension + title: MigsOrg combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016020 + MigsOrgFoodFoodProductionFacility: + description: MIxS Data that comply with the MigsOrg checklist and the FoodFoodProductionFacility Extension + title: MigsOrg combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016021 + MigsOrgFoodHumanFoods: + description: MIxS Data that comply with the MigsOrg checklist and the FoodHumanFoods Extension + title: MigsOrg combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016022 + MigsOrgHostAssociated: + description: MIxS Data that comply with the MigsOrg checklist and the HostAssociated Extension + title: MigsOrg combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016002 + MigsOrgHumanAssociated: + description: MIxS Data that comply with the MigsOrg checklist and the HumanAssociated Extension + title: MigsOrg combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016003 + MigsOrgHumanGut: + description: MIxS Data that comply with the MigsOrg checklist and the HumanGut Extension + title: MigsOrg combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016004 + MigsOrgHumanOral: + description: MIxS Data that comply with the MigsOrg checklist and the HumanOral Extension + title: MigsOrg combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016005 + MigsOrgHumanSkin: + description: MIxS Data that comply with the MigsOrg checklist and the HumanSkin Extension + title: MigsOrg combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016006 + MigsOrgHumanVaginal: + description: MIxS Data that comply with the MigsOrg checklist and the HumanVaginal Extension + title: MigsOrg combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016007 + MigsOrgHydrocarbonResourcesCores: + description: MIxS Data that comply with the MigsOrg checklist and the HydrocarbonResourcesCores Extension + title: MigsOrg combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016015 + MigsOrgHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the MigsOrg checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: MigsOrg combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016016 + MigsOrgMicrobialMatBiofilm: + description: MIxS Data that comply with the MigsOrg checklist and the MicrobialMatBiofilm Extension + title: MigsOrg combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016008 + MigsOrgMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the MigsOrg checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: MigsOrg combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016009 + MigsOrgPlantAssociated: + description: MIxS Data that comply with the MigsOrg checklist and the PlantAssociated Extension + title: MigsOrg combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016010 + MigsOrgSediment: + description: MIxS Data that comply with the MigsOrg checklist and the Sediment Extension + title: MigsOrg combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016011 + MigsOrgSoil: + description: MIxS Data that comply with the MigsOrg checklist and the Soil Extension + title: MigsOrg combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016012 + MigsOrgSymbiontAssociated: + description: MIxS Data that comply with the MigsOrg checklist and the SymbiontAssociated Extension + title: MigsOrg combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016023 + MigsOrgWastewaterSludge: + description: MIxS Data that comply with the MigsOrg checklist and the WastewaterSludge Extension + title: MigsOrg combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016013 + MigsOrgWater: + description: MIxS Data that comply with the MigsOrg checklist and the Water Extension + title: MigsOrg combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016014 + MigsPlAgriculture: + description: MIxS Data that comply with the MigsPl checklist and the Agriculture Extension + title: MigsPl combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - MigsPl + class_uri: MIXS:0010004_0016018 + MigsPlAir: + description: MIxS Data that comply with the MigsPl checklist and the Air Extension + title: MigsPl combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - MigsPl + class_uri: MIXS:0010004_0016000 + MigsPlBuiltEnvironment: + description: MIxS Data that comply with the MigsPl checklist and the BuiltEnvironment Extension + title: MigsPl combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016001 + MigsPlFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the MigsPl checklist and the FoodAnimalAndAnimalFeed Extension + title: MigsPl combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsPl + class_uri: MIXS:0010004_0016019 + MigsPlFoodFarmEnvironment: + description: MIxS Data that comply with the MigsPl checklist and the FoodFarmEnvironment Extension + title: MigsPl combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016020 + MigsPlFoodFoodProductionFacility: + description: MIxS Data that comply with the MigsPl checklist and the FoodFoodProductionFacility Extension + title: MigsPl combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - MigsPl + class_uri: MIXS:0010004_0016021 + MigsPlFoodHumanFoods: + description: MIxS Data that comply with the MigsPl checklist and the FoodHumanFoods Extension + title: MigsPl combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - MigsPl + class_uri: MIXS:0010004_0016022 + MigsPlHostAssociated: + description: MIxS Data that comply with the MigsPl checklist and the HostAssociated Extension + title: MigsPl combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016002 + MigsPlHumanAssociated: + description: MIxS Data that comply with the MigsPl checklist and the HumanAssociated Extension + title: MigsPl combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016003 + MigsPlHumanGut: + description: MIxS Data that comply with the MigsPl checklist and the HumanGut Extension + title: MigsPl combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - MigsPl + class_uri: MIXS:0010004_0016004 + MigsPlHumanOral: + description: MIxS Data that comply with the MigsPl checklist and the HumanOral Extension + title: MigsPl combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - MigsPl + class_uri: MIXS:0010004_0016005 + MigsPlHumanSkin: + description: MIxS Data that comply with the MigsPl checklist and the HumanSkin Extension + title: MigsPl combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - MigsPl + class_uri: MIXS:0010004_0016006 + MigsPlHumanVaginal: + description: MIxS Data that comply with the MigsPl checklist and the HumanVaginal Extension + title: MigsPl combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - MigsPl + class_uri: MIXS:0010004_0016007 + MigsPlHydrocarbonResourcesCores: + description: MIxS Data that comply with the MigsPl checklist and the HydrocarbonResourcesCores Extension + title: MigsPl combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - MigsPl + class_uri: MIXS:0010004_0016015 + MigsPlHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the MigsPl checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: MigsPl combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsPl + class_uri: MIXS:0010004_0016016 + MigsPlMicrobialMatBiofilm: + description: MIxS Data that comply with the MigsPl checklist and the MicrobialMatBiofilm Extension + title: MigsPl combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - MigsPl + class_uri: MIXS:0010004_0016008 + MigsPlMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the MigsPl checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: MigsPl combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016009 + MigsPlPlantAssociated: + description: MIxS Data that comply with the MigsPl checklist and the PlantAssociated Extension + title: MigsPl combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016010 + MigsPlSediment: + description: MIxS Data that comply with the MigsPl checklist and the Sediment Extension + title: MigsPl combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016011 + MigsPlSoil: + description: MIxS Data that comply with the MigsPl checklist and the Soil Extension + title: MigsPl combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - MigsPl + class_uri: MIXS:0010004_0016012 + MigsPlSymbiontAssociated: + description: MIxS Data that comply with the MigsPl checklist and the SymbiontAssociated Extension + title: MigsPl combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016023 + MigsPlWastewaterSludge: + description: MIxS Data that comply with the MigsPl checklist and the WastewaterSludge Extension + title: MigsPl combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - MigsPl + class_uri: MIXS:0010004_0016013 + MigsPlWater: + description: MIxS Data that comply with the MigsPl checklist and the Water Extension + title: MigsPl combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - MigsPl + class_uri: MIXS:0010004_0016014 + MigsViAgriculture: + description: MIxS Data that comply with the MigsVi checklist and the Agriculture Extension + title: MigsVi combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - MigsVi + class_uri: MIXS:0010005_0016018 + MigsViAir: + description: MIxS Data that comply with the MigsVi checklist and the Air Extension + title: MigsVi combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - MigsVi + class_uri: MIXS:0010005_0016000 + MigsViBuiltEnvironment: + description: MIxS Data that comply with the MigsVi checklist and the BuiltEnvironment Extension + title: MigsVi combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016001 + MigsViFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the MigsVi checklist and the FoodAnimalAndAnimalFeed Extension + title: MigsVi combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsVi + class_uri: MIXS:0010005_0016019 + MigsViFoodFarmEnvironment: + description: MIxS Data that comply with the MigsVi checklist and the FoodFarmEnvironment Extension + title: MigsVi combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016020 + MigsViFoodFoodProductionFacility: + description: MIxS Data that comply with the MigsVi checklist and the FoodFoodProductionFacility Extension + title: MigsVi combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - MigsVi + class_uri: MIXS:0010005_0016021 + MigsViFoodHumanFoods: + description: MIxS Data that comply with the MigsVi checklist and the FoodHumanFoods Extension + title: MigsVi combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - MigsVi + class_uri: MIXS:0010005_0016022 + MigsViHostAssociated: + description: MIxS Data that comply with the MigsVi checklist and the HostAssociated Extension + title: MigsVi combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016002 + MigsViHumanAssociated: + description: MIxS Data that comply with the MigsVi checklist and the HumanAssociated Extension + title: MigsVi combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016003 + MigsViHumanGut: + description: MIxS Data that comply with the MigsVi checklist and the HumanGut Extension + title: MigsVi combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - MigsVi + class_uri: MIXS:0010005_0016004 + MigsViHumanOral: + description: MIxS Data that comply with the MigsVi checklist and the HumanOral Extension + title: MigsVi combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - MigsVi + class_uri: MIXS:0010005_0016005 + MigsViHumanSkin: + description: MIxS Data that comply with the MigsVi checklist and the HumanSkin Extension + title: MigsVi combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - MigsVi + class_uri: MIXS:0010005_0016006 + MigsViHumanVaginal: + description: MIxS Data that comply with the MigsVi checklist and the HumanVaginal Extension + title: MigsVi combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - MigsVi + class_uri: MIXS:0010005_0016007 + MigsViHydrocarbonResourcesCores: + description: MIxS Data that comply with the MigsVi checklist and the HydrocarbonResourcesCores Extension + title: MigsVi combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - MigsVi + class_uri: MIXS:0010005_0016015 + MigsViHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the MigsVi checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: MigsVi combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsVi + class_uri: MIXS:0010005_0016016 + MigsViMicrobialMatBiofilm: + description: MIxS Data that comply with the MigsVi checklist and the MicrobialMatBiofilm Extension + title: MigsVi combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - MigsVi + class_uri: MIXS:0010005_0016008 + MigsViMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the MigsVi checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: MigsVi combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016009 + MigsViPlantAssociated: + description: MIxS Data that comply with the MigsVi checklist and the PlantAssociated Extension + title: MigsVi combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016010 + MigsViSediment: + description: MIxS Data that comply with the MigsVi checklist and the Sediment Extension + title: MigsVi combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016011 + MigsViSoil: + description: MIxS Data that comply with the MigsVi checklist and the Soil Extension + title: MigsVi combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - MigsVi + class_uri: MIXS:0010005_0016012 + MigsViSymbiontAssociated: + description: MIxS Data that comply with the MigsVi checklist and the SymbiontAssociated Extension + title: MigsVi combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016023 + MigsViWastewaterSludge: + description: MIxS Data that comply with the MigsVi checklist and the WastewaterSludge Extension + title: MigsVi combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - MigsVi + class_uri: MIXS:0010005_0016013 + MigsViWater: + description: MIxS Data that comply with the MigsVi checklist and the Water Extension + title: MigsVi combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - MigsVi + class_uri: MIXS:0010005_0016014 + MimagAgriculture: + description: MIxS Data that comply with the Mimag checklist and the Agriculture Extension + title: Mimag combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - Mimag + class_uri: MIXS:0010011_0016018 + MimagAir: + description: MIxS Data that comply with the Mimag checklist and the Air Extension + title: Mimag combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - Mimag + class_uri: MIXS:0010011_0016000 + MimagBuiltEnvironment: + description: MIxS Data that comply with the Mimag checklist and the BuiltEnvironment Extension + title: Mimag combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - Mimag + class_uri: MIXS:0010011_0016001 + MimagFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the Mimag checklist and the FoodAnimalAndAnimalFeed Extension + title: Mimag combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - Mimag + class_uri: MIXS:0010011_0016019 + MimagFoodFarmEnvironment: + description: MIxS Data that comply with the Mimag checklist and the FoodFarmEnvironment Extension + title: Mimag combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - Mimag + class_uri: MIXS:0010011_0016020 + MimagFoodFoodProductionFacility: + description: MIxS Data that comply with the Mimag checklist and the FoodFoodProductionFacility Extension + title: Mimag combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - Mimag + class_uri: MIXS:0010011_0016021 + MimagFoodHumanFoods: + description: MIxS Data that comply with the Mimag checklist and the FoodHumanFoods Extension + title: Mimag combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - Mimag + class_uri: MIXS:0010011_0016022 + MimagHostAssociated: + description: MIxS Data that comply with the Mimag checklist and the HostAssociated Extension + title: Mimag combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016002 + MimagHumanAssociated: + description: MIxS Data that comply with the Mimag checklist and the HumanAssociated Extension + title: Mimag combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016003 + MimagHumanGut: + description: MIxS Data that comply with the Mimag checklist and the HumanGut Extension + title: Mimag combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - Mimag + class_uri: MIXS:0010011_0016004 + MimagHumanOral: + description: MIxS Data that comply with the Mimag checklist and the HumanOral Extension + title: Mimag combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - Mimag + class_uri: MIXS:0010011_0016005 + MimagHumanSkin: + description: MIxS Data that comply with the Mimag checklist and the HumanSkin Extension + title: Mimag combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - Mimag + class_uri: MIXS:0010011_0016006 + MimagHumanVaginal: + description: MIxS Data that comply with the Mimag checklist and the HumanVaginal Extension + title: Mimag combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - Mimag + class_uri: MIXS:0010011_0016007 + MimagHydrocarbonResourcesCores: + description: MIxS Data that comply with the Mimag checklist and the HydrocarbonResourcesCores Extension + title: Mimag combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - Mimag + class_uri: MIXS:0010011_0016015 + MimagHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the Mimag checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: Mimag combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - Mimag + class_uri: MIXS:0010011_0016016 + MimagMicrobialMatBiofilm: + description: MIxS Data that comply with the Mimag checklist and the MicrobialMatBiofilm Extension + title: Mimag combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - Mimag + class_uri: MIXS:0010011_0016008 + MimagMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the Mimag checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: Mimag combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - Mimag + class_uri: MIXS:0010011_0016009 + MimagPlantAssociated: + description: MIxS Data that comply with the Mimag checklist and the PlantAssociated Extension + title: Mimag combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016010 + MimagSediment: + description: MIxS Data that comply with the Mimag checklist and the Sediment Extension + title: Mimag combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - Mimag + class_uri: MIXS:0010011_0016011 + MimagSoil: + description: MIxS Data that comply with the Mimag checklist and the Soil Extension + title: Mimag combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - Mimag + class_uri: MIXS:0010011_0016012 + MimagSymbiontAssociated: + description: MIxS Data that comply with the Mimag checklist and the SymbiontAssociated Extension + title: Mimag combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016023 + MimagWastewaterSludge: + description: MIxS Data that comply with the Mimag checklist and the WastewaterSludge Extension + title: Mimag combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - Mimag + class_uri: MIXS:0010011_0016013 + MimagWater: + description: MIxS Data that comply with the Mimag checklist and the Water Extension + title: Mimag combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - Mimag + class_uri: MIXS:0010011_0016014 + MimarksCAgriculture: + description: MIxS Data that comply with the MimarksC checklist and the Agriculture Extension + title: MimarksC combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - MimarksC + class_uri: MIXS:0010009_0016018 + MimarksCAir: + description: MIxS Data that comply with the MimarksC checklist and the Air Extension + title: MimarksC combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - MimarksC + class_uri: MIXS:0010009_0016000 + MimarksCBuiltEnvironment: + description: MIxS Data that comply with the MimarksC checklist and the BuiltEnvironment Extension + title: MimarksC combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016001 + MimarksCFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the MimarksC checklist and the FoodAnimalAndAnimalFeed Extension + title: MimarksC combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - MimarksC + class_uri: MIXS:0010009_0016019 + MimarksCFoodFarmEnvironment: + description: MIxS Data that comply with the MimarksC checklist and the FoodFarmEnvironment Extension + title: MimarksC combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016020 + MimarksCFoodFoodProductionFacility: + description: MIxS Data that comply with the MimarksC checklist and the FoodFoodProductionFacility Extension + title: MimarksC combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - MimarksC + class_uri: MIXS:0010009_0016021 + MimarksCFoodHumanFoods: + description: MIxS Data that comply with the MimarksC checklist and the FoodHumanFoods Extension + title: MimarksC combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - MimarksC + class_uri: MIXS:0010009_0016022 + MimarksCHostAssociated: + description: MIxS Data that comply with the MimarksC checklist and the HostAssociated Extension + title: MimarksC combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016002 + MimarksCHumanAssociated: + description: MIxS Data that comply with the MimarksC checklist and the HumanAssociated Extension + title: MimarksC combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016003 + MimarksCHumanGut: + description: MIxS Data that comply with the MimarksC checklist and the HumanGut Extension + title: MimarksC combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - MimarksC + class_uri: MIXS:0010009_0016004 + MimarksCHumanOral: + description: MIxS Data that comply with the MimarksC checklist and the HumanOral Extension + title: MimarksC combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - MimarksC + class_uri: MIXS:0010009_0016005 + MimarksCHumanSkin: + description: MIxS Data that comply with the MimarksC checklist and the HumanSkin Extension + title: MimarksC combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - MimarksC + class_uri: MIXS:0010009_0016006 + MimarksCHumanVaginal: + description: MIxS Data that comply with the MimarksC checklist and the HumanVaginal Extension + title: MimarksC combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - MimarksC + class_uri: MIXS:0010009_0016007 + MimarksCHydrocarbonResourcesCores: + description: MIxS Data that comply with the MimarksC checklist and the HydrocarbonResourcesCores Extension + title: MimarksC combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - MimarksC + class_uri: MIXS:0010009_0016015 + MimarksCHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the MimarksC checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: MimarksC combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MimarksC + class_uri: MIXS:0010009_0016016 + MimarksCMicrobialMatBiofilm: + description: MIxS Data that comply with the MimarksC checklist and the MicrobialMatBiofilm Extension + title: MimarksC combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - MimarksC + class_uri: MIXS:0010009_0016008 + MimarksCMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the MimarksC checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: MimarksC combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016009 + MimarksCPlantAssociated: + description: MIxS Data that comply with the MimarksC checklist and the PlantAssociated Extension + title: MimarksC combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016010 + MimarksCSediment: + description: MIxS Data that comply with the MimarksC checklist and the Sediment Extension + title: MimarksC combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016011 + MimarksCSoil: + description: MIxS Data that comply with the MimarksC checklist and the Soil Extension + title: MimarksC combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - MimarksC + class_uri: MIXS:0010009_0016012 + MimarksCSymbiontAssociated: + description: MIxS Data that comply with the MimarksC checklist and the SymbiontAssociated Extension + title: MimarksC combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016023 + MimarksCWastewaterSludge: + description: MIxS Data that comply with the MimarksC checklist and the WastewaterSludge Extension + title: MimarksC combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - MimarksC + class_uri: MIXS:0010009_0016013 + MimarksCWater: + description: MIxS Data that comply with the MimarksC checklist and the Water Extension + title: MimarksC combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - MimarksC + class_uri: MIXS:0010009_0016014 + MimarksSAgriculture: + description: MIxS Data that comply with the MimarksS checklist and the Agriculture Extension + title: MimarksS combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - MimarksS + class_uri: MIXS:0010008_0016018 + MimarksSAir: + description: MIxS Data that comply with the MimarksS checklist and the Air Extension + title: MimarksS combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - MimarksS + class_uri: MIXS:0010008_0016000 + MimarksSBuiltEnvironment: + description: MIxS Data that comply with the MimarksS checklist and the BuiltEnvironment Extension + title: MimarksS combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016001 + MimarksSFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the MimarksS checklist and the FoodAnimalAndAnimalFeed Extension + title: MimarksS combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - MimarksS + class_uri: MIXS:0010008_0016019 + MimarksSFoodFarmEnvironment: + description: MIxS Data that comply with the MimarksS checklist and the FoodFarmEnvironment Extension + title: MimarksS combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016020 + MimarksSFoodFoodProductionFacility: + description: MIxS Data that comply with the MimarksS checklist and the FoodFoodProductionFacility Extension + title: MimarksS combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - MimarksS + class_uri: MIXS:0010008_0016021 + MimarksSFoodHumanFoods: + description: MIxS Data that comply with the MimarksS checklist and the FoodHumanFoods Extension + title: MimarksS combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - MimarksS + class_uri: MIXS:0010008_0016022 + MimarksSHostAssociated: + description: MIxS Data that comply with the MimarksS checklist and the HostAssociated Extension + title: MimarksS combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016002 + MimarksSHumanAssociated: + description: MIxS Data that comply with the MimarksS checklist and the HumanAssociated Extension + title: MimarksS combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016003 + MimarksSHumanGut: + description: MIxS Data that comply with the MimarksS checklist and the HumanGut Extension + title: MimarksS combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - MimarksS + class_uri: MIXS:0010008_0016004 + MimarksSHumanOral: + description: MIxS Data that comply with the MimarksS checklist and the HumanOral Extension + title: MimarksS combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - MimarksS + class_uri: MIXS:0010008_0016005 + MimarksSHumanSkin: + description: MIxS Data that comply with the MimarksS checklist and the HumanSkin Extension + title: MimarksS combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - MimarksS + class_uri: MIXS:0010008_0016006 + MimarksSHumanVaginal: + description: MIxS Data that comply with the MimarksS checklist and the HumanVaginal Extension + title: MimarksS combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - MimarksS + class_uri: MIXS:0010008_0016007 + MimarksSHydrocarbonResourcesCores: + description: MIxS Data that comply with the MimarksS checklist and the HydrocarbonResourcesCores Extension + title: MimarksS combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - MimarksS + class_uri: MIXS:0010008_0016015 + MimarksSHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the MimarksS checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: MimarksS combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MimarksS + class_uri: MIXS:0010008_0016016 + MimarksSMicrobialMatBiofilm: + description: MIxS Data that comply with the MimarksS checklist and the MicrobialMatBiofilm Extension + title: MimarksS combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - MimarksS + class_uri: MIXS:0010008_0016008 + MimarksSMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the MimarksS checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: MimarksS combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016009 + MimarksSPlantAssociated: + description: MIxS Data that comply with the MimarksS checklist and the PlantAssociated Extension + title: MimarksS combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016010 + MimarksSSediment: + description: MIxS Data that comply with the MimarksS checklist and the Sediment Extension + title: MimarksS combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016011 + MimarksSSoil: + description: MIxS Data that comply with the MimarksS checklist and the Soil Extension + title: MimarksS combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - MimarksS + class_uri: MIXS:0010008_0016012 + MimarksSSymbiontAssociated: + description: MIxS Data that comply with the MimarksS checklist and the SymbiontAssociated Extension + title: MimarksS combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016023 + MimarksSWastewaterSludge: + description: MIxS Data that comply with the MimarksS checklist and the WastewaterSludge Extension + title: MimarksS combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - MimarksS + class_uri: MIXS:0010008_0016013 + MimarksSWater: + description: MIxS Data that comply with the MimarksS checklist and the Water Extension + title: MimarksS combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - MimarksS + class_uri: MIXS:0010008_0016014 + MimsAgriculture: + description: MIxS Data that comply with the Mims checklist and the Agriculture Extension + title: Mims combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - Mims + class_uri: MIXS:0010007_0016018 + MimsAir: + description: MIxS Data that comply with the Mims checklist and the Air Extension + title: Mims combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - Mims + class_uri: MIXS:0010007_0016000 + MimsBuiltEnvironment: + description: MIxS Data that comply with the Mims checklist and the BuiltEnvironment Extension + title: Mims combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - Mims + class_uri: MIXS:0010007_0016001 + MimsFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the Mims checklist and the FoodAnimalAndAnimalFeed Extension + title: Mims combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - Mims + class_uri: MIXS:0010007_0016019 + MimsFoodFarmEnvironment: + description: MIxS Data that comply with the Mims checklist and the FoodFarmEnvironment Extension + title: Mims combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - Mims + class_uri: MIXS:0010007_0016020 + MimsFoodFoodProductionFacility: + description: MIxS Data that comply with the Mims checklist and the FoodFoodProductionFacility Extension + title: Mims combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - Mims + class_uri: MIXS:0010007_0016021 + MimsFoodHumanFoods: + description: MIxS Data that comply with the Mims checklist and the FoodHumanFoods Extension + title: Mims combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - Mims + class_uri: MIXS:0010007_0016022 + MimsHostAssociated: + description: MIxS Data that comply with the Mims checklist and the HostAssociated Extension + title: Mims combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016002 + MimsHumanAssociated: + description: MIxS Data that comply with the Mims checklist and the HumanAssociated Extension + title: Mims combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016003 + MimsHumanGut: + description: MIxS Data that comply with the Mims checklist and the HumanGut Extension + title: Mims combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - Mims + class_uri: MIXS:0010007_0016004 + MimsHumanOral: + description: MIxS Data that comply with the Mims checklist and the HumanOral Extension + title: Mims combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - Mims + class_uri: MIXS:0010007_0016005 + MimsHumanSkin: + description: MIxS Data that comply with the Mims checklist and the HumanSkin Extension + title: Mims combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - Mims + class_uri: MIXS:0010007_0016006 + MimsHumanVaginal: + description: MIxS Data that comply with the Mims checklist and the HumanVaginal Extension + title: Mims combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - Mims + class_uri: MIXS:0010007_0016007 + MimsHydrocarbonResourcesCores: + description: MIxS Data that comply with the Mims checklist and the HydrocarbonResourcesCores Extension + title: Mims combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - Mims + class_uri: MIXS:0010007_0016015 + MimsHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the Mims checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: Mims combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - Mims + class_uri: MIXS:0010007_0016016 + MimsMicrobialMatBiofilm: + description: MIxS Data that comply with the Mims checklist and the MicrobialMatBiofilm Extension + title: Mims combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - Mims + class_uri: MIXS:0010007_0016008 + MimsMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the Mims checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: Mims combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - Mims + class_uri: MIXS:0010007_0016009 + MimsPlantAssociated: + description: MIxS Data that comply with the Mims checklist and the PlantAssociated Extension + title: Mims combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016010 + MimsSediment: + description: MIxS Data that comply with the Mims checklist and the Sediment Extension + title: Mims combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - Mims + class_uri: MIXS:0010007_0016011 + MimsSoil: + description: MIxS Data that comply with the Mims checklist and the Soil Extension + title: Mims combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - Mims + class_uri: MIXS:0010007_0016012 + MimsSymbiontAssociated: + description: MIxS Data that comply with the Mims checklist and the SymbiontAssociated Extension + title: Mims combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016023 + MimsWastewaterSludge: + description: MIxS Data that comply with the Mims checklist and the WastewaterSludge Extension + title: Mims combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - Mims + class_uri: MIXS:0010007_0016013 + MimsWater: + description: MIxS Data that comply with the Mims checklist and the Water Extension + title: Mims combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - Mims + class_uri: MIXS:0010007_0016014 + MisagAgriculture: + description: MIxS Data that comply with the Misag checklist and the Agriculture Extension + title: Misag combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - Misag + class_uri: MIXS:0010010_0016018 + MisagAir: + description: MIxS Data that comply with the Misag checklist and the Air Extension + title: Misag combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - Misag + class_uri: MIXS:0010010_0016000 + MisagBuiltEnvironment: + description: MIxS Data that comply with the Misag checklist and the BuiltEnvironment Extension + title: Misag combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - Misag + class_uri: MIXS:0010010_0016001 + MisagFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the Misag checklist and the FoodAnimalAndAnimalFeed Extension + title: Misag combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - Misag + class_uri: MIXS:0010010_0016019 + MisagFoodFarmEnvironment: + description: MIxS Data that comply with the Misag checklist and the FoodFarmEnvironment Extension + title: Misag combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - Misag + class_uri: MIXS:0010010_0016020 + MisagFoodFoodProductionFacility: + description: MIxS Data that comply with the Misag checklist and the FoodFoodProductionFacility Extension + title: Misag combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - Misag + class_uri: MIXS:0010010_0016021 + MisagFoodHumanFoods: + description: MIxS Data that comply with the Misag checklist and the FoodHumanFoods Extension + title: Misag combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - Misag + class_uri: MIXS:0010010_0016022 + MisagHostAssociated: + description: MIxS Data that comply with the Misag checklist and the HostAssociated Extension + title: Misag combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - Misag + class_uri: MIXS:0010010_0016002 + MisagHumanAssociated: + description: MIxS Data that comply with the Misag checklist and the HumanAssociated Extension + title: Misag combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - Misag + class_uri: MIXS:0010010_0016003 + MisagHumanGut: + description: MIxS Data that comply with the Misag checklist and the HumanGut Extension + title: Misag combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - Misag + class_uri: MIXS:0010010_0016004 + MisagHumanOral: + description: MIxS Data that comply with the Misag checklist and the HumanOral Extension + title: Misag combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - Misag + class_uri: MIXS:0010010_0016005 + MisagHumanSkin: + description: MIxS Data that comply with the Misag checklist and the HumanSkin Extension + title: Misag combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - Misag + class_uri: MIXS:0010010_0016006 + MisagHumanVaginal: + description: MIxS Data that comply with the Misag checklist and the HumanVaginal Extension + title: Misag combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - Misag + class_uri: MIXS:0010010_0016007 + MisagHydrocarbonResourcesCores: + description: MIxS Data that comply with the Misag checklist and the HydrocarbonResourcesCores Extension + title: Misag combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - Misag + class_uri: MIXS:0010010_0016015 + MisagHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the Misag checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: Misag combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - Misag + class_uri: MIXS:0010010_0016016 + MisagMicrobialMatBiofilm: + description: MIxS Data that comply with the Misag checklist and the MicrobialMatBiofilm Extension + title: Misag combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - Misag + class_uri: MIXS:0010010_0016008 + MisagMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the Misag checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: Misag combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - Misag + class_uri: MIXS:0010010_0016009 + MisagPlantAssociated: + description: MIxS Data that comply with the Misag checklist and the PlantAssociated Extension + title: Misag combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - Misag + class_uri: MIXS:0010010_0016010 + MisagSediment: + description: MIxS Data that comply with the Misag checklist and the Sediment Extension + title: Misag combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - Misag + class_uri: MIXS:0010010_0016011 + MisagSoil: + description: MIxS Data that comply with the Misag checklist and the Soil Extension + title: Misag combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - Misag + class_uri: MIXS:0010010_0016012 + MisagSymbiontAssociated: + description: MIxS Data that comply with the Misag checklist and the SymbiontAssociated Extension + title: Misag combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - Misag + class_uri: MIXS:0010010_0016023 + MisagWastewaterSludge: + description: MIxS Data that comply with the Misag checklist and the WastewaterSludge Extension + title: Misag combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - Misag + class_uri: MIXS:0010010_0016013 + MisagWater: + description: MIxS Data that comply with the Misag checklist and the Water Extension + title: Misag combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - Misag + class_uri: MIXS:0010010_0016014 + MiuvigAgriculture: + description: MIxS Data that comply with the Miuvig checklist and the Agriculture Extension + title: Miuvig combined with Agriculture + in_subset: + - combination_classes + is_a: Agriculture + mixins: + - Miuvig + class_uri: MIXS:0010012_0016018 + MiuvigAir: + description: MIxS Data that comply with the Miuvig checklist and the Air Extension + title: Miuvig combined with Air + in_subset: + - combination_classes + is_a: Air + mixins: + - Miuvig + class_uri: MIXS:0010012_0016000 + MiuvigBuiltEnvironment: + description: MIxS Data that comply with the Miuvig checklist and the BuiltEnvironment Extension + title: Miuvig combined with BuiltEnvironment + in_subset: + - combination_classes + is_a: BuiltEnvironment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016001 + MiuvigFoodAnimalAndAnimalFeed: + description: MIxS Data that comply with the Miuvig checklist and the FoodAnimalAndAnimalFeed Extension + title: Miuvig combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + is_a: FoodAnimalAndAnimalFeed + mixins: + - Miuvig + class_uri: MIXS:0010012_0016019 + MiuvigFoodFarmEnvironment: + description: MIxS Data that comply with the Miuvig checklist and the FoodFarmEnvironment Extension + title: Miuvig combined with FoodFarmEnvironment + in_subset: + - combination_classes + is_a: FoodFarmEnvironment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016020 + MiuvigFoodFoodProductionFacility: + description: MIxS Data that comply with the Miuvig checklist and the FoodFoodProductionFacility Extension + title: Miuvig combined with FoodFoodProductionFacility + in_subset: + - combination_classes + is_a: FoodFoodProductionFacility + mixins: + - Miuvig + class_uri: MIXS:0010012_0016021 + MiuvigFoodHumanFoods: + description: MIxS Data that comply with the Miuvig checklist and the FoodHumanFoods Extension + title: Miuvig combined with FoodHumanFoods + in_subset: + - combination_classes + is_a: FoodHumanFoods + mixins: + - Miuvig + class_uri: MIXS:0010012_0016022 + MiuvigHostAssociated: + description: MIxS Data that comply with the Miuvig checklist and the HostAssociated Extension + title: Miuvig combined with HostAssociated + in_subset: + - combination_classes + is_a: HostAssociated + mixins: + - Miuvig + class_uri: MIXS:0010012_0016002 + MiuvigHumanAssociated: + description: MIxS Data that comply with the Miuvig checklist and the HumanAssociated Extension + title: Miuvig combined with HumanAssociated + in_subset: + - combination_classes + is_a: HumanAssociated + mixins: + - Miuvig + class_uri: MIXS:0010012_0016003 + MiuvigHumanGut: + description: MIxS Data that comply with the Miuvig checklist and the HumanGut Extension + title: Miuvig combined with HumanGut + in_subset: + - combination_classes + is_a: HumanGut + mixins: + - Miuvig + class_uri: MIXS:0010012_0016004 + MiuvigHumanOral: + description: MIxS Data that comply with the Miuvig checklist and the HumanOral Extension + title: Miuvig combined with HumanOral + in_subset: + - combination_classes + is_a: HumanOral + mixins: + - Miuvig + class_uri: MIXS:0010012_0016005 + MiuvigHumanSkin: + description: MIxS Data that comply with the Miuvig checklist and the HumanSkin Extension + title: Miuvig combined with HumanSkin + in_subset: + - combination_classes + is_a: HumanSkin + mixins: + - Miuvig + class_uri: MIXS:0010012_0016006 + MiuvigHumanVaginal: + description: MIxS Data that comply with the Miuvig checklist and the HumanVaginal Extension + title: Miuvig combined with HumanVaginal + in_subset: + - combination_classes + is_a: HumanVaginal + mixins: + - Miuvig + class_uri: MIXS:0010012_0016007 + MiuvigHydrocarbonResourcesCores: + description: MIxS Data that comply with the Miuvig checklist and the HydrocarbonResourcesCores Extension + title: Miuvig combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + is_a: HydrocarbonResourcesCores + mixins: + - Miuvig + class_uri: MIXS:0010012_0016015 + MiuvigHydrocarbonResourcesFluidsSwabs: + description: MIxS Data that comply with the Miuvig checklist and the HydrocarbonResourcesFluidsSwabs Extension + title: Miuvig combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - Miuvig + class_uri: MIXS:0010012_0016016 + MiuvigMicrobialMatBiofilm: + description: MIxS Data that comply with the Miuvig checklist and the MicrobialMatBiofilm Extension + title: Miuvig combined with MicrobialMatBiofilm + in_subset: + - combination_classes + is_a: MicrobialMatBiofilm + mixins: + - Miuvig + class_uri: MIXS:0010012_0016008 + MiuvigMiscellaneousNaturalOrArtificialEnvironment: + description: MIxS Data that comply with the Miuvig checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension + title: Miuvig combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016009 + MiuvigPlantAssociated: + description: MIxS Data that comply with the Miuvig checklist and the PlantAssociated Extension + title: Miuvig combined with PlantAssociated + in_subset: + - combination_classes + is_a: PlantAssociated + mixins: + - Miuvig + class_uri: MIXS:0010012_0016010 + MiuvigSediment: + description: MIxS Data that comply with the Miuvig checklist and the Sediment Extension + title: Miuvig combined with Sediment + in_subset: + - combination_classes + is_a: Sediment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016011 + MiuvigSoil: + description: MIxS Data that comply with the Miuvig checklist and the Soil Extension + title: Miuvig combined with Soil + in_subset: + - combination_classes + is_a: Soil + mixins: + - Miuvig + class_uri: MIXS:0010012_0016012 + MiuvigSymbiontAssociated: + description: MIxS Data that comply with the Miuvig checklist and the SymbiontAssociated Extension + title: Miuvig combined with SymbiontAssociated + in_subset: + - combination_classes + is_a: SymbiontAssociated + mixins: + - Miuvig + class_uri: MIXS:0010012_0016023 + MiuvigWastewaterSludge: + description: MIxS Data that comply with the Miuvig checklist and the WastewaterSludge Extension + title: Miuvig combined with WastewaterSludge + in_subset: + - combination_classes + is_a: WastewaterSludge + mixins: + - Miuvig + class_uri: MIXS:0010012_0016013 + MiuvigWater: + description: MIxS Data that comply with the Miuvig checklist and the Water Extension + title: Miuvig combined with Water + in_subset: + - combination_classes + is_a: Water + mixins: + - Miuvig + class_uri: MIXS:0010012_0016014 +settings: + agrochemical_name: .* + amount: '[-+]?[0-9]*\.?[0-9]+' + add_recov_methods: Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other + DOI: ^doi:10.\d{2,9}/.*$ + NCBItaxon_id: NCBITaxon:\d+ + PMID: ^PMID:\d+$ + URL: ^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$ + adapter: '[ACGTRKSYMWBHDVN]+' + adapter_A_DNA_sequence: '[ACGTRKSYMWBHDVN]+' + adapter_B_DNA_sequence: '[ACGTRKSYMWBHDVN]+' + ambiguous_nucleotides: '[ACGTRKSYMWBHDVN]+' + country: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + date_time_stamp: (\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\d|3[01])(T([01]\d|2[0-3]):([0-5]\d):([0-5]\d)(\.\d+)?(Z|([+-][01]\d:[0-5]\d))?)?)?)?$ + duration: P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W) + float: '[-+]?[0-9]*\.?[0-9]+' + integer: '[1-9][0-9]*' + lat: (-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) + lon: -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2}) + name: .* + parameters: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + particulate_matter_name: .* + region: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + room_name: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + room_number: '[1-9][0-9]*' + scientific_float: '[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?' + software: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + specific_location: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + storage_condition_type: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + termID: '[a-zA-Z]{2,}:[a-zA-Z0-9]\d+' + termLabel: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + text: .* + unit: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) + version: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+) diff --git a/src/scripts/describe_enums_by_slots_using.py b/src/scripts/describe_enums_by_slots_using.py index a8d688ab16..8de9eb36c7 100644 --- a/src/scripts/describe_enums_by_slots_using.py +++ b/src/scripts/describe_enums_by_slots_using.py @@ -4,9 +4,19 @@ @click.command() -@click.option('--schema_file', type=str, default="../mixs/schema/mixs.yaml", help="Path to the input schema file.") -@click.option('--output_file', type=str, default='../../mixs_with_enum_descriptions.yaml', show_default=True, - help="Path to the output schema file with updated enum descriptions.") +@click.option( + "--schema_file", + type=str, + default="../mixs/schema/mixs.yaml", + help="Path to the input schema file.", +) +@click.option( + "--output_file", + type=str, + default="../../mixs_with_enum_descriptions.yaml", + show_default=True, + help="Path to the output schema file with updated enum descriptions.", +) def update_enum_descriptions(schema_file: str, output_file: str) -> None: """ Update enum descriptions in the given schema file. @@ -15,6 +25,8 @@ def update_enum_descriptions(schema_file: str, output_file: str) -> None: by other terms (slots). The descriptions will indicate whether an enum is used by any term, and if so, by how many terms and which ones. + Note: Does not overwrite existing descriptions + :param schema_file: Path to the input schema file. :param output_file: Path to the output schema file where the updated schema will be saved. """ @@ -26,16 +38,24 @@ def update_enum_descriptions(schema_file: str, output_file: str) -> None: user_names = [u.name for u in users] user_names.sort() - if len(user_names) == 0: - ev.description = "Permissible values, not used by any term" - elif len(user_names) == 1: - ev.description = f"Permissible values, used by term {user_names[0]}" - else: # len(user_names) > 1 - ev.description = f"Permissible values, used by {len(user_names)} terms: {', '.join(user_names)}" + new_desc = "" + + if ev.description is None or ev.description == "": + if len(user_names) == 0: + new_desc = "Permissible values, not used by any term" + elif len(user_names) == 1: + new_desc = f"Permissible values, used by term {user_names[0]}" + else: # len(user_names) > 1 + new_desc = f"Permissible values, used by {len(user_names)} terms: {', '.join(user_names)}" + ev.description = new_desc + else: + click.echo( + f"Enum {ek} already has description '{ev.description}'. Do not overwrite with new description." + ) yaml_dumper.dump(schema_view.schema, output_file) click.echo(f"Enum descriptions updated and saved to {output_file}") -if __name__ == '__main__': +if __name__ == "__main__": update_enum_descriptions()