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NF.yaml
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#######################################
# Portal
#######################################
# Note: this template definition uses the alternate syntax with 'attribute'
id: https://w3id.org/nfosi/
name: nfosi
default_curi_maps:
- semweb_context
prefixes:
nf: https://w3id.org/synapse/nfosi/vocab/
personinfo: https://w3id.org/linkml/examples/personinfo/
linkml: https://w3id.org/linkml/
schema: http://schema.org/
rdfs: http://www.w3.org/2000/01/rdf-schema#
skos: http://www.w3.org/2004/02/skos/core#
prov: http://www.w3.org/ns/prov#
htan: https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld
default_prefix: nf
default_range: string
emit_prefixes:
- rdf
- rdfs
- xsd
- skos
imports:
- linkml:types
slots:
Component:
description: Type of metadata template; provide the same one for all items/rows.
required: true
Filename:
description: The name of the file.
required: false
GIST:
description: Characterization of the manifestation of Gastrointestinal stromal tumor (GIST).
range: PresenceEnum
required: false
InChIKey:
description: >
A unique hash key for a compound, e.g. for “Selumetinib”, the key is CYOHGALHFOKKQC-UHFFFAOYSA-N (https://pubchem.ncbi.nlm.nih.gov/compound/10127622#section=InChI-Key). This is a more reliable identifier than the compound name and should be used if available.
required: false
IrisLischNodules:
description: Characterization of the manifestation of Iris Lisch Nodules.
range: PresenceEnum
required: false
title: Iris Lisch nodules
MPNSTCharacterization:
description: Characterization of the manifestation of MPNST.
range: PresenceEnum
required: false
title: MPNST Characterization
MRISequence:
description: A mode used in MRI imaging
range: MRISequenceEnum
required: false
Resource_id:
description: A UUID for a Resource from the NF Research Tools Database
required: false
WHOPerformanceStatus:
description: Score on the WHO scale describing patient's functional abilities.
range: WHOPerformanceStatusScores
title: WHO performance status
accessRequirements:
description: Statement describing access requirements for an entity.
required: false
accessType:
description: Indicates access type / possible procedures needed for access to the resource.
range: AccessTypeEnum
required: true
see_also:
- accessRequirements
acknowledgementStatements:
description: Statement describing how resource use should be acknowledged.
required: false
age:
description: A numeric value representing age of the individual. Use with `ageUnit`.
required: false
ageUnit:
description: A time unit that can be used with a given age value, e.g. years.
range: TimeUnit
required: false
aliquotID:
description: A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.
required: false
antibodyID:
description: Antibody ID such as RRID if available, otherwise use vendor ID.
required: false
aqueductalStenosis:
description: Characterization of the manifestation of aqueductal stenosis.
range: PresenceEnum
required: false
title: Aqueductal stenosis
assay:
description: The technology used to generate the data in this file.
range: AssayEnum
required: true
assayTarget:
description: Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.
required: false
attentionDeficitDisorder:
description: Characterization of the manifestation of Attention Deficit Disorder.
range: PresenceEnum
required: false
title: Attention deficit disorder
author:
title: Author(s)
description: The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.
range: string
multivalued: true
required: false
auxiliaryAsset:
description: >
URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity.
required: false
averageBaseQuality:
description: Average base quality collected from samtools
required: false
averageInsertSize:
description: Average insert size as reported by samtools
required: false
averageReadLength:
description: Average read length collected from samtools
required: false
batchID:
description: Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.
required: false
benefactorId:
description: The id of the resource from which access control is inherited.
required: false
bisulfiteConversionKitID:
description: Name of kit used in bisulfite conversion.
required: false
bodySite:
comments:
- Helpful to consider where /cell samples came from, e.g. something like "schwannoma" gets put in `tumorType`, but `bodySite` gives us the original location of the tumor.
description: Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts.
range: BodyPartEnum
required: false
slot_uri: https://cancerdhc.github.io/ccdhmodel/v1.1/BodySite/
breastCancer:
description: Characterization of the manifestation of Breast cancer.
range: PresenceEnum
required: false
title: Breast cancer
cafeaulaitMacules:
description: Characterization of cafe-au-lait macules.
range: PresenceEnum
title: Six or more cafe-au-lait macules
captureArea:
description: >
One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.
required: false
cellID:
description: Also known as cell barcode, this value can be added for single-cell experiments to identify data at the cell level.
required: false
cellType:
description: A cell type is a distinct morphological or functional form of cell.
range: Cell
required: false
channel:
description: Color channel used to generate data file.
required: true
range: ChannelEnum
source: https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
chipID:
description: User-specified identifier for the chip used to perform the methylation microarray.
required: false
source: https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
chipPosition:
description: User-specified identifier for the specific position on the chip that the sample was loaded into to perform the methylation microarray.
required: false
source: https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
citation:
title: Citation
description: Citation (e.g. doi) that usage of data or resource should be cited with.
range: string
required: false
comments:
title: Comments
description: Brief free-text comments that may also be important to understanding the resource.
range: string
required: false
compoundDose:
description: A dose quantity for the treatment compound. To be used with compoundDoseUnit.
required: false
compoundDoseUnit:
description: A unit associated with the value(s) in compoundDose.
required: false
compoundName:
description: Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)
required: false
concentrationMaterial:
description: Numeric value for concentration of the material
required: false
concentrationMaterialUnit:
description: Unit used for the material concentration, e.g. mg/mL
range: ConcentrationUnit
required: false
concentrationNaCl:
description: Numeric value for NaCl concentration
required: false
concentrationNaClUnit:
description: Unit used for the NaCl concentration, e.g. mM
range: ConcentrationUnit
required: false
concreteType:
description: Refers to the class model the data platform uses for representing the resource. This is a low-level field set by the platform and is not a user annotation.
required: false
contentSize:
description: (Files only) File size, usually calculated by the backend.
required: false
contentType:
description: Refers to the type of content.
notes:
- Used by schematic (entities with value = dataset) to detect which folders to surface.
required: false
contributor:
description: An entity responsible for making contributions to the resource.
range: string
required: false
see_also: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#contributor
createdBy:
description: Refers to the user who created the resource.
required: false
createdOn:
description: Refers to when the resource was created.
required: false
creator:
description: An entity responsible for making the resource.
notes:
- Recommended practice is to identify the creator with a URI. If this is not possible or feasible, a literal value that identifies the creator may be provided.
range: string
required: true
see_also: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#creator
currentVersion:
description: (Versionable entities only) The current version number of the resource.
required: false
see_also: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_version
dataCollectionMode:
description: Mode of data collection in tandem MS assays. Either DDA (data-dependent acquisition) or DIA (data-independent) acquisition.
required: true
dataFileHandleId:
description: (Files only) Refers to the id of the file.
required: false
dataStatus:
description: Overall status of data in a study.
range: DataStatusEnum
required: true
dataSubtype:
description: Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.
range: DataSubtypeEnum
required: true
dataType:
any_of:
- range: Data
- range: Metadata
description: >
Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.
required: true
datasetItemCount:
description: Count of files in dataset. Auto-calculated by Synapse.
required: false
datasetSizeInBytes:
description: Size of dataset entity in bytes. Auto-calculated by Synapse.
required: false
dermalNeurofibromas:
description: Characterization of the manifestation of Dermal neurofibromas.
range: NeurofibromaManifestationEnum
required: false
title: Dermal neurofibromas
dermalSchwannoma:
description: Characterization of the manifestation of Dermal schwannoma.
range: PresenceEnum
required: false
title: Dermal schwannoma
description:
description: Text describing a resource.
range: string
required: false
diagnosis:
description: Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.
range: DiagnosisEnum
required: true
diagnosisAgeGroup:
description: Age group of the individual at the time of diagnosis.
range: AgeGroupEnum
title: Diagnosis age group
diffuseDermalNeurofibromas:
description: Characterization of the manifestation of Diffuse dermal neurofibromas.
range: NeurofibromaManifestationEnum
required: false
title: Diffuse dermal neurofibromas
diseaseFocus:
description: Disease that acts as the main topic.
range: string
required: false
dissociationMethod:
description: Procedure by which a biological specimen is dissociated into individual cells or a cell suspension
range: DissociationMethodEnum
required: false
documentation:
description: URL to any documentation describing the resource and its use.
required: false
doi:
description: Digital object identifier of the resource.
required: false
drugScreenType:
description: String describing general class of drug screen
range: DrugScreen
required: false
epidemiologyMetric:
description: Common metrics used in epidemiology studies.
required: true
etag:
description: Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. The E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date.
required: false
experimentId:
description: When applicable, an optional identifier that can be used to distinguish or group the experiments that generated the data; also can be used to denote internal batch reference if needed.
required: false
experimentalCondition:
description: A free-text description of the experimental condition (e.g. 5 mM doxorubicin).
required: false
experimentalFactor:
description: An ontology concept for experimental factor measured with this data.
notes:
- Note that this enforces a concept term from EFO (currently preferred), while the related `experimentalCondition` is free-text and much more specific.
range: Measurement
required: false
experimentalTimepoint:
description: The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit
required: false
expressionUnit:
description: Measure used for transcript expression quantification
range: ExpressionUnitEnum
required: false
failedQC:
description: Whether the sample or data failed QC checks (Yes, No)
range: BooleanEnum
required: false
fileCount:
description: Number of files in the resource collection.
notes:
- This is auto-generated by Synapse for datasets.
required: false
fileFormat:
description: Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software
range: FileFormatEnum
required: true
fileSize:
description: Size of file in bytes.
required: false
fundingAgency:
description: Refers to the funding organization for the generated resource. This annotation is handled by the DCC.
range: string
required: false
genePerturbationTechnology:
description: Technology used to perturb gene
range: GenePerturbationMethodEnum
required: false
genePerturbationType:
description: Specific way in which a single gene was perturbed in a sample
range: GenePerturbationTechnologyEnum
required: false
genePerturbed:
description: The HUGO gene symbol for the gene that is perturbed.
required: false
genomicReference:
description: Version of genome reference used for alignment in processing workflow
notes:
- Currently used with nextflow-processed data.
required: true
genomicReferenceLink:
description: Link to genome reference data file used for alignment in processing workflow
required: false
gliomaOrEpendymoma:
description: Characterization of the manifestation of Glioma or ependymoma.
range: BinaryImagingDiagnosisEnum
required: false
title: Glioma or ependymoma
glomusTumor:
description: Characterization of the manifestation of Glomus tumor.
range: PresenceEnum
required: false
title: Glomus tumor
grantDOI:
description: Doi of a grant (e.g. in ProposalCentral) that can be associated with the entity.
range: string
required: false
heartDefect:
description: Characterization of the manifestation of Heart defect.
range: PresenceEnum
required: false
title: Heart defect
id:
description: The entity id for the resource automatically assigned by the platform.
required: false
immersion:
description: Immersion medium
required: false
individualID:
description: A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.
required: true
individualIdSource:
description: Database or repository to which individual ID maps
notes:
- Legacy key used in a couple of old studies
required: false
inheritance:
description: Describes whether known inheritance from a parent.
range: InheritanceEnum
title: Inheritance
initiative:
description: Refers to a funding initiative. Typically handled by the DCC.
range: string
required: false
institution:
description: Link to affiliated institution.
range: Institution
required: false
intellectualDisability:
description: Characterization of the manifestation of Intellectual disability.
range: PresenceEnum
required: false
title: Intellectual disability
isCellLine:
description: Whether or not sample source is a cell line (Yes; No)
range: BooleanEnum
required: false
isFilteredReads:
description: Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator
required: false
isMultiIndividual:
description: Whether or not a file has data for multiple individuals (Yes; No)
range: BooleanEnum
required: false
isMultiSpecimen:
description: Whether or not a file has data for multiple specimens (Yes; No)
range: BooleanEnum
required: false
isPairedEnd:
deprecated: Note that this can be inferred as 'Yes' when runType=pairedEnd; current templates actually use runType to capture this info.
description: (Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No).
range: BooleanEnum
required: false
isPrimaryCell:
description: Whether or not cellType is primary (Yes; No)
range: BooleanEnum
required: false
isStranded:
description: Whether or not the library is stranded (Yes; No)
range: BooleanEnum
required: false
isXenograft:
description: Whether or not sample source is a xenograft (Yes; No)
range: BooleanEnum
required: false
learningDisability:
description: Characterization of the manifestation of Learning disability.
range: PresenceEnum
required: false
title: Learning disability
lensAperture:
description: Numerical aperture of the lens. Floating point value > 0.
required: false
lenticularOpacity:
description: Characterization of the manifestation of Lenticular opacity.
range: PresenceEnum
required: false
title: Lenticular opacity
leukemia:
description: Characterization of the manifestation of Leukemia.
range: PresenceEnum
required: false
title: Leukemia
libraryKitID:
description: Library kit ID.
required: true
libraryPrep:
description: The general strategy by which the library was prepared
range: LibraryPrepEnum
required: false
libraryPreparationMethod:
description: Method by which library was prepared
range: LibraryPreparationMethodEnum
required: true
libraryStrand:
any_of:
- range: StrandednessEnum
- range: NotApplicableEnum
description: Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.
notes:
- Meaning originally captured with combination of readPairOrientation and readStrandOrigin.
- https://littlebitofdata.com/en/2017/08/strandness_in_rnaseq/
required: true
license:
title: License
description: Link to a license or name of license applicable for the resource.
range: License
required: false
longBoneDysplasia:
description: Characterization of the manifestation of Long bone dysplasia.
range: PresenceEnum
required: false
title: Long bone dysplasia
manifestation:
description: An associated phenotype characteristic.
range: string
required: false
materialType:
description: Type of material in the characterization
required: false
meanCoverage:
description: Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools
required: false
meningioma:
description: Characterization of the manifestation of Meningioma.
range: MultipleImagingDiagnosisEnum
required: false
title: Meningioma
modelSystemName:
any_of:
- range: CellLineModel
- range: MouseModel
description: 'A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)'
required: false
modifiedBy:
description: Refers to a user who last modified the resource on the platform.
required: false
mosaicism:
description: Whether individual is mosaic.
range: MosaicismEnum
title: Mosaicism
nf1Genotype:
any_of:
- range: Genotype
- range: UnknownEnum
description: Genotype of NF1 gene in the biospecimen from which the data were derived, if known.
required: false
see_also:
- nf1Variant
- nf2Genotype
germlineMutationIndicator:
description: Indicates a summary testing result for individual's germline mutation only.
range: TestSummaryEnum
germlineMutation:
description: The individual's actual germline mutation.
notes:
- More sensitive information than germlineMutationIndicator.
- Free-text field that possibly suggests *any* mutations could be put here, while nf1GermlineMutation, etc. are more specific in terms of disease.
nf1GermlineMutation:
description: NF1 germline mutation.
notes:
- Unlike nf1Variant, this is free-text and not constrained to enumerated values of known variants, making it more flexible for new mutations and different nomenclatures.
required: false
nf1SomaticMutation:
description: NF1 somatic mutation, i.e. in tumor samples.
required: false
nf2Genotype:
any_of:
- range: Genotype
- range: UnknownEnum
description: Genotype of NF2 gene in the biospecimen from which the data were derived, if known
required: false
nominalMagnification:
description: magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens.
required: false
nonopticGlioma:
description: Characterization of the manifestation of Nonoptic glioma.
range: PresenceEnum
required: false
title: Nonoptic glioma
nonvestibularCranialSchwannoma:
description: Characterization of the manifestation of Nonvestibular cranial schwannoma.
range: BinaryImagingDiagnosisEnum
required: false
title: Nonvestibular cranial schwannoma
nonvestibularSchwannomas:
description: Characterization of the manifestation of Nonvestibular schwannomas.
range: NonvestibularSchwannomaManifestationEnum
required: false
title: Nonvestibular schwannomas
nucleicAcidSource:
description: Source of the extracted nucleic acid used in the experiment
range: NucleicAcidSourceEnum
required: false
numberOfSchwannomas:
description: Number of schwannomas.
range: SchwannomaManifestationEnum
required: false
title: Number of schwannomas
objective:
description: Microscope objective.
required: false
opticGlioma:
description: Characterization of the manifestation of Optic glioma.
range: OpticGliomaManifestationEnum
required: false
title: Optic glioma
organ:
description: A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.
range: OrganEnum
required: false
otherTumors:
description: Characterization of the manifestation of other tumors.
range: PresenceEnum
required: false
title: Other tumors
pH:
description: Numeric value for pH (range 0-14)
required: false
painStatus:
description: Pain status rating.
range: PainEnum
title: Pain status
pairsOnDifferentChr:
description: Pairs on different chromosomes collected from samtools
required: false
parentId:
description: 'The id of the parent resource, i.e. the parent folder on the platform. '
required: false
parentSpecimenID:
description: |
A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning.
required: false
peripheralNeuropathy:
description: Characterization of the manifestation of Peripheral neuropathy.
range: PresenceEnum
required: false
title: Peripheral neuropathy
pheochromocytoma:
description: Characterization of the manifestation of Pheochromocytoma.
range: PresenceEnum
required: false
title: Pheochromocytoma
plateName:
description: User-specified identifier of the plate used to prepare the sample for analysis.
required: false
source: https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
plateWell:
description: User-specified identifier for the specific well of the plate used to prepare the sample for analysis.
required: false
source: https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
platform:
description: A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.
range: PlatformEnum
required: true
plexiformNeurofibromas:
description: Characterization of the manifestation of Plexiform neurofibromas.
range: PlexiformNeurofibromaManifestationEnum
required: false
title: Plexiform neurofibromas
populationCoverage:
description: Describes population coverage of the present data.
required: false
programmingLanguage:
description: A computer programming language
required: false
progressReportNumber:
description: 'Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1'
required: false
proportionCoverage10x:
description: Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools
required: false
proportionCoverage30x:
description: Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools
required: false
proteinExtractSource:
description: Source of the extracted protein used in the experiment
range: ProteinExtractSourceEnum
required: false
protocolAssay:
title: Protocol assay
description: >
Main assay type that this protocol is related to, e.g. this is a prep protocol for single-cell RNA-seq assay. This is especially helpful for newly-developed or in-house assays.
range: AssayEnum
required: false
protocolPurpose:
title: Protocol purpose
description: Brief description of the protocol purpose.
range: string
required: false
pubertyOnset:
description: Puberty onset.
range: PubertyOnsetEnum
required: false
title: Puberty onset
publisher:
description: An entity responsible for making the resource available.
range: string
required: false
see_also: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/publisher
readDepth:
description: If available, the coverage statistic as output from bedtools coverage or samtools stats.
required: false
readLength:
description: Number of base pairs (bp) sequenced for a read
required: false
readPair:
description: The read of origin, Read 1 or Read 2
required: false
readPairOrientation:
deprecated: See `libraryStrand`.
description: The relative orientation of the reads in a paired-end protocol
range: ReadPairOrientationEnum
required: false
readStrandOrigin:
deprecated: See `libraryStrand`.
description: The strand from which the read originates in a strand-specific protocol
range: ReadStrandOriginEnum
required: false
readsDuplicatedPercent:
description: Percent of duplicated reads collected from samtools
required: false
readsMappedPercent:
description: Percent of mapped reads collected from samtools
required: false
recordingSource:
description: Source of electrophysiology recording.
required: false
referenceSequence:
description: Syntactic sequences that has a role as reference of an annotation.
required: false
referenceSet:
description: A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data.
range: GenomicReferenceEnum
required: false
relatedDataset:
description: Reference to a relevant dataset entity.
required: false
relatedResource:
description: A related resource.
required: false
relatedStudies:
description: Studies similar to the current study. Subproperty of `relatedResource`.
multivalued: true
range: string
required: false
reporterGene:
description: A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.
required: false
reporterSubstance:
description: A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
required: false
notes:
- Need to make enums for this.
resourceType:
description: The type of resource being stored and annotated
range: Resource
required: true
runType:
description: Sequencing run type.
notes:
- Includes some of same information as concept `library layout` and has been removed in favor of libraryStrand
range: RunTypeEnum
required: false
runtimePlatform:
description: Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).
required: false
sampleType:
title: Sample type
description: Type of sample used
range: string
required: false
scoliosis:
description: Characterization of the manifestation of Scoliosis.
range: PresenceEnum
required: false
title: Scoliosis
series:
description: Title of a custom series that this resource is part of, if any.
range: string
required: false
see_also: http://www.w3.org/ns/dcat#inSeries
sex:
any_of:
- range: SexEnum
- range: UnknownEnum
- range: NotApplicableEnum
description: Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.
required: false
skinFoldFreckling:
description: Characterization of skin fold freckling.
range: PresenceEnum
title: Skin fold freckling
slideID:
description: >
Unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123.
required: false
slideVersion:
description: Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.
required: false
sourceName:
description: >
Intended for non-biological samples, tf the sample is a nanoparticle sample or some chemical substance not derived from a biological material, the corresponding source name should refer to the starting sample that was modified by a protocol for the assay.
required: false
species:
description: The name of a species (typically a taxonomic group) of organism.
range: SpeciesEnum
required: true
specimenID:
description: >
A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen.
required: true
specimenIDSource:
description: Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.
required: false
specimenPreparationMethod:
description: Term that represents preservation of the sample before usage in, e.g. sequencing
range: SpecimenPreparationMethodEnum
required: true
specimenType:
any_of:
- range: Tissue
- range: OrganismSubstance
description: >
The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances.
required: false
sphenoidDysplasia:
description: Characterization of the manifestation of Sphenoid dysplasia.
range: PresenceEnum
required: false
title: Sphenoid dysplasia
spinalNeurofibromas:
description: Characterization of the manifestation of Spinal neurofibromas.
range: SpinalNeuromaManifestationEnum
required: false
title: Spinal neurofibromas
spinalSchwannoma:
description: Characterization of the manifestation of Spinal schwannoma.
range: MultipleImagingDiagnosisEnum
required: false
title: Spinal schwannoma
stature:
description: Stature of the individual.
range: Percentiles-2SD
required: false
title: Stature
studyFileviewId:
description: Links a Synapse project to its fileview.
range: string
required: false
studyId:
description: Id of study.
range: string
required: true
studyLeads:
description: Individuals with lead roles in a study.
multivalued: true
required: true
studyName:
description: Name of a study.
range: string
required: true
studyStatus:
description: Status of a study.
range: StudyStatusEnum
required: true
subcutaneousNodularNeurofibromas:
description: Characterization of the manifestation of Subcutaneous nodular neurofibromas.
range: NeurofibromaManifestationEnum
required: false
title: Subcutaneous nodular neurofibromas
summary:
description: A short description (an abstract).
range: string
required: true
targetCaptureKitID:
description: >
A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.
required: false
targetDepth:
description: The targeted read depth prior to sequencing.
required: false
timepointUnit:
description: For timed experiments this represents the unit of time measured
range: TimeUnit
required: false
title:
description: Title of a resource.
range: string
required: true
see_also: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_title
totalReads:
description: If available, the total number of reads collected from samtools.
required: false
transplantationRecipientSpecies:
description: Species into which donor was grown
required: false
transplantationRecipientTissue:
description: Tissue into which a xenograph sample is transplanted
range: Tissue
required: false
transplantationType:
description: Type of transplantation involved in the experiment, derived from MESH
range: TransplantationType
required: false
tumorTreatmentStatus:
description: Tumor treatment status for the individual.
range: TumorTreatmentEnum
title: Tumor treatment status
tumorType:
description: The type of tumor that the biospecimen used to generate the data were collected from.
range: Tumor
required: true
type:
description: Refers to the type of the resource on the platform, e.g. “file”.
required: false
vascularDisease:
description: Characterization of the manifestation of Vascular disease.
range: PresenceEnum
required: false
title: Vascular disease
vestibularSchwannoma:
description: Characterization of the manifestation of Vestibular schwannoma.
range: LateralManifestationEnum
required: false
title: Vestibular schwannoma
vitalStatus:
description: Vital status of the patient.
range: VitalStatusEnum
title: Vital status
workflow:
description: Name and version of the workflow used to generate/analyze the data
range: WorkflowEnum
required: false
workflowLink:
description: Workflow URL reference
required: false
workingDistance:
description: Working distance of the lens expressed as a floating point number > 0.
required: false
workingDistanceUnit:
description: Unit for working distance.
range: WorkingDistanceUnitEnum
required: false
yearProcessed:
description: "Year in which the resource was processed/derived, if applicable. This is only required for data processed by NF-OSI for tracking purposes, optional for community-contributed datasets. \n"
notes:
- There is no 'year' validation rule and `date` rule requires actual date format
range: integer
required: false
yearPublished:
description: Year in which the resource was published/generally made available.
range: integer
required: false
peakCallingAlgorithm:
description: A list of commonly used peak-calling algorithms for ChIP-Seq data analysis.
required: false
enums:
AssayEnum:
title: Assay
permissible_values:
2D AlamarBlue absorbance:
description: Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the absorbance-based assay, absorbance can be read at 570 nm.
meaning: https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html
2D AlamarBlue fluorescence:
description: Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the fluorescence-based assay, color change and fluorescence can be detected using 560/590 nm (excitation/emission).
meaning: https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html
3D confocal imaging:
description: Confocal microscopy with 3D reconstruction of the sample tissue.
meaning: https://pubmed.ncbi.nlm.nih.gov/34331281
3D electron microscopy:
description: Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
meaning: http://purl.obolibrary.org/obo/MI_0410
3D imaging:
description: Technique to produce 3D images to visualize important structures in great detail. To produce 3D images, many scans are made, and then combined by computers to produce a 3D model, which can then be manipulated. 3D ultrasounds are produced using a somewhat similar technique.
meaning: http://purl.obolibrary.org/obo/NCIT_C18485
3D microtissue viability:
description: Cell viability assay on a 3D microtissue model.
meaning: https://www.ncbi.nlm.nih.gov/books/NBK343426/
actigraphy:
description: Use of a portable device (actigraph) to study sleep-wake patterns and circadian rhythms by assessing movement.
meaning: http://purl.obolibrary.org/obo/MAXO_0000914
AlgometRx Nociometer:
description: Assay that can selectively measure the sensitivity of three different nerve fiber types. An overall score can be derived to indicate the type of pain a person is experiencing and can be used to monitor how well a patient responds to treatment of pain.
auditory brainstem response:
description: ABR is a gold standard for evaluating hearing in mice. A non-invasive method that measures the electrical activity generated by the auditory nerve and brainstem in response to sound stimuli. Electrodes are placed on the scalp of the mouse, and sound is delivered through a speaker or earphone.
ATAC-seq:
description: Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment
meaning: http://purl.obolibrary.org/obo/OBI_0002039
ATPase activity assay:
description: As an assay used for drug discovery, measures enzymatic ATP hydrolysis to help assess levels of enzymatic activity induced by a candidate drug molecule.
meaning: http://purl.obolibrary.org/obo/MI_0880
notes:
- See also https://www.bellbrooklabs.com/atpase-activity-assay-for-drug-discovery/ for discussion
BrdU proliferation assay:
description: A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle).
meaning: http://purl.obolibrary.org/obo/OBI_0000664
CAPP-seq: