diff --git a/schema/cat-vrs/core/cat-vrs-core-source.yaml b/schema/cat-vrs/core/cat-vrs-core-source.yaml index 6554d52..f7bc9f4 100644 --- a/schema/cat-vrs/core/cat-vrs-core-source.yaml +++ b/schema/cat-vrs/core/cat-vrs-core-source.yaml @@ -67,7 +67,7 @@ $defs: type: object inherits: Constraint description: >- - The location or location-state, congruent with other reference sequences, + The location or location-state, congruent with other reference sequences, about which categorical variation is being described. properties: type: @@ -91,8 +91,8 @@ $defs: description: >- Defined relationships between members of the categorical variant and the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a - human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` - refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` + human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` + refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. required: - definingContext @@ -133,7 +133,7 @@ $defs: items: properties: code: - enum: + enum: - EFO:0030069 - EFO:0020073 - EFO:0030068 diff --git a/schema/cat-vrs/core/def/DefiningContextConstraint.rst b/schema/cat-vrs/core/def/DefiningContextConstraint.rst index 6633aed..27dcb1f 100644 --- a/schema/cat-vrs/core/def/DefiningContextConstraint.rst +++ b/schema/cat-vrs/core/def/DefiningContextConstraint.rst @@ -1,6 +1,6 @@ **Computational Definition** -The location or location-state, congruent with other reference sequences, about which categorical variation is being described. +The location or location-state, congruent with other reference sequences, about which categorical variation is being described. **Information Model** @@ -27,4 +27,4 @@ Some DefiningContextConstraint attributes are inherited from :ref:`Constraint`. * - relations - _Not Specified_ - 0..m - - Defined relationships between members of the categorical variant and the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. + - Defined relationships between members of the categorical variant and the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. diff --git a/schema/cat-vrs/core/json/DefiningContextConstraint b/schema/cat-vrs/core/json/DefiningContextConstraint index f4d0b3c..065c167 100644 --- a/schema/cat-vrs/core/json/DefiningContextConstraint +++ b/schema/cat-vrs/core/json/DefiningContextConstraint @@ -4,7 +4,7 @@ "title": "DefiningContextConstraint", "type": "object", "maturity": "draft", - "description": "The location or location-state, congruent with other reference sequences, about which categorical variation is being described.", + "description": "The location or location-state, congruent with other reference sequences, about which categorical variation is being described.", "properties": { "type": { "type": "string", @@ -35,7 +35,7 @@ "codon_translation" ] }, - "description": "Defined relationships between members of the categorical variant and the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. \"GRCh37\" and \"GRCh38\") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept." + "description": "Defined relationships between members of the categorical variant and the defining context. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. \"GRCh37\" and \"GRCh38\") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept." } }, "required": [ diff --git a/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst b/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst index e6e6cbf..5bb090e 100644 --- a/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst +++ b/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst @@ -17,5 +17,5 @@ Cat-VRS Constraints found in Canonical Alleles. - Description * - constraints - _Not Specified_ - - 0..1 + - 1..1 - diff --git a/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst b/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst index d7b26d0..acdd353 100644 --- a/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst +++ b/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst @@ -17,5 +17,5 @@ Cat-VRS Constraints found in CategoricalCnvs. - Description * - constraints - _Not Specified_ - - 0..1 + - 1..1 - diff --git a/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst b/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst index acb18b8..0b1eaef 100644 --- a/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst +++ b/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst @@ -17,5 +17,5 @@ Cat-VRS Constraints found in Protein Sequence Consequences. - Description * - constraints - _Not Specified_ - - 0..1 + - 1..1 - diff --git a/schema/cat-vrs/profiles/json/CanonicalAlleleProperties b/schema/cat-vrs/profiles/json/CanonicalAlleleProperties index 964b2e2..f4cc583 100644 --- a/schema/cat-vrs/profiles/json/CanonicalAlleleProperties +++ b/schema/cat-vrs/profiles/json/CanonicalAlleleProperties @@ -27,7 +27,8 @@ "const": "transcript_projection" } } - ] + ], + "maxContains": 2 } } } @@ -35,5 +36,7 @@ } } }, - "required": [] + "required": [ + "constraints" + ] } \ No newline at end of file diff --git a/schema/cat-vrs/profiles/json/CategoricalCnvProperties b/schema/cat-vrs/profiles/json/CategoricalCnvProperties index ade56ca..4f0ad60 100644 --- a/schema/cat-vrs/profiles/json/CategoricalCnvProperties +++ b/schema/cat-vrs/profiles/json/CategoricalCnvProperties @@ -42,5 +42,7 @@ ] } }, - "required": [] + "required": [ + "constraints" + ] } \ No newline at end of file diff --git a/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties b/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties index 3c4a887..d983263 100644 --- a/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties +++ b/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties @@ -18,7 +18,8 @@ "relations": { "contains": { "const": "codon_translation" - } + }, + "maxContains": 1 } } } @@ -26,5 +27,7 @@ } } }, - "required": [] + "required": [ + "constraints" + ] } \ No newline at end of file