diff --git a/docs/schema_markdown/Biospecimen.md b/docs/schema_markdown/Biospecimen.md index bcec8bea..77831224 100644 --- a/docs/schema_markdown/Biospecimen.md +++ b/docs/schema_markdown/Biospecimen.md @@ -37,6 +37,7 @@ URI: [GHGA:Biospecimen](https://w3id.org/GHGA/Biospecimen) * [Biospecimen➞isolation](Biospecimen_isolation.md) 0..1 * Description: Method or device employed for collecting/isolating a biospecimen or a sample. * Range: [String](types/String.md) + * in subsets: (ontology) * [Biospecimen➞storage](Biospecimen_storage.md) 0..1 * Description: Methods by which a biospecimen or a sample is stored (e.g. frozen in liquid nitrogen). * Range: [String](types/String.md) @@ -51,6 +52,7 @@ URI: [GHGA:Biospecimen](https://w3id.org/GHGA/Biospecimen) * Range: [VitalStatusEnum](VitalStatusEnum.md) * [Biospecimen➞tissue](Biospecimen_tissue.md) 1..1 * Range: [String](types/String.md) + * in subsets: (ontology) ### Mixed in from IdentifiedByAliasMixin: diff --git a/docs/schema_markdown/Biospecimen_isolation.md b/docs/schema_markdown/Biospecimen_isolation.md index 625672d6..2c8d4795 100644 --- a/docs/schema_markdown/Biospecimen_isolation.md +++ b/docs/schema_markdown/Biospecimen_isolation.md @@ -21,3 +21,10 @@ URI: [GHGA:Biospecimen_isolation](https://w3id.org/GHGA/Biospecimen_isolation) ## Used by * [Biospecimen](Biospecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/Biospecimen_tissue.md b/docs/schema_markdown/Biospecimen_tissue.md index 0d8c54a1..efe72da2 100644 --- a/docs/schema_markdown/Biospecimen_tissue.md +++ b/docs/schema_markdown/Biospecimen_tissue.md @@ -21,3 +21,10 @@ URI: [GHGA:Biospecimen_tissue](https://w3id.org/GHGA/Biospecimen_tissue) ## Used by * [Biospecimen](Biospecimen.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/Individual.md b/docs/schema_markdown/Individual.md index b1749eae..2676386b 100644 --- a/docs/schema_markdown/Individual.md +++ b/docs/schema_markdown/Individual.md @@ -40,12 +40,15 @@ URI: [GHGA:Individual](https://w3id.org/GHGA/Individual) * [Individual➞geographical_region](Individual_geographical_region.md) 0..1 * Description: The geographical region where the Individual is located. Any demarcated area of the Earth; may be determined by both natural and human boundaries. * Range: [String](types/String.md) + * in subsets: (ontology) * [Individual➞ancestries](Individual_ancestries.md) 0..\* * Description: A person's descent or lineage, from a person or from a population. * Range: [String](types/String.md) + * in subsets: (ontology) * [Individual➞phenotypic_features](Individual_phenotypic_features.md) 0..\* * Description: The Phenotypic Feature entity that is associated with this Biospecimen at the time of retrieval from the organism. Typically, a concept from Human Phenotype Ontology. For example, 'HP:0100244' indicates that the Individual - from_which_the_Biospecimen was extracted from - exhibits_'Fibrosarcoma'_as_one_of_its_phenotype. * Range: [String](types/String.md) + * in subsets: (ontology) ### Mixed in from IdentifiedByAliasMixin: diff --git a/docs/schema_markdown/Individual_ancestries.md b/docs/schema_markdown/Individual_ancestries.md index e0e7d58c..f6e2051f 100644 --- a/docs/schema_markdown/Individual_ancestries.md +++ b/docs/schema_markdown/Individual_ancestries.md @@ -21,3 +21,10 @@ URI: [GHGA:Individual_ancestries](https://w3id.org/GHGA/Individual_ancestries) ## Used by * [Individual](Individual.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/Individual_geographical_region.md b/docs/schema_markdown/Individual_geographical_region.md index 7247396c..e850be2d 100644 --- a/docs/schema_markdown/Individual_geographical_region.md +++ b/docs/schema_markdown/Individual_geographical_region.md @@ -21,3 +21,10 @@ URI: [GHGA:Individual_geographical_region](https://w3id.org/GHGA/Individual_geog ## Used by * [Individual](Individual.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/Individual_phenotypic_features.md b/docs/schema_markdown/Individual_phenotypic_features.md index 234ea2cc..81a849bf 100644 --- a/docs/schema_markdown/Individual_phenotypic_features.md +++ b/docs/schema_markdown/Individual_phenotypic_features.md @@ -21,3 +21,10 @@ URI: [GHGA:Individual_phenotypic_features](https://w3id.org/GHGA/Individual_phen ## Used by * [Individual](Individual.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/Ontology.md b/docs/schema_markdown/Ontology.md new file mode 100644 index 00000000..e08bd12b --- /dev/null +++ b/docs/schema_markdown/Ontology.md @@ -0,0 +1,35 @@ + +# Subset: ontology + + +This slot is part of an ontology which is currently not otherwise encoded in the schema. + +URI: [GHGA:ontology](https://w3id.org/GHGA/ontology) + + +### Classes + + +### Mixins + + +### Slots + + * [Biospecimen➞isolation](Biospecimen_isolation.md) + * [Biospecimen➞tissue](Biospecimen_tissue.md) + * [Individual➞ancestries](Individual_ancestries.md) + * [Individual➞geographical_region](Individual_geographical_region.md) + * [Individual➞phenotypic_features](Individual_phenotypic_features.md) - The Phenotypic Feature entity that is associated with this Biospecimen at the time of retrieval from the organism. Typically, a concept from Human Phenotype Ontology. For example, 'HP:0100244' indicates that the Individual - from_which_the_Biospecimen was extracted from - exhibits_'Fibrosarcoma'_as_one_of_its_phenotype. + * [Sample➞isolation](Sample_isolation.md) + * [Sample➞type](Sample_type.md) - The type of sample. + * [ancestries](ancestries.md) - A person's descent or lineage, from a person or from a population. + * [geographical_region](geographical_region.md) - The geographical region where the Individual is located. Any demarcated area of the Earth; may be determined by both natural and human boundaries. + * [isolation](isolation.md) - Method or device employed for collecting/isolating a biospecimen or a sample. + * [phenotypic_features](phenotypic_features.md) - Phenotypic feature concepts that the entity is associated with. + * [tissue](tissue.md) + +### Types + + +### Enums + diff --git a/docs/schema_markdown/Sample.md b/docs/schema_markdown/Sample.md index e671d8e0..af9d5c25 100644 --- a/docs/schema_markdown/Sample.md +++ b/docs/schema_markdown/Sample.md @@ -33,12 +33,14 @@ URI: [GHGA:Sample](https://w3id.org/GHGA/Sample) * [Sample➞type](Sample_type.md) 0..1 * Description: The type of sample. * Range: [SampleTypeEnum](SampleTypeEnum.md) + * in subsets: (ontology) * [Sample➞description](Sample_description.md) 1..1 * Description: Short textual description of the sample (How the sample was collected, sample source, Protocol followed for processing the sample etc). * Range: [String](types/String.md) * [Sample➞isolation](Sample_isolation.md) 0..1 * Description: Method or device employed for collecting/isolating a biospecimen or a sample. * Range: [String](types/String.md) + * in subsets: (ontology) * [Sample➞storage](Sample_storage.md) 0..1 * Description: Methods by which a biospecimen or a sample is stored (e.g. frozen in liquid nitrogen). * Range: [String](types/String.md) diff --git a/docs/schema_markdown/Sample_isolation.md b/docs/schema_markdown/Sample_isolation.md index c13f1b9f..8db34bcd 100644 --- a/docs/schema_markdown/Sample_isolation.md +++ b/docs/schema_markdown/Sample_isolation.md @@ -21,3 +21,10 @@ URI: [GHGA:Sample_isolation](https://w3id.org/GHGA/Sample_isolation) ## Used by * [Sample](Sample.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/Sample_type.md b/docs/schema_markdown/Sample_type.md index b1514eb2..93c74fd3 100644 --- a/docs/schema_markdown/Sample_type.md +++ b/docs/schema_markdown/Sample_type.md @@ -21,3 +21,10 @@ URI: [GHGA:Sample_type](https://w3id.org/GHGA/Sample_type) ## Used by * [Sample](Sample.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/ancestries.md b/docs/schema_markdown/ancestries.md index a59139c9..31dcd541 100644 --- a/docs/schema_markdown/ancestries.md +++ b/docs/schema_markdown/ancestries.md @@ -20,3 +20,10 @@ None → 0..\* [String](types/String.md) ## Used by + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/geographical_region.md b/docs/schema_markdown/geographical_region.md index e68e772b..94d0fc53 100644 --- a/docs/schema_markdown/geographical_region.md +++ b/docs/schema_markdown/geographical_region.md @@ -20,3 +20,10 @@ None → 0..1 [String](types/String.md) ## Used by + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/index.md b/docs/schema_markdown/index.md index 21e0506b..f54ee7de 100644 --- a/docs/schema_markdown/index.md +++ b/docs/schema_markdown/index.md @@ -4,7 +4,7 @@ **metamodel version:** 1.7.0 -**version:** 1.0.1 +**version:** 1.1.0 The submission centric metadata schema for the German Human Genome-Phenome Archive (GHGA). @@ -340,6 +340,7 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi ### Subsets + * [Ontology](Ontology.md) - This slot is part of an ontology which is currently not otherwise encoded in the schema. ### Types diff --git a/docs/schema_markdown/isolation.md b/docs/schema_markdown/isolation.md index 3dd45ccc..1ebb8ba5 100644 --- a/docs/schema_markdown/isolation.md +++ b/docs/schema_markdown/isolation.md @@ -21,3 +21,10 @@ None → 0..1 [String](types/String.md) ## Used by + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/phenotypic_features.md b/docs/schema_markdown/phenotypic_features.md index 068a2232..e5138587 100644 --- a/docs/schema_markdown/phenotypic_features.md +++ b/docs/schema_markdown/phenotypic_features.md @@ -20,3 +20,10 @@ None → 0..\* [String](types/String.md) ## Used by + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/docs/schema_markdown/tissue.md b/docs/schema_markdown/tissue.md index 78b1ee06..fe5aea86 100644 --- a/docs/schema_markdown/tissue.md +++ b/docs/schema_markdown/tissue.md @@ -20,3 +20,10 @@ None → 0..1 [String](types/String.md) ## Used by + +## Other properties + +| | | | +| --- | --- | --- | +| **In Subsets:** | | ontology | + diff --git a/scripts/generate_xlsx.py b/scripts/generate_xlsx.py index ae1e5967..8032e21d 100755 --- a/scripts/generate_xlsx.py +++ b/scripts/generate_xlsx.py @@ -95,10 +95,24 @@ def mv_help(self) -> str: """The multiple values help text""" return "multiple values" if self.slot_def.multivalued else "single value" + def in_ontology_subset(self, slot_def: SlotDefinition) -> bool: + """Returns a bool indicating whether or not the given slot is marked as + non-implemented ontology slot.""" + SUBSET_NAME="ontology" + in_subset_usage = slot_def.in_subset + in_subset_root = self.schema.get_slot(slot_def.name).in_subset + return ( + isinstance(in_subset_usage, list) and SUBSET_NAME in in_subset_usage or + isinstance(in_subset_root, list) and SUBSET_NAME in in_subset_root or + in_subset_usage == SUBSET_NAME or + in_subset_root == SUBSET_NAME + ) + + @property def restriction_help(self) -> str: """The restriction help text""" - if self.enum_name or self.slot_def.pattern: + if self.enum_name or self.slot_def.pattern or self.in_ontology_subset(self.slot_def): return "controlled vocabulary" elif self.cls_name: id_slot = self.schema.get_identifier_slot(self.cls_name) diff --git a/spreadsheets/ghga_submission_full.xlsx b/spreadsheets/ghga_submission_full.xlsx index cab74fa1..2ed99f86 100644 Binary files a/spreadsheets/ghga_submission_full.xlsx and b/spreadsheets/ghga_submission_full.xlsx differ diff --git a/spreadsheets/ghga_submission_individual.xlsx b/spreadsheets/ghga_submission_individual.xlsx index 8465ed63..65111c17 100644 Binary files a/spreadsheets/ghga_submission_individual.xlsx and b/spreadsheets/ghga_submission_individual.xlsx differ diff --git a/spreadsheets/ghga_submission_minimal.xlsx b/spreadsheets/ghga_submission_minimal.xlsx index 07a44211..cf1f0a57 100644 Binary files a/spreadsheets/ghga_submission_minimal.xlsx and b/spreadsheets/ghga_submission_minimal.xlsx differ diff --git a/spreadsheets/ghga_submission_sample.xlsx b/spreadsheets/ghga_submission_sample.xlsx index 2fcd35c1..88b69fd9 100644 Binary files a/spreadsheets/ghga_submission_sample.xlsx and b/spreadsheets/ghga_submission_sample.xlsx differ diff --git a/spreadsheets/ghga_submission_seq.xlsx b/spreadsheets/ghga_submission_seq.xlsx index d6a4df55..f1ed248f 100644 Binary files a/spreadsheets/ghga_submission_seq.xlsx and b/spreadsheets/ghga_submission_seq.xlsx differ diff --git a/src/schema/submission.yaml b/src/schema/submission.yaml index fc40cff5..ad0e1a02 100644 --- a/src/schema/submission.yaml +++ b/src/schema/submission.yaml @@ -2,7 +2,7 @@ id: https://w3id.org/GHGA-Submission-Metadata-Schema name: GHGA-Submission-Metadata-Schema description: >- The submission centric metadata schema for the German Human Genome-Phenome Archive (GHGA). -version: 1.0.1 +version: 1.1.0 imports: - linkml:types @@ -437,6 +437,8 @@ classes: description: >- The type of sample. range: SampleTypeEnum + in_subset: + - ontology required: false description: description: >- @@ -1053,7 +1055,8 @@ slots: phenotypic_features: description: Phenotypic feature concepts that the entity is associated with. - pattern: .* + in_subset: + - ontology # range: PhenotypicFeaturesEnum multivalued: true @@ -1072,7 +1075,8 @@ slots: ancestries: description: >- A person's descent or lineage, from a person or from a population. - pattern: HANCESTRO:.* + in_subset: + - ontology # range: AncestryEnum multivalued: true @@ -1353,7 +1357,8 @@ slots: isolation: description: >- Method or device employed for collecting/isolating a biospecimen or a sample. - pattern: SNOMED:.* + in_subset: + - ontology # range: IsolationEnum storage: @@ -1385,7 +1390,8 @@ slots: description: >- The geographical region where the Individual is located. Any demarcated area of the Earth; may be determined by both natural and human boundaries. - pattern: HANCESTRO:.* + in_subset: + - ontology # range: GeographicalRegionEnum vital_status: @@ -1471,7 +1477,8 @@ slots: DOI identifier of a publication. tissue: - pattern: BTO:.* + in_subset: + - ontology # range: TissueEnum trios: @@ -1479,6 +1486,12 @@ slots: range: Trio multivalued: true +subsets: + ontology: + description: >- + This slot is part of an ontology which is currently not otherwise encoded + in the schema. + enums: DataUseModifierEnum: description: Permitted values for data use modifier