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Fixed openapi.yml.
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‎node_normalizer/resources/openapi.yml‎

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@@ -50,6 +50,7 @@ paths:
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<a href="https://github.com/NCATSTranslator/NodeNormalization/blob/master/documentation/API.md#status">NodeNorm API documentation</a>.'
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responses:
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'200':
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description: Successful result describing this NodeNorm instance.
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content:
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application/json:
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schema:
@@ -68,15 +69,15 @@ paths:
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description: 'Returns the curies and their hit count for a semantic type(s). You can read more about this endpoint
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in the <a href="https://github.com/NCATSTranslator/NodeNormalization/blob/master/documentation/API.md#get_curie_prefixes">NodeNorm API documentation</a>.'
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parameters:
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- in: query
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name: semantic_type
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schema:
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example:
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- biolink:ChemicalEntity
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- biolink:AnatomicalEntity
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items:
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type: string
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type: array
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- in: query
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name: semantic_type
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schema:
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example:
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- biolink:ChemicalEntity
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- biolink:AnatomicalEntity
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items:
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type: string
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type: array
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responses:
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'200':
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content:
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"KEGG.COMPOUND": "16039"
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"biolink:AnatomicalEntity":
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curie_prefix:
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"UMLS": "159941",
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"FMA": "98631",
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"UBERON": "14564",
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"ZFA": "606",
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"NCIT": "10286",
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"MESH": "1992",
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"EMAPA": "966",
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"FBbt": "117",
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"WBbt": "18",
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"GO": "4041",
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"SNOMEDCT": "1422",
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"UMLS": "159941"
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"FMA": "98631"
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"UBERON": "14564"
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"ZFA": "606"
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"NCIT": "10286"
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"MESH": "1992"
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"EMAPA": "966"
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"FBbt": "117"
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"WBbt": "18"
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"GO": "4041"
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"SNOMEDCT": "1422"
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"CL": "3043"
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type: object
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description: Results
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summary: Return the number of times each CURIE prefix appears in an equivalent
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identifier for a semantic type
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tags:
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- Interfaces
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- Interfaces
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/get_normalized_nodes:
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get:
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description: 'Returns the equivalent identifiers and semantic types for the CURIEs entered.
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You can optionally <a href="https://github.com/NCATSTranslator/Babel/blob/master/docs/Conflation.md">conflate identifiers</a> if needed.
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You can read more about this endpoint in the
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<a href="https://github.com/NCATSTranslator/NodeNormalization/blob/master/documentation/API.md#get_normalized_nodes">NodeNorm API documentation</a>.'
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parameters:
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- in: query
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name: curie
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schema:
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example:
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- MESH:D014867
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- NCIT:C34373
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items:
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type: string
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type: array
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- in: query
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name: curie
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schema:
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example:
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- MESH:D014867
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- NCIT:C34373
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items:
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type: string
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type: array
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responses:
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'200':
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content:
@@ -146,56 +147,56 @@ paths:
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identifier: CHEBI:15377
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label: Water
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equivalent_identifiers:
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- identifier: CHEBI:15377
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label: Water
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- identifier: CHEMBL.COMPOUND:CHEMBL1098659
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label: WATER
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- identifier: DRUGBANK:DB09145
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- identifier: PUBCHEM:22247451
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- identifier: PUBCHEM:962
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- identifier: MESH:D014867
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- identifier: HMDB:HMDB0002111
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- identifier: INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N
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- identifier: UNII:059QF0K00R
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- identifier: KEGG.COMPOUND:C00001
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- identifier: CHEBI:15377
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label: Water
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- identifier: CHEMBL.COMPOUND:CHEMBL1098659
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label: WATER
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- identifier: DRUGBANK:DB09145
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- identifier: PUBCHEM:22247451
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- identifier: PUBCHEM:962
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- identifier: MESH:D014867
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- identifier: HMDB:HMDB0002111
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- identifier: INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N
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- identifier: UNII:059QF0K00R
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- identifier: KEGG.COMPOUND:C00001
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type:
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- biolink:SmallMolecule
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- biolink:MolecularEntity
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- biolink:ChemicalEntity
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- biolink:PhysicalEssence
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- biolink:ChemicalOrDrugOrTreatment
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- biolink:ChemicalEntityOrGeneOrGeneProduct
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- biolink:ChemicalEntityOrProteinOrPolypeptide
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- biolink:NamedThing
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- biolink:PhysicalEssenceOrOccurrent
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- biolink:SmallMolecule
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- biolink:MolecularEntity
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- biolink:ChemicalEntity
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- biolink:PhysicalEssence
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- biolink:ChemicalOrDrugOrTreatment
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- biolink:ChemicalEntityOrGeneOrGeneProduct
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- biolink:ChemicalEntityOrProteinOrPolypeptide
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- biolink:NamedThing
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- biolink:PhysicalEssenceOrOccurrent
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information_content: 47.5
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NCIT:C34373:
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equivalent_identifiers:
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- identifier: MONDO:0004976
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label: amyotrophic lateral sclerosis
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- identifier: DOID:332
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- identifier: OPPHANET:803
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- identifier: UMLS:C0393554
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- identifier: MESH:D000690
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- identifier: MEDDRA:10002026
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- identifier: NCIT:C34373
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- identifier: HP:0007354
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label: Amyotrophic lateral sclerosis
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- identifier: MONDO:0004976
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label: amyotrophic lateral sclerosis
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- identifier: DOID:332
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- identifier: OPPHANET:803
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- identifier: UMLS:C0393554
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- identifier: MESH:D000690
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- identifier: MEDDRA:10002026
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- identifier: NCIT:C34373
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- identifier: HP:0007354
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label: Amyotrophic lateral sclerosis
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id:
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identifier: MONDO:0004976
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label: amyotrophic lateral sclerosis
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type:
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- biolink:Disease
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- biolink:DiseaseorPhenotypicFeature
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- biolink:BiologicalEntity
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- biolink:ThingWithTaxon
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- biolink:NamedThing
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- biolink:Disease
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- biolink:DiseaseorPhenotypicFeature
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- biolink:BiologicalEntity
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- biolink:ThingWithTaxon
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- biolink:NamedThing
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information_content: 74.9
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type: object
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description: Results
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summary: Get the equivalent identifiers and semantic types for the CURIEs entered.
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tags:
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- Interfaces
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- Interfaces
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/get_semantic_types:
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get:
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description: 'Returns a distinct set of the semantic types discovered in the
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summary: Return a list of BioLink semantic types for which normalization has
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been attempted.
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tags:
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- Interfaces
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- Interfaces
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/get_allowed_conflations:
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get:
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description: 'Returns a list of allowed conflation options. Conflation allows cliques to be combined on-the-fly
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on the basis of two different criteria:
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<ol>
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<li><code>GeneProtein</code> conflation merges protein-coding genes with the proteins they encode. The gene(s) always
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appear first in the combined clique.
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<li><code>DrugChemical</code> conflation merges chemicals based on their active ingredient. We attempt to ensure that
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the active ingredient appears before any formulations in the combined clique.
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</ol>
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You can read <a href="https://github.com/NCATSTranslator/Babel/blob/master/docs/Conflation.md">more about conflation</a> or
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<a href="https://github.com/NCATSTranslator/NodeNormalization/blob/master/documentation/API.md#get_allowed_conflations">more about this endpoint</a>.'
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on the basis of two different criteria:
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<ol>
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<li><code>GeneProtein</code> conflation merges protein-coding genes with the proteins they encode. The gene(s) always
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appear first in the combined clique.
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<li><code>DrugChemical</code> conflation merges chemicals based on their active ingredient. We attempt to ensure that
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the active ingredient appears before any formulations in the combined clique.
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</ol>
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You can read <a href="https://github.com/NCATSTranslator/Babel/blob/master/docs/Conflation.md">more about conflation</a> or
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<a href="https://github.com/NCATSTranslator/NodeNormalization/blob/master/documentation/API.md#get_allowed_conflations">more about this endpoint</a>.'
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responses:
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'200':
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content:
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description: Results
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summary: Return a list of named conflations.
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tags:
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- Interfaces
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- Interfaces
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/get_setid:
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get:
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description: 'Returns the set ID for a given set of CURIEs. A set ID is an identifier that can be used to identify

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