release 2.2.10

biolink · Nov 19, 2021 · d01ad1f · d01ad1f
1 parent 8a59e63
commit d01ad1f
Show file tree

Hide file tree

Showing 6 changed files with 44 additions and 19 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -1,5 +1,10 @@
 CHANGES
 =======
+2.2.10
+------
+mapping fixes - remove obsolete mappings, swap text based mappings with ids where applicable
+add associated with predicate along with associated with sensitivity to predicates. 
+
 2.2.9
 -----
 many fixes to mappings

diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -5,7 +5,7 @@ license: https://creativecommons.org/publicdomain/zero/1.0/
 
 # Version should be kept in sync with primary Git repository release tag
 
-version: 2.2.9
+version: 2.2.10
 
 ## ------------
 ## PREFIXES
@@ -72,7 +72,7 @@ prefixes:
   HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'
   HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'
   HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'
-  ICD10: ' https://icd.codes/icd9cm/'
+  ICD10: 'https://icd.codes/icd9cm/'
   ICD9: 'http://translator.ncats.nih.gov/ICD9_'
   interpro: 'https://www.ebi.ac.uk/interpro/entry/'
   INO: 'http://purl.obolibrary.org/obo/INO_'
@@ -7245,7 +7245,6 @@ classes:
       - HMDB
       - KEGG.COMPOUND
       - ChemBank
-      - Aeolus
       - PUBCHEM.SUBSTANCE
       - SIDER.DRUG
       - INCHI

diff --git a/biolink/model.py b/biolink/model.py
@@ -1,5 +1,5 @@
 # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0
-# Generation date: 2021-11-09T16:59:43
+# Generation date: 2021-11-18 16:34
 # Schema: Biolink-Model
 #
 # id: https://w3id.org/biolink/biolink-model
@@ -32,7 +32,7 @@
 
 # Namespaces
 APO = CurieNamespace('APO', 'http://purl.obolibrary.org/obo/APO_')
-AEOLUS = CurieNamespace('Aeolus', 'http://translator.ncats.nih.gov/Aeolus_')
+AEOLUS = CurieNamespace('Aeolus', 'http://example.org/UNKNOWN/Aeolus/')
 BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_')
 BIGG_METABOLITE = CurieNamespace('BIGG_METABOLITE', 'http://identifiers.org/bigg.metabolite/')
 BIGG_REACTION = CurieNamespace('BIGG_REACTION', 'http://identifiers.org/bigg.reaction/')
@@ -58,7 +58,10 @@
 COAR_RESOURCE = CurieNamespace('COAR_RESOURCE', 'http://purl.org/coar/resource_type/')
 COG = CurieNamespace('COG', 'https://www.ncbi.nlm.nih.gov/research/cog-project/')
 CPT = CurieNamespace('CPT', 'https://www.ama-assn.org/practice-management/cpt/')
-CTD = CurieNamespace('CTD', 'http://translator.ncats.nih.gov/CTD_')
+CTD = CurieNamespace('CTD', 'http://ctdbase.org/')
+CTD_CHEMICAL = CurieNamespace('CTD_CHEMICAL', 'http://ctdbase.org/detail.go?type=chem&acc=')
+CTD_DISEASE = CurieNamespace('CTD_DISEASE', 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc=')
+CTD_GENE = CurieNamespace('CTD_GENE', 'http://ctdbase.org/detail.go?type=gene&acc=')
 CHEMBANK = CurieNamespace('ChemBank', 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=')
 CLINVARVARIANT = CurieNamespace('ClinVarVariant', 'http://www.ncbi.nlm.nih.gov/clinvar/variation/')
 DBSNP = CurieNamespace('DBSNP', 'http://identifiers.org/dbsnp/')
@@ -67,7 +70,7 @@
 DOID = CurieNamespace('DOID', 'http://purl.obolibrary.org/obo/DOID_')
 DOID_PROPERTY = CurieNamespace('DOID-PROPERTY', 'http://purl.obolibrary.org/obo/doid#')
 DRUGBANK = CurieNamespace('DRUGBANK', 'http://identifiers.org/drugbank/')
-DRUGCENTRAL = CurieNamespace('DrugCentral', 'http://translator.ncats.nih.gov/DrugCentral_')
+DRUGCENTRAL = CurieNamespace('DrugCentral', 'http://drugcentral.org/drugcard/')
 EC = CurieNamespace('EC', 'http://www.enzyme-database.org/query.php?ec=')
 ECO = CurieNamespace('ECO', 'http://purl.obolibrary.org/obo/ECO_')
 ECTO = CurieNamespace('ECTO', 'http://purl.obolibrary.org/obo/ECTO_')
@@ -105,8 +108,7 @@
 HP = CurieNamespace('HP', 'http://purl.obolibrary.org/obo/HP_')
 HSAPDV = CurieNamespace('HsapDv', 'http://purl.obolibrary.org/obo/HsapDv_')
 IAO = CurieNamespace('IAO', 'http://purl.obolibrary.org/obo/IAO_')
-ICD0 = CurieNamespace('ICD0', 'http://translator.ncats.nih.gov/ICD0_')
-ICD10 = CurieNamespace('ICD10', 'http://translator.ncats.nih.gov/ICD10_')
+ICD10 = CurieNamespace('ICD10', 'https://icd.codes/icd9cm/')
 ICD9 = CurieNamespace('ICD9', 'http://translator.ncats.nih.gov/ICD9_')
 IDO = CurieNamespace('IDO', 'http://purl.obolibrary.org/obo/IDO_')
 INCHI = CurieNamespace('INCHI', 'http://identifiers.org/inchi/')
@@ -141,7 +143,6 @@
 MP = CurieNamespace('MP', 'http://purl.obolibrary.org/obo/MP_')
 MPATH = CurieNamespace('MPATH', 'http://purl.obolibrary.org/obo/MPATH_')
 MSIGDB = CurieNamespace('MSigDB', 'https://www.gsea-msigdb.org/gsea/msigdb/')
-METACYC = CurieNamespace('MetaCyc', 'http://translator.ncats.nih.gov/MetaCyc_')
 NBO = CurieNamespace('NBO', 'http://purl.obolibrary.org/obo/NBO_')
 NBO_PROPERTY = CurieNamespace('NBO-PROPERTY', 'http://purl.obolibrary.org/obo/nbo#')
 NCBIGENE = CurieNamespace('NCBIGene', 'http://identifiers.org/ncbigene/')
@@ -164,7 +165,6 @@
 PANTHER_PATHWAY = CurieNamespace('PANTHER_PATHWAY', 'http://identifiers.org/panther.pathway/')
 PATO = CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_')
 PCO = CurieNamespace('PCO', 'http://purl.obolibrary.org/obo/PCO_')
-PDQ = CurieNamespace('PDQ', 'https://www.cancer.gov/publications/pdq#')
 PFAM = CurieNamespace('PFAM', 'http://identifiers.org/pfam/')
 PHARMGKB_PATHWAYS = CurieNamespace('PHARMGKB_PATHWAYS', 'http://identifiers.org/pharmgkb.pathways/')
 PHAROS = CurieNamespace('PHAROS', 'http://pharos.nih.gov')
@@ -187,7 +187,6 @@
 RHEA = CurieNamespace('RHEA', 'http://identifiers.org/rhea/')
 RNACENTRAL = CurieNamespace('RNACENTRAL', 'http://identifiers.org/rnacentral/')
 RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_')
-RTXKG1 = CurieNamespace('RTXKG1', 'http://kg1endpoint.rtx.ai/')
 RXCUI = CurieNamespace('RXCUI', 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=')
 RXNORM = CurieNamespace('RXNORM', 'http://purl.bioontology.org/ontology/RXNORM/')
 RESEARCHID = CurieNamespace('ResearchID', 'https://publons.com/researcher/')
@@ -201,7 +200,6 @@
 SMPDB = CurieNamespace('SMPDB', 'http://identifiers.org/smpdb/')
 SNOMED = CurieNamespace('SNOMED', 'http://www.snomedbrowser.com/Codes/Details/')
 SNOMEDCT = CurieNamespace('SNOMEDCT', 'http://www.snomedbrowser.com/Codes/Details/')
-SNPEFF = CurieNamespace('SNPEFF', 'http://translator.ncats.nih.gov/SNPEFF_')
 SO = CurieNamespace('SO', 'http://purl.obolibrary.org/obo/SO_')
 STATO = CurieNamespace('STATO', 'http://purl.obolibrary.org/obo/STATO_')
 STY = CurieNamespace('STY', 'http://purl.bioontology.org/ontology/STY/')
@@ -240,8 +238,8 @@
 APOLLO = CurieNamespace('apollo', 'https://github.com/GMOD/Apollo')
 BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/')
 BIOSCHEMAS = CurieNamespace('bioschemas', 'https://bioschemas.org/')
-CHEMBIO = CurieNamespace('chembio', 'http://translator.ncats.nih.gov/chembio_')
 DCAT = CurieNamespace('dcat', 'http://www.w3.org/ns/dcat#')
+DCID = CurieNamespace('dcid', 'https://datacommons.org/browser/')
 DCT = CurieNamespace('dct', 'http://purl.org/dc/terms/')
 DCTYPES = CurieNamespace('dctypes', 'http://purl.org/dc/dcmitype/')
 DICTYBASE = CurieNamespace('dictyBase', 'http://dictybase.org/gene/')
@@ -253,13 +251,13 @@
 GFF3 = CurieNamespace('gff3', 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#')
 GPI = CurieNamespace('gpi', 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#')
 GTPO = CurieNamespace('gtpo', 'https://rdf.guidetopharmacology.org/ns/gtpo#')
-HETIO = CurieNamespace('hetio', 'http://translator.ncats.nih.gov/hetio_')
 INTERPRO = CurieNamespace('interpro', 'https://www.ebi.ac.uk/interpro/entry/')
 ISBN = CurieNamespace('isbn', 'https://www.isbn-international.org/identifier/')
 ISNI = CurieNamespace('isni', 'https://isni.org/isni/')
 ISSN = CurieNamespace('issn', 'https://portal.issn.org/resource/ISSN/')
 LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
 MEDGEN = CurieNamespace('medgen', 'https://www.ncbi.nlm.nih.gov/medgen/')
+METACYC_REACTION = CurieNamespace('metacyc_reaction', 'https://identifiers.org/metacyc.reaction:')
 MIRBASE = CurieNamespace('mirbase', 'http://identifiers.org/mirbase')
 OBOINOWL = CurieNamespace('oboInOwl', 'http://www.geneontology.org/formats/oboInOwl#')
 OBOFORMAT = CurieNamespace('oboformat', 'http://www.geneontology.org/formats/oboInOwl#')
@@ -3181,6 +3179,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
 @dataclass
 class PhenotypicFeature(DiseaseOrPhenotypicFeature):
+    """
+    A combination of entity and quality that makes up a phenotyping statement.
+    """
     _inherited_slots: ClassVar[List[str]] = ["in_taxon"]
 
     class_class_uri: ClassVar[URIRef] = BIOLINK.PhenotypicFeature
@@ -8516,6 +8517,9 @@ class slots:
 slots.related_to_at_instance_level = Slot(uri=BIOLINK.related_to_at_instance_level, name="related to at instance level", curie=BIOLINK.curie('related_to_at_instance_level'),
                    model_uri=BIOLINK.related_to_at_instance_level, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]])
 
+slots.associated_with = Slot(uri=BIOLINK.associated_with, name="associated with", curie=BIOLINK.curie('associated_with'),
+                   model_uri=BIOLINK.associated_with, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]])
+
 slots.superclass_of = Slot(uri=BIOLINK.superclass_of, name="superclass of", curie=BIOLINK.curie('superclass_of'),
                    model_uri=BIOLINK.superclass_of, domain=None, range=Optional[Union[Union[dict, "OntologyClass"], List[Union[dict, "OntologyClass"]]]])
 
@@ -8624,6 +8628,24 @@ class slots:
 slots.affected_by = Slot(uri=BIOLINK.affected_by, name="affected by", curie=BIOLINK.curie('affected_by'),
                    model_uri=BIOLINK.affected_by, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]])
 
+slots.associated_with_sensitivity_to = Slot(uri=BIOLINK.associated_with_sensitivity_to, name="associated with sensitivity to", curie=BIOLINK.curie('associated_with_sensitivity_to'),
+                   model_uri=BIOLINK.associated_with_sensitivity_to, domain=NamedThing, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]])
+
+slots.sensitivity_associated_with = Slot(uri=BIOLINK.sensitivity_associated_with, name="sensitivity associated with", curie=BIOLINK.curie('sensitivity_associated_with'),
+                   model_uri=BIOLINK.sensitivity_associated_with, domain=ChemicalEntity, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]])
+
+slots.associated_with_resistance_to = Slot(uri=BIOLINK.associated_with_resistance_to, name="associated with resistance to", curie=BIOLINK.curie('associated_with_resistance_to'),
+                   model_uri=BIOLINK.associated_with_resistance_to, domain=NamedThing, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]])
+
+slots.resistance_associated_with = Slot(uri=BIOLINK.resistance_associated_with, name="resistance associated with", curie=BIOLINK.curie('resistance_associated_with'),
+                   model_uri=BIOLINK.resistance_associated_with, domain=ChemicalEntity, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]])
+
+slots.diagnoses = Slot(uri=BIOLINK.diagnoses, name="diagnoses", curie=BIOLINK.curie('diagnoses'),
+                   model_uri=BIOLINK.diagnoses, domain=None, range=Optional[Union[Union[str, DiseaseOrPhenotypicFeatureId], List[Union[str, DiseaseOrPhenotypicFeatureId]]]])
+
+slots.is_diagnosed_by = Slot(uri=BIOLINK.is_diagnosed_by, name="is diagnosed by", curie=BIOLINK.curie('is_diagnosed_by'),
+                   model_uri=BIOLINK.is_diagnosed_by, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]])
+
 slots.increases_amount_or_activity_of = Slot(uri=BIOLINK.increases_amount_or_activity_of, name="increases amount or activity of", curie=BIOLINK.curie('increases_amount_or_activity_of'),
                    model_uri=BIOLINK.increases_amount_or_activity_of, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]])
 

diff --git a/json-schema/biolink-model.json b/json-schema/biolink-model.json
@@ -11237,7 +11237,7 @@
       },
       "PhenotypicFeature": {
          "additionalProperties": false,
-         "description": "",
+         "description": "A combination of entity and quality that makes up a phenotyping statement.",
          "properties": {
             "category": {
                "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}",
@@ -14863,7 +14863,6 @@
    "$schema": "http://json-schema.org/draft-07/schema#",
    "additionalProperties": true,
    "properties": {},
-   "required": [],
    "title": "Biolink-Model",
    "type": "object"
 }

diff --git a/setup.cfg b/setup.cfg
@@ -1,7 +1,7 @@
 [metadata]
 name = biolink_model
 description = 'A high level datamodel of biological entities and associations'
-version = 2.2.9
+version = 2.2.10
 url = https://github.com/biolink/biolink-model
 author = Harold Solbrig
 author-email = [email protected]

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
     REQUIREMENTS = FH.readlines()
 
 NAME = 'biolink-model'
-VERSION = '2.2.9'
+VERSION = '2.2.10'
 DESCRIPTION = 'Biolink Model: A high level datamodel of biological entities and associations'
 URL = 'https://github.com/biolink/biolink-model'
 AUTHOR = 'Deepak Unni', 'Sierra Moxon'