bioregistry 0.13.3__tar.gz → 0.13.4__tar.gz

{bioregistry-0.13.3 → bioregistry-0.13.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.3
+Version: 0.13.4
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt

{bioregistry-0.13.3 → bioregistry-0.13.4}/pyproject.toml

@@ -10,7 +10,7 @@ markers = [
 
 [project]
 name = "bioregistry"
-version = "0.13.3"
+version = "0.13.4"
 description = "Integrated registry of biological databases and nomenclatures"
 readme = "README.md"
 authors = [
@@ -254,7 +254,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.13.3"
+current_version = "0.13.4"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{bioregistry-0.13.3 → bioregistry-0.13.4}/src/bioregistry/data/bioregistry.json

@@ -3609,6 +3609,49 @@
     },
     "part_of_database": "aop"
   },
+  "aopo": {
+    "comment": "There's no associated primary publication to my knowledge. The class and property CURIE format strings are somewhat inconsistent, but all conform to http://aopkb.org/aop_ontology#AdverseOutcomePathway, http://aopkb.org/aop_ontology#has_key_event or http://aopkb.org/aop_ontology#hasProcess. It is not indexed in the OLS but supports the AOP-WIKI RDF (see https://doi.org/10.1089/aivt.2021.0010 or https://aopwiki.rdf.bigcat-bioinformatics.org/).",
+    "contact": {
+      "github": "DataSciBurgoon",
+      "name": "Lyle Burgoon",
+      "orcid": "0000-0003-4977-5352"
+    },
+    "contributor": {
+      "email": "javier.millanacosta@maastrichtuniversity.nl",
+      "github": "jmillanacosta",
+      "name": "Javier Millán Acosta",
+      "orcid": "0000-0001-5608-781X"
+    },
+    "description": "The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.",
+    "download_owl": "https://github.com/DataSciBurgoon/aop-ontology/raw/refs/heads/master/aopo.owl",
+    "example": "AdverseOutcomePathway",
+    "github_request_issue": 1744,
+    "homepage": "https://github.com/DataSciBurgoon/aop-ontology",
+    "keywords": [
+      "adverse outcome pathway",
+      "ontology"
+    ],
+    "license": "Apache-2.0",
+    "name": "Adverse Outcome Pathway Ontology",
+    "pattern": "^[A-Za-z_]+$",
+    "publications": [
+      {
+        "doi": "10.1089/aivt.2017.0017",
+        "pmc": "PMC6060416",
+        "pubmed": "30057931",
+        "title": "Creating a Structured Adverse Outcome Pathway Knowledgebase via Ontology-Based Annotations",
+        "year": 2017
+      }
+    ],
+    "repository": "https://github.com/DataSciBurgoon/aop-ontology",
+    "reviewer": {
+      "email": "cthoyt@gmail.com",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "http://aopkb.org/aop_ontology#$1"
+  },
   "apaonto": {
     "aberowl": {
       "description": "APA thesaurus . Flat ontology file",
@@ -83308,6 +83351,13 @@
         "homepage": "https://scholia.toolforge.org/",
         "name": "Scholia",
         "uri_format": "https://scholia.toolforge.org/ncbi-taxon/$1"
+      },
+      {
+        "code": "bioportal.purl",
+        "description": "BioPortal assigns their own PURLs to entities in NCBI taxonomy database.",
+        "homepage": "https://purl.bioontology.org/ontology/NCBITAXON",
+        "name": "BioPortal",
+        "uri_format": "http://purl.bioontology.org/ontology/NCBITAXON/$1"
       }
     ],
     "publications": [
@@ -88854,6 +88904,37 @@
     },
     "pattern": "^\\d+$"
   },
+  "ocdo": {
+    "contact": {
+      "email": "a.azocar.guzman@fz-juelich.de",
+      "github": "aazocar",
+      "name": "Abril Azocar Guzman",
+      "orcid": "0000-0001-7564-7990"
+    },
+    "contributor": {
+      "email": "philip.stroemert@tib.eu",
+      "github": "StroemPhi",
+      "name": "Philip Strömert",
+      "orcid": "0000-0002-1595-3213"
+    },
+    "description": "The Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.",
+    "download_owl": "https://github.com/OCDO/cdco/raw/refs/heads/main/cdco.owl",
+    "example": "hasDefectComplex",
+    "github_request_issue": 1742,
+    "homepage": "https://github.com/OCDO/cdco",
+    "license": "CC-BY-4.0",
+    "logo": "https://raw.githubusercontent.com/OCDO/.github/refs/heads/main/profile/ocdo_logo.png",
+    "name": "Crystallographic Defect Core Ontology",
+    "publications": [],
+    "repository": "https://github.com/OCDO/cdco",
+    "reviewer": {
+      "email": "cthoyt@gmail.com",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "http://purls.helmholtz-metadaten.de/cdos/cdco/$1"
+  },
   "oci": {
     "biocontext": {
       "prefix": "OCI"
@@ -131717,6 +131798,42 @@
     "name": "WGS84 Geo Positioning",
     "uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1"
   },
+  "who.va": {
+    "contributor": {
+      "email": "b.gyori@northeastern.edu",
+      "github": "bgyori",
+      "name": "Benjamin M. Gyori",
+      "orcid": "0000-0001-9439-5346"
+    },
+    "description": "Identifiers assigned by the World Health Organization for coding causes of death from verbal autopsy (VA) reports. These codes are produced as outputs in standard VA analysis software.",
+    "example": "VAs-09.01",
+    "example_extras": [
+      "VAs-09"
+    ],
+    "github_request_issue": 1739,
+    "homepage": "https://www.who.int/publications/m/item/verbal-autopsy-standards-the-2016-who-verbal-autopsy-instrument",
+    "keywords": [
+      "cause of death",
+      "verbal autopsy"
+    ],
+    "name": "World Health Organization Verbal Autopsy Code",
+    "pattern": "^VAs-\\d{2}(?:\\.\\d{2})?$",
+    "publications": [
+      {
+        "doi": "10.1371/journal.pmed.1002486",
+        "pmc": "PMC5761828",
+        "pubmed": "29320495",
+        "title": "The WHO 2016 verbal autopsy instrument: An international standard suitable for automated analysis by InterVA, InSilicoVA, and Tariff 2.0",
+        "year": 2018
+      }
+    ],
+    "reviewer": {
+      "email": "cthoyt@gmail.com",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    }
+  },
   "wicell": {
     "cellosaurus": {
       "category": "Cell line collections (Providers)",

{bioregistry-0.13.3 → bioregistry-0.13.4}/src/bioregistry/parse_iri.py

@@ -38,6 +38,9 @@ def curie_from_iri(
         instead of the canonicalized Bioregistry prefix.
 
     :returns: A CURIE string, if the IRI can be parsed.
+
+    >>> curie_from_iri("http://purl.bioontology.org/ontology/NCBITAXON/131567")
+    'ncbitaxon:131567'
     """
     rv = parse_iri(
         iri, use_preferred=use_preferred, on_failure_return_type=FailureReturnType.single

{bioregistry-0.13.3 → bioregistry-0.13.4}/src/bioregistry/version.py

@@ -11,7 +11,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.13.3"
+VERSION = "0.13.4"
 
 
 def get_git_hash() -> str | None: