bioregistry 0.13.14__py3-none-any.whl → 0.13.16__py3-none-any.whl

bioregistry/app/impl.py

@@ -68,7 +68,7 @@ BIOREGISTRY_FOOTER_DEFAULT = dedent(f"""\
 
     <p class="small text-center text-muted">
     Developed with ❤️ by the
-    <a href="https://www.iac.rwth-aachen.de">Institute for Inorganic Chemistry</a> at RWTH Aachen University
+    <a href="https://www.iac.rwth-aachen.de">Institute of Inorganic Chemistry</a> at RWTH Aachen University
     </br> and the
     <a href="https://gyorilab.github.io">Gyori Lab for Computational Biomedicine</a>
     at Northeastern University.<br/>

bioregistry/curation/bulk_import.py

@@ -19,7 +19,6 @@ from __future__ import annotations
 
 import sys
 from collections import defaultdict
-from collections.abc import Mapping
 from typing import Any
 
 import click
@@ -32,7 +31,7 @@ from bioregistry.utils import norm
 NESTED = {"contact", "contributor"}
 
 
-def _resource_from_row(row: Mapping[str, Any]) -> Resource:
+def _resource_from_row(row: dict[str, Any]) -> Resource:
     kwargs = {}
     nested: defaultdict[str, dict[str, str]] = defaultdict(dict)
     for key, value in row.items():
@@ -60,7 +59,7 @@ def _resource_from_row(row: Mapping[str, Any]) -> Resource:
 
 def _bulk_import_df(df: pd.DataFrame) -> None:
     for _, row in df.iterrows():
-        resource = _resource_from_row(row.to_dict())
+        resource = _resource_from_row(row.to_dict())  # type:ignore[arg-type]
         try:
             add_resource(resource)
         except KeyError as e:

bioregistry/data/bioregistry.json

@@ -1797,10 +1797,11 @@
   "afo": {
     "aberowl": {
       "description": "<p><strong>Allotrope Merged Ontology Suite</strong></p> <p>The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.</p> <p>license: http://purl.allotrope.org/voc/creative-commons-attribution-license<br/> rights: http://purl.allotrope.org/voc/copyright<br/></p>",
-      "download_owl": "http://aber-owl.net/media/ontologies/AFO/42/afo.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/AFO/43/afo.owl",
+      "homepage": "http://purl.allotrope.org",
       "name": "Allotrope Merged Ontology Suite",
       "prefix": "AFO",
-      "version": "REC/2025/06"
+      "version": "REC/2025/12"
     },
     "bioportal": {
       "contact": {
@@ -4122,7 +4123,7 @@
   "apo": {
     "aberowl": {
       "description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
-      "download_owl": "http://aber-owl.net/media/ontologies/APO/64/apo.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/APO/65/apo.owl",
       "homepage": "http://www.yeastgenome.org/",
       "name": "Ascomycete phenotype ontology",
       "prefix": "APO"
@@ -4228,8 +4229,8 @@
       "name": "Ascomycete Phenotype Ontology (APO)",
       "prefix": "apo",
       "tracker": "https://github.com/obophenotype/ascomycete-phenotype-ontology/issues",
-      "version": "2025-11-10",
-      "version.iri": "http://purl.obolibrary.org/obo/apo/releases/2025-11-10/apo.owl"
+      "version": "2025-12-19",
+      "version.iri": "http://purl.obolibrary.org/obo/apo/releases/2025-12-19/apo.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -4928,7 +4929,7 @@
           "year": 2019
         }
       ],
-      "repository": "https://github.com/arpcard/aro/blob/master/README.md",
+      "repository": "https://github.com/arpcard/aro",
       "subjects": [
         "Genetics"
       ],
@@ -7989,11 +7990,11 @@
   },
   "bervo": {
     "aberowl": {
-      "description": "The Biological and Environmental Research Variable Ontology (BERVO) is a model of the experimental variables, conditions, and concepts used in the study of environmental research, including studies in earth science, plant science, and geochemistry. , None",
-      "download_owl": "http://aber-owl.net/media/ontologies/BERVO/4/bervo.owl",
+      "description": "The Biological and Environmental Research Variable Ontology (BERVO) is a model of the experimental variables, conditions, and concepts used in the study of environmental research, including studies in earth science, plant science, and geochemistry. , None, \"An ontology of variables for earth system simulation, partially derived from the EcoSIM framework.\"",
+      "download_owl": "http://aber-owl.net/media/ontologies/BERVO/5/bervo.owl",
       "name": "The Biological and Environmental Research Variable Ontology",
       "prefix": "BERVO",
-      "version": "2025-11-07"
+      "version": "2025-12-22"
     },
     "bioportal": {
       "contact": {
@@ -19758,7 +19759,7 @@
   "cl": {
     "aberowl": {
       "description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.",
-      "download_owl": "http://aber-owl.net/media/ontologies/CL/117/cl.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/CL/118/cl.owl",
       "homepage": "https://obophenotype.github.io/cell-ontology/",
       "name": "Cell Ontology",
       "prefix": "CL"
@@ -19817,14 +19818,15 @@
         "name": "Alexander Diehl",
         "orcid": "0000-0001-9990-8331"
       },
-      "description": "The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies.",
+      "description": "Cell Ontology (CL) is an ontology designed to classify and describe cell types across different organisms. It serves as a resource for model organism and bioinformatics databases. The ontology covers a broad range of cell types in animal cells, with over 2700 cell type classes, and provides high-level cell type classes as mapping points for cell type classes in ontologies representing other species, such as the Plant Ontology or Drosophila Anatomy Ontology. Integration with other ontologies such as Uberon, GO, CHEBI, PR, and PATO enables linking cell types to anatomical structures, biological processes, and other relevant concepts.\n\nThe Cell Ontology was created in 2004 and has been a core OBO Foundry ontology since the start of the Foundry.",
       "domains": [
         "Annotation",
         "cell",
         "morphology"
       ],
       "homepage": "https://github.com/obophenotype/cell-ontology",
-      "license": "CC-BY-3.0",
+      "license": "CC-BY-4.0",
+      "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbm9IIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--d544c9b28a1342673bbc8f0346aeee1c9220104e/107354015-9375bb00-6ac5-11eb-9394-7318df343ec2.png?disposition=inline",
       "name": "Cell Ontology",
       "prefix": "FAIRsharing.j9y503",
       "publications": [
@@ -33218,7 +33220,7 @@
   "doid": {
     "aberowl": {
       "description": "An ontology for describing the classification of human diseases organized by etiology.",
-      "download_owl": "http://aber-owl.net/media/ontologies/DOID/701/doid.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/DOID/702/doid.owl",
       "homepage": "https://disease-ontology.org",
       "name": "Human Disease Ontology",
       "prefix": "DOID"
@@ -34675,7 +34677,7 @@
   "dron": {
     "aberowl": {
       "description": "An ontology to support comparative effectiveness researchers studying claims data.",
-      "download_owl": "http://aber-owl.net/media/ontologies/DRON/33/dron.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/DRON/34/dron.owl",
       "homepage": "https://github.com/ufbmi/dron",
       "name": "The Drug Ontology",
       "prefix": "DRON"
@@ -34782,8 +34784,8 @@
       "name": "The Drug Ontology",
       "prefix": "dron",
       "tracker": "https://github.com/ufbmi/dron/issues",
-      "version": "2025-11-20",
-      "version.iri": "http://purl.obolibrary.org/obo/dron/releases/2025-11-20/dron.owl"
+      "version": "2025-12-19",
+      "version.iri": "http://purl.obolibrary.org/obo/dron/releases/2025-12-19/dron.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -48227,7 +48229,7 @@
       "name": "FoodOn",
       "prefix": "FOODON",
       "repository": "https://github.com/FoodOntology/foodon",
-      "version": "2025-08-01"
+      "version": "2025-12-30"
     },
     "biocontext": {
       "prefix": "FOODON"
@@ -49347,12 +49349,12 @@
         "name": "Valerie Wood",
         "orcid": "0000-0001-6330-7526"
       },
-      "description": "FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource (www.pombase.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.",
+      "description": "The Fission Yeast Phenotype Ontology (FYPO) is a formal ontology of phenotypes observed in fission yeast. FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource.",
       "domains": [
         "GO-term enrichment data",
         "phenotype"
       ],
-      "homepage": "http://sourceforge.net/apps/trac/pombase/wiki/FissionYeastPhenotypeOntology",
+      "homepage": "https://github.com/pombase/fypo",
       "license": "CC-BY-4.0",
       "name": "Fission Yeast Phenotype Ontology",
       "prefix": "FAIRsharing.4vr0ys",
@@ -78919,6 +78921,62 @@
       "orcid": "0000-0003-4423-4370"
     }
   },
+  "metpo": {
+    "aberowl": {
+      "description": "An ontology of ecophysiological traits of microbes, including tolerated and preferred growth conditions, Microbial ecophysiological trait and phenotype ontology",
+      "download_owl": "http://aber-owl.net/media/ontologies/METPO/18/metpo.owl",
+      "homepage": "https://github.com/berkeleybop/metpo",
+      "name": "METPO",
+      "prefix": "METPO",
+      "version": "2025-12-12"
+    },
+    "contact": {
+      "email": "mam@lbl.gov",
+      "github": "turbomam",
+      "name": "Mark Andrew Miller",
+      "orcid": "0000-0001-9076-6066"
+    },
+    "contributor": {
+      "email": "mam@lbl.gov",
+      "github": "turbomam",
+      "name": "Mark Andrew Miller",
+      "orcid": "0000-0001-9076-6066"
+    },
+    "description": "METPO (Microbial Ecophysiological Trait and Phenotype Ontology) provides standardized terms for describing microbial phenotypes, growth characteristics, and culture conditions. It includes classes for growth media, temperature tolerances, pH tolerances, and relationships like \"grows in\" and \"does not grow in\".",
+    "download_json": "https://w3id.org/metpo/metpo.json",
+    "download_obo": "https://w3id.org/metpo/metpo.obo",
+    "download_owl": "https://w3id.org/metpo/metpo.owl",
+    "example": "1004005",
+    "github_request_issue": 1794,
+    "homepage": "https://github.com/berkeleybop/metpo",
+    "keywords": [
+      "microbes",
+      "ontology",
+      "phenotypes"
+    ],
+    "mappings": {
+      "aberowl": "METPO"
+    },
+    "name": "Microbial Ecophysiological Trait and Phenotype Ontology",
+    "owners": [
+      {
+        "name": "Lawrence Berkeley National Laboratory",
+        "partnered": false,
+        "ror": "02jbv0t02",
+        "wikidata": "Q1133630"
+      }
+    ],
+    "pattern": "^\\d+$",
+    "preferred_prefix": "METPO",
+    "repository": "https://github.com/berkeleybop/metpo",
+    "reviewer": {
+      "email": "cthoyt@gmail.com",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "https://w3id.org/metpo/$1"
+  },
   "mex": {
     "biocontext": {
       "prefix": "MEX"
@@ -82546,7 +82604,7 @@
   "mmo": {
     "aberowl": {
       "description": "A representation of the variety of methods used to make clinical and phenotype measurements.",
-      "download_owl": "http://aber-owl.net/media/ontologies/MMO/118/mmo.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/MMO/119/mmo.owl",
       "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000",
       "name": "Measurement method ontology",
       "prefix": "MMO"
@@ -84503,7 +84561,7 @@
   "mp": {
     "aberowl": {
       "description": "Standard terms for annotating mammalian phenotypic data.",
-      "download_owl": "http://aber-owl.net/media/ontologies/MP/134/mp.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/MP/135/mp.owl",
       "homepage": "https://www.informatics.jax.org/vocab/mp_ontology/",
       "name": "Mammalian Phenotype Ontology",
       "prefix": "MP"
@@ -84670,8 +84728,8 @@
       "name": "The Mammalian Phenotype Ontology",
       "prefix": "mp",
       "tracker": "https://github.com/mgijax/mammalian-phenotype-ontology/issues",
-      "version": "2025-11-19",
-      "version.iri": "http://purl.obolibrary.org/obo/mp/releases/2025-11-19/mp-international.owl"
+      "version": "2025-12-18",
+      "version.iri": "http://purl.obolibrary.org/obo/mp/releases/2025-12-18/mp-international.owl"
     },
     "ontobee": {
       "library": "Library",
@@ -99680,6 +99738,49 @@
       "https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25488"
     ]
   },
+  "pahg": {
+    "contact": {
+      "email": "baoym@big.ac.cn",
+      "name": "Yiming Bao",
+      "orcid": "0000-0002-9922-9723"
+    },
+    "contributor": {
+      "email": "ji.kang@northeastern.edu",
+      "github": "kanghosaeyo",
+      "name": "Kangho Ji",
+      "orcid": "0009-0009-3402-8013"
+    },
+    "description": "Identifiers correspond to curated multigene families in the human genome from the Phylogenomic Analysis of Human Genome (PAHG) database, focusing on evolutionary relationships and gene duplication events across vertebrates.",
+    "example": "92",
+    "github_request_issue": 1796,
+    "homepage": "https://www.pahgncb.com",
+    "keywords": [
+      "gene duplication",
+      "human genome",
+      "multigene families",
+      "paralogons",
+      "phylogenomics",
+      "vertebrate evolution"
+    ],
+    "name": "Phylogenomic Analysis of Human Genome",
+    "pattern": "^\\d+$",
+    "publications": [
+      {
+        "doi": "10.1186/s12863-025-01361-y",
+        "pmc": "PMC12522930",
+        "pubmed": "41087926",
+        "title": "PAHG: the database of human multi-gene families",
+        "year": 2025
+      }
+    ],
+    "reviewer": {
+      "email": "cthoyt@gmail.com",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "https://www.pahgncb.com/genomedb/public/genefamily/$1"
+  },
   "paleodb": {
     "biocontext": {
       "prefix": "PALEODB"
@@ -106025,6 +106126,45 @@
     ],
     "uri_format": "http://localhost/plosthes.2017-1#$1"
   },
+  "pmads": {
+    "contact": {
+      "email": "wanglab.tj@outlook.com",
+      "name": "Haiyun Wang",
+      "orcid": "0000-0001-8364-8328"
+    },
+    "contributor": {
+      "email": "ji.kang@northeastern.edu",
+      "github": "kanghosaeyo",
+      "name": "Kangho Ji",
+      "orcid": "0009-0009-3402-8013"
+    },
+    "description": "Identifiers correspond to curated and proteomics-inferred associations between protein post-translational modifications (PTM) and drug sensitivity.",
+    "example": "acc0079",
+    "github_request_issue": 1799,
+    "homepage": "https://pmads-db.org",
+    "keywords": [
+      "drug sensitivity",
+      "modification",
+      "proteomics"
+    ],
+    "name": "PMADS",
+    "pattern": "^acc\\d{4}$",
+    "publications": [
+      {
+        "doi": "10.1093/nar/gkaf1033",
+        "pubmed": "41099621",
+        "title": "PMADS: an integrated database of curated and proteomics-inferred associations between protein post-translational modifications and drug sensitivity.",
+        "year": 2025
+      }
+    ],
+    "reviewer": {
+      "email": "b.gyori@northeastern.edu",
+      "github": "bgyori",
+      "name": "Benjamin M. Gyori",
+      "orcid": "0000-0001-9439-5346"
+    },
+    "uri_format": "https://pmads-db.org/result/?id=$1"
+  },
   "pmap.cutdb": {
     "biocontext": {
       "prefix": "PMAP.CUTDB"
@@ -110081,7 +110221,7 @@
   "pso": {
     "aberowl": {
       "description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.",
-      "download_owl": "http://aber-owl.net/media/ontologies/PSO/5/pso.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/PSO/6/pso.owl",
       "homepage": "https://github.com/Planteome/plant-stress-ontology",
       "name": "Plant Stress Ontology",
       "prefix": "PSO"
@@ -111242,7 +111382,7 @@
   "pw": {
     "aberowl": {
       "description": "A controlled vocabulary for annotating gene products to pathways.",
-      "download_owl": "http://aber-owl.net/media/ontologies/PW/97/pw.owl",
+      "download_owl": "http://aber-owl.net/media/ontologies/PW/98/pw.owl",
       "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
       "name": "Pathway ontology",
       "prefix": "PW"
@@ -116391,6 +116531,7 @@
         "strain"
       ],
       "homepage": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457",
+      "license": "CC-BY-4.0",
       "name": "Rat Strain Ontology",
       "prefix": "FAIRsharing.vajn3f",
       "publications": [
@@ -134939,7 +135080,8 @@
     "fairsharing": {
       "abbreviation": "TGMA",
       "description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
-      "homepage": "https://www.vectorbase.org/ontology-browser",
+      "homepage": "http://purl.obolibrary.org/obo/tgma.owl",
+      "license": "CC0-1.0",
       "name": "Mosquito gross anatomy",
       "prefix": "FAIRsharing.dqnfkg",
       "publications": [
@@ -135887,7 +136029,7 @@
         "structure",
         "life cycle"
       ],
-      "homepage": "http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab",
+      "homepage": "https://github.com/Planteome/plant-trait-ontology",
       "license": "CC-BY-4.0",
       "name": "Plant Trait Ontology",
       "prefix": "FAIRsharing.w69t6r",
@@ -135897,6 +136039,11 @@
           "pubmed": "29186578",
           "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics",
           "year": 2017
+        },
+        {
+          "doi": "10.1093/nar/gkad1028",
+          "title": "Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology",
+          "year": 2024
         }
       ],
       "repository": "https://github.com/Planteome/plant-trait-ontology",
@@ -148170,7 +148317,7 @@
     "example": "0005926",
     "fairsharing": {
       "abbreviation": "ZFA",
-      "description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish. If you work on the project responsible for \"Zebrafish anatomy and development\" then please consider helping us by claiming this record and updating it appropriately.",
+      "description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish. The anatomical ontology is a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version of the zebrafish anatomical ontology is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science.",
       "domains": [
         "morphology",
         "structure",
@@ -148178,6 +148325,7 @@
         "life cycle stage"
       ],
       "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
+      "license": "CC-BY-3.0",
       "name": "Zebrafish anatomy and development",
       "prefix": "FAIRsharing.s3r6sk",
       "publications": [

bioregistry/data/curated_papers.tsv

@@ -362,3 +362,5 @@ pubmed	relevant	orcid	date_curated	relevancy_type	pr_added	notes
 40811252	1	0009-0009-3402-8013	2025-09-30	new_provider	1710	Publication for abpdb
 40812678	1	0009-0009-3402-8013	2025-09-13	new_prefix	1700	Publication for tsrna
 40842115	1	0009-0009-3402-8013	2025-11-25	new_prefix	1771	Publication for molgluedb
+41087926	1	0009-0009-3402-8013	2025-12-21	new_prefix	1796	Publication for pahg
+41099621	1	0009-0009-3402-8013	2025-12-26	new_prefix	1799	Publication for pmads