bioregistry 0.13.15__tar.gz → 0.13.16__tar.gz

{bioregistry-0.13.15 → bioregistry-0.13.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.15
+Version: 0.13.16
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt

{bioregistry-0.13.15 → bioregistry-0.13.16}/pyproject.toml

@@ -10,7 +10,7 @@ markers = [
 
 [project]
 name = "bioregistry"
-version = "0.13.15"
+version = "0.13.16"
 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 = "0.13.15"
+current_version = "0.13.16"
 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-0.13.15 → bioregistry-0.13.16}/src/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-0.13.15 → bioregistry-0.13.16}/src/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-0.13.15 → bioregistry-0.13.16}/src/bioregistry/data/bioregistry.json

@@ -4929,7 +4929,7 @@
           "year": 2019
         }
       ],
-      "repository": "https://github.com/arpcard/aro/blob/master/README.md",
+      "repository": "https://github.com/arpcard/aro",
       "subjects": [
         "Genetics"
       ],
@@ -33220,7 +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"
@@ -48229,7 +48229,7 @@
       "name": "FoodOn",
       "prefix": "FOODON",
       "repository": "https://github.com/FoodOntology/foodon",
-      "version": "2025-08-01"
+      "version": "2025-12-30"
     },
     "biocontext": {
       "prefix": "FOODON"
@@ -78921,6 +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/$1"
+  },
   "mex": {
     "biocontext": {
       "prefix": "MEX"
@@ -99682,6 +99738,49 @@
       "https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25488"
     ]
   },
+  "pahg": {
+    "contact": {
+      "email": "baoym@big.ac.cn",
+      "name": "Yiming Bao",
+      "orcid": "0000-0002-9922-9723"
+    },
+    "contributor": {
+      "email": "ji.kang@northeastern.edu",
+      "github": "kanghosaeyo",
+      "name": "Kangho Ji",
+      "orcid": "0009-0009-3402-8013"
+    },
+    "description": "Identifiers correspond to curated multigene families in the human genome from the Phylogenomic Analysis of Human Genome (PAHG) database, focusing on evolutionary relationships and gene duplication events across vertebrates.",
+    "example": "92",
+    "github_request_issue": 1796,
+    "homepage": "https://www.pahgncb.com",
+    "keywords": [
+      "gene duplication",
+      "human genome",
+      "multigene families",
+      "paralogons",
+      "phylogenomics",
+      "vertebrate evolution"
+    ],
+    "name": "Phylogenomic Analysis of Human Genome",
+    "pattern": "^\\d+$",
+    "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"
@@ -106027,6 +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"
@@ -116393,6 +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": [
@@ -135890,7 +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",
@@ -135900,6 +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",
@@ -148173,7 +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",
@@ -148181,6 +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-0.13.15 → bioregistry-0.13.16}/src/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

{bioregistry-0.13.15 → bioregistry-0.13.16}/src/bioregistry/external/aberowl/processed.json

@@ -2334,7 +2334,7 @@
   },
   "DOID": {
     "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"
@@ -2620,10 +2620,10 @@
   },
   "EDEM-CONNECTONTO": {
     "description": "The EDEM-CONNECTONTO has been created to incorporate domain knowledge about the various types of agitation observed in people with dementia (PwD), as well as the dyadic relationship existing between PwD and their informal caregivers. Furthermore, it offers a structured framework for non-pharmacological interventions, enabling caregivers to effectively manage and mitigate the bidirectional effects of agitation in PwD.",
-    "download_owl": "http://aber-owl.net/media/ontologies/EDEM-CONNECTONTO/1/edem-connectonto.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/EDEM-CONNECTONTO/2/edem-connectonto.owl",
     "name": "eDEM-Connect: Ontology of Dementia-related Agitation and Relationship between Informal Caregivers and Persons with Dementia",
     "prefix": "EDEM-CONNECTONTO",
-    "version": "Version 1.0"
+    "version": "Version_2.0"
   },
   "EDONTOLOGY": {
     "description": "This research work contributes in the field of Information logistics and ontology development in healthcare. An ontology based model that can fix information flow problems in the ward-round process of hospital unit. The ontology based model can be used to provide relevant information to the domain users according to their needs and demands. The ontology based model projects domain users profiling and describes their roles, information demands with competencies: skills, qualifications and experiences. The ontology based model will be implemented in OWL language that can be used in an application to support ward-round activities for achieving effective patient’s treatment process. For ontology development is concerned, different ontology development methodologies have been reviewed from literature review by the author to analyze the existing problems in the ward-round. This thesis incorporates Hybrid Methodology (HM) that helps to develop ontology based model that addresses information flow problems in ward-round. The proposed ontology based model is developed in web Ontology Language (OWL) supported tool protégé 4.0.2 that can be considered as foundation to develop a software product with the help of IT practitioners and developers to fulfill medical practitioner’s demands in ward-round’s context.",
@@ -8179,10 +8179,10 @@
   },
   "PHASES": {
     "description": "PHASES provides an ontology for integrating research in solitude and gerotranscendence. By integrating these areas of study, we aim to deepen our understanding of each and how they promote healthy aging.",
-    "download_owl": "http://aber-owl.net/media/ontologies/PHASES/1/phases.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/PHASES/2/phases.owl",
     "name": "Promoting Health Aging through Semantic Enrichment of Solitude Research",
     "prefix": "PHASES",
-    "version": "2025-05-16"
+    "version": "2025-12-23"
   },
   "PHENX": {
     "description": "Standard measures related to complex diseases, phenotypic traits and environmental exposures",
@@ -8915,7 +8915,7 @@
   "ROADMAP": {
     "description": "ROADMAP provides a controlled terminology for the metadata that describe AI models and datasets. It builds on \"model cards\" and \"datasheets for datasets\" with imaging-specific descriptors. It includes a comprehensive set of metrics to assess the performance of AI models that work with images, text, and/or discrete data.",
     "download_owl": "http://aber-owl.net/media/ontologies/ROADMAP/4/roadmap.owl",
-    "name": "Radiology Ontology of AI Models, Datasets and Projects",
+    "name": "Radiology Ontology of AI Datasets, Models and Projects",
     "prefix": "ROADMAP",
     "version": "2025-11"
   },
@@ -10327,10 +10327,10 @@
   },
   "VFB_DRIVERS": {
     "description": "An ontology of Drosophila melanogaster drivers and expression patterns., An ontology of Drosophila melanogaster drivers and expression patterns. All genetic objects are created using data taken directly from FlyBase.",
-    "download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/197/vfb_drivers.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/198/vfb_drivers.owl",
     "name": "vfb_drivers",
     "prefix": "VFB_DRIVERS",
-    "version": "2025-12-22"
+    "version": "2025-12-29"
   },
   "VHO": {
     "description": "Ontology of terms used for annotating data in Virtual Fly Brain, including anatomical templates.",

{bioregistry-0.13.15 → bioregistry-0.13.16}/src/bioregistry/external/bartoc/processed.json

@@ -17071,7 +17071,7 @@
     "prefix": "20557"
   },
   "20558": {
-    "description": "The National Science and Technology Standard Classification System is a national standard classification framework for information management and distribution, efficient human resource management, and efficient planning and management of R&D projects in the field of science and technology, and is an independent two-dimensional classification system for research and application fields. The research field is a three-tier classification system, consisting of 33 major categories, 369 subcategories, and 2,899 subcategories, and the application field is a one-tier classification system, consisting of 32 major categories.",
+    "description": "The National Science and Technology Standard Classification System is a national standard classification framework for information management and distribution, efficient human resource management, and efficient planning and management of R&D projects in the field of science and technology, and is an independent two-dimensional classification system for research and application fields. The research field is a three-tier classification system, consisting of 22 major categories, 277 subcategories, and 2,799 detailed Area, and the application field is a one-tier classification system, consisting of 22 major categories. \nThe specialized agency for the classification system is the Korea Institute of Science and Technology Evaluation and Planning (KISTEP), which prepares a draft of the National Standard Classification Table for Science and Technology for the establishment of the National Science and Technology Standard Classification System. Based on this draft, the Minister of Science and ICT finalizes and promulgates the National Standard Classification Table for Science and Technology following deliberation by the Presidential Advisory Council on Science and Technology.",
     "homepage": "https://www.kistep.re.kr/board.es?mid=a10305080000&bid=0002&act=view&list_no=43328",
     "name": "National Science and Technology Standard Classification System",
     "prefix": "20558"

{bioregistry-0.13.15 → bioregistry-0.13.16}/src/bioregistry/external/bioportal/agroportal.json

@@ -71,6 +71,7 @@
     },
     "description": "Agroforestry Ontology is a knowledge model that provides a unifying framework for structuring agroforestry data and knowledge. It's an ontology designed to define the different types of agroforestry systems., Ontologie des systèmes agroforestiers, Ontology of agroforestry systems",
     "example_uri": "https://agroportal.lirmm.fr/check_resolvability?url=https://w3id.org/afy/StructuralElement",
+    "homepage": "https://agroforesterie.github.io/",
     "license": "CC-BY-4.0",
     "name": "Agroforestry Ontology",
     "prefix": "AFY",
@@ -225,7 +226,7 @@
       "name": "Filipi Miranda Soares"
     },
     "description": "The Agriculture Product Types Ontology (APTO) is an ontology of types, meaning it does not contain individuals and is intended as a classification system for agricultural commodities price index databases in Brazil. This ontology contains labels and comments in both Portuguese and English. There are two main modules: :Organism and :Product_type. The :Organism class contains subclasses that represent the taxonomy of species related to the production of given product types. It imports taxonomic information from the Global Biodiversity Information Facility (GBIF) Backbone Taxonomy via API. The :Product_type class has six main subclasses organized into major groups: :Inorganic_compound :Animal_product :Plant_product :Raw_product :Processed_product :By-product The :Animal_product and :Plant_product classes include subclasses indicating the type of processing the product has undergone. These subclasses are also children of :Raw_product, :Processed_product, and :By-product. Object Properties APTO defines nine object properties: :has_ingredient and :is_ingredient_of (inverse properties): Indicate that a product type is used in the manufacturing of a processed product type (e.g., :Cow_cheese :has_ingredient :Cow_milk). :derives_from and :derives_in (inverse properties, imported from the Relations Ontology (RO)): Indicate that a product type originates from another product type (e.g., :Cocoa_almond :derives_from :Cocoa). :member_of_taxon (imported from the Biological Collections Ontology (BCO)): Indicates that an organismal entity belongs to a taxon (e.g., :Pacu :member_of_taxon :Piaractus_mesopotamicus). :produced_by and :produces (inverse properties, imported from RO): Indicate that an organismal entity produces a given type of product. For example, :Assai :produced_by :Assai_palm, and :Assai_palm :member_of_taxon :Euterpe_oleracea. If only the final product is listed in commodity databases and the rest of the organism holds no commercial value, the product is linked directly to the taxon (e.g., :Pineapple :produced_by :Ananas_comosus). :residue_of: Indicates that a by-product is the residue of manufacturing another product (e.g., :Whey :residue_of :Cheese). :is_a_hybrid_of: Specific to the :Organism subclasses, indicating a hybrid of two species (e.g., :Citrus_aurantium :is_a_hybrid_of ( :Citrus_reticulata and :Citrus_maxima ))., meaning it does not contain individuals and is intended as a classification system for agricultural commodities price index databases in Brazil. This ontology contains labels and comments in both Portuguese and English. There are two main modules: :Organism and :Product_type. The :Organism class contains subclasses that represent the taxonomy of species related to the production of given product types. It imports taxonomic information from the Global Biodiversity Information Facility (GBIF) Backbone Taxonomy via API. The :Product_type class has six main subclasses organized into major groups: :Inorganic_compound :Animal_product :Plant_product :Raw_product :Processed_product :By-product The :Animal_product and :Plant_product classes include subclasses indicating the type of processing the product has undergone.",
-    "example_uri": "https://w3id.org/APTO#Product_type",
+    "example_uri": "https://w3id.org/APTO#PT0051",
     "homepage": "https://almescore.github.io/APTO/",
     "license": "CC-BY-4.0",
     "name": "Agriculture Product Types Ontology",
@@ -245,9 +246,11 @@
     },
     "description": "The Aquatic Food Ontology (AQFO) is currently being developed to enable easy aggregation and analysis of data generated by the CGIAR Initiative on Aquatic Foods. The ontology covers two domains - aquaculture and small scale fisheries. The development of AQFO is currently led by WorldFish and supported by the Alliance of Bioversity and CIAT.",
     "example_uri": "http://w3id.org/aqfo/aqfo_00002088",
+    "homepage": "https://worldfishcenter.org/aquadata-ontology",
     "license": "CC-BY-4.0",
     "name": "Aquatic Food Ontology",
-    "prefix": "AQFO"
+    "prefix": "AQFO",
+    "repository": "https://github.com/WorldFishCenter/fish-ontology"
   },
   "ASCOPAIN-T": {
     "contact": {
@@ -1623,7 +1626,7 @@
     "name": "FoodOn",
     "prefix": "FOODON",
     "repository": "https://github.com/FoodOntology/foodon",
-    "version": "2025-08-01"
+    "version": "2025-12-30"
   },
   "FOWL": {
     "contact": {
@@ -1946,7 +1949,7 @@
     "license": "CC-BY-4.0",
     "name": "A lexicon of water related textual and geophysicla data - Un lexique de données textuelles et géophysiques sur l'eau",
     "prefix": "LEXEAU",
-    "version": "2.3"
+    "version": "2.4"
   },
   "LHO": {
     "contact": {
@@ -2292,7 +2295,8 @@
     },
     "description": "The Ploutos Common Semantic Model (PCSM) is a small, shared semantic model with common concepts and relations for the different pilots in the Ploutos project focussing on the agrifood supply chain from farmer to consumer (https://ploutosproject.org). The model itself is in the Turtle file ploutos.ttl. Various existing ontologies are being reused, like Saref4Agri, ENVO, GS1. In sip1.ttl through sip9.ttl are example data that showcase how the PCSM is used in the different sustainable innovation pilots (SIPs). Other various files are from other authors and mostly used as imports for the PCSM.",
     "name": "Ploutos Common Semantic Model",
-    "prefix": "PCSM"
+    "prefix": "PCSM",
+    "repository": "https://gitlab.com/Ploutos-project/ploutos-common-semantic-model"
   },
   "PDO_CAS": {
     "contact": {
@@ -2580,6 +2584,7 @@
       "email": "ga.ubbiali@gmail.com",
       "name": "Giorgio A. Ubbiali"
     },
+    "description": "The Sustainability Core Ontology (SCO) is a middle-level ontology, covering the terminology related to the three major theoretical challenges of sustainability: 1) The polysemy of the term sustainability. 2) The relationship between sustainability and sustainable development. 3) The complexity underlying sustainability. SCO is designed to be the pivotal resource upon which to harmonize and integrate ontologies regarding sustainability. The ultimate goal is to establish a family of interoperable sustainability ontologies. Currently, SCO employs Basic Formal Ontology (BFO) and Unified Foundational Ontology (UFO) as the upper-level ontologies. SCO V1.1.0 is the current release and is comprised of two segments: SCO-B (B for BFO) and SCO-U (U for UFO). SCO-B aligns the SCO vocabulary with BFO. SCO-U aligns the SCO vocabulary with gUFO (UFO implementation in the Web Ontology Language (OWL)). SCO V1.1.0. conforms to OBO-Foundry principles. The most recent version of SCO-B segment can always be found at https://w3id.org/sco. The most recent version of SCO-U segment can always be found at https://w3id.org/sco/sco-u. This file provides SCO-B segment. References – TLOs: https://github.com/BFO-ontology/BFO-2020 https://ontouml.readthedocs.io/en/latest/intro/ufo.html https://nemo-ufes.github.io/gufo/",
     "homepage": "https://www.w3id.org/sco/repo",
     "license": "CC-BY-4.0",
     "name": "Sustainability Core Ontology",
@@ -2594,6 +2599,7 @@
       "email": "ga.ubbiali@gmail.com",
       "name": "Giorgio A. Ubbiali"
     },
+    "description": "SCO is a middle-level ontology, representing the major theoretical challenges to sustainability: 1) The polysemy of the term sustainability. 2) The relationship between sustainability and sustainable development. 3) The complexity underlying sustainability. SCO aims to play a pivotal role in harmonizing and integrating top-level and domain ontologies regarding sustainability., SCO V1.1.0 aligns with two Top-Level Ontologies (TLOs), Basic Formal Ontology (BFO) and Unified Foundational Ontology (UFO). SCO V1.1.0 is comprised of two segments: SCO-B (B for BFO) and SCO-U (U for UFO). SCO-B aligns the SCO vocabulary with BFO (as SCO V1.0.0). SCO-U aligns the SCO vocabulary with gUFO (UFO implementation in the Web Ontology Language (OWL)). This file provides SCO-U segment. References – TLOs: https://github.com/BFO-ontology/BFO-2020 https://ontouml.readthedocs.io/en/latest/intro/ufo.html https://nemo-ufes.github.io/gufo/",
     "homepage": "https://www.w3id.org/sco/repo",
     "license": "CC-BY-4.0",
     "name": "Sustainability Core Ontology - Segment U",

{bioregistry-0.13.15 → bioregistry-0.13.16}/src/bioregistry/external/fairsharing/processed.json

@@ -549,11 +549,11 @@
       "name": "Goksel Misirli",
       "orcid": "0000-0002-2454-7188"
     },
-    "description": "Ontology for mapping ontological terms to SBOL Visual glyphs.",
+    "description": "The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited Markdown files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items.",
     "domains": [
       "Knowledge representation"
     ],
-    "homepage": "https://vows.sbolstandard.org",
+    "homepage": "https://sbolstandard.org/sbol-visual-ontology/",
     "license": "CC0-1.0",
     "name": "Synthetic Biology Open Language Visual 2 Ontology",
     "publications": [
@@ -561,6 +561,11 @@
         "doi": "10.1021/acssynbio.0c00046",
         "title": "SBOL Visual 2 Ontology",
         "year": 2020
+      },
+      {
+        "doi": "10.1021/acssynbio.9b00139",
+        "title": "Communicating Structure and Function in Synthetic Biology Diagrams",
+        "year": 2019
       }
     ],
     "repository": "https://github.com/dissys/sbol-visual-ontology",
@@ -3984,7 +3989,7 @@
       "name": "Federica Viti",
       "orcid": "0000-0002-9651-8896"
     },
-    "description": "Ontology for the field of Tissue Engineering, especially bone and cartilage tissues.",
+    "description": "Ontology for the field of Tissue Engineering, especially bone and cartilage tissues. Note that although the BioPortal record and publication remain available, they have not been updated since 2014 and therefore this ontology should be used with care. Please get in touch with us if you have any information.",
     "domains": [
       "bone element"
     ],
@@ -4986,11 +4991,12 @@
   },
   "FAIRsharing.7p0xdg": {
     "abbreviation": "DSEO",
-    "description": "Simple SKOS Taxonomy denoting subfields of study in data science for use in educational applications.",
-    "homepage": "http://bigdatau.org/about_erudite",
+    "description": "The Data Science Education Ontology (DSEO) is a collection of concepts that aims to capture learning needs in data science. It was designed with a data science practicioner’s workflow in mind. The platform collects and organizes online data science training resources and materials and provides an interface for learners to search, explore, recommend, and collect resources they find valuable. Overall, the platform aims to teach data science while leveraging techniques from data science. Specifically, the DSEO is part of the Educational Resource Discovery Index, ERuDIte, and it serves to provide additional descriptors to learning resource metadata.",
+    "homepage": "https://www.pagestudy.org/DSEO/",
+    "license": "CC BY-SA 3.0",
     "name": "Data Science Education Ontology",
+    "repository": "https://github.com/bioint/DSEO",
     "subjects": [
-      "Knowledge and Information Systems",
       "Education Science"
     ]
   },
@@ -8808,12 +8814,19 @@
   },
   "FAIRsharing.bkejsq": {
     "abbreviation": "HUPSON",
-    "description": "Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.",
+    "description": "Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. HuPSON was created as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.",
     "domains": [
       "algorithm"
     ],
     "homepage": "http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html",
     "name": "Human Physiology Simulation Ontology",
+    "publications": [
+      {
+        "doi": "10.1186/2041-1480-4-35",
+        "title": "HuPSON: the human physiology simulation ontology",
+        "year": 2013
+      }
+    ],
     "subjects": [
       "Systems Biology",
       "Medical Informatics"
@@ -10001,7 +10014,7 @@
         "year": 2019
       }
     ],
-    "repository": "https://github.com/arpcard/aro/blob/master/README.md",
+    "repository": "https://github.com/arpcard/aro",
     "subjects": [
       "Genetics"
     ],
@@ -12574,13 +12587,13 @@
   },
   "FAIRsharing.hqyeb7": {
     "abbreviation": "FIRE",
-    "description": "The ontology of Fire was created in order to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies.",
+    "description": "The ontology of Fire was created in order to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies. Please note that the documentation appears incomplete in places and the ontology has not been updated since its first release in 2014. ",
     "domains": [
       "combustion process",
       "climate",
       "ecosystem"
     ],
-    "homepage": "http://bioportal.bioontology.org/ontologies/FIRE",
+    "homepage": "http://cerrado.linkeddata.es/ecology/fire#",
     "name": "Fire Ontology",
     "subjects": [
       "Environmental Science",
@@ -16230,7 +16243,7 @@
   },
   "FAIRsharing.s3r6sk": {
     "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",
@@ -16238,6 +16251,7 @@
       "life cycle stage"
     ],
     "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
+    "license": "CC-BY-3.0",
     "name": "Zebrafish anatomy and development",
     "publications": [
       {
@@ -17119,6 +17133,7 @@
       "strain"
     ],
     "homepage": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457",
+    "license": "CC-BY-4.0",
     "name": "Rat Strain Ontology",
     "publications": [
       {
@@ -17628,7 +17643,7 @@
       "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",
     "publications": [
@@ -17637,6 +17652,11 @@
         "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",

{bioregistry-0.13.15 → bioregistry-0.13.16}/src/bioregistry/external/integbio/__init__.py

@@ -131,18 +131,18 @@ def get_integbio(*, force_download: bool = False) -> dict[str, dict[str, Any]]:
         inplace=True,
     )
     for key in SKIP:
-        del df[key]
+        del df[key]  # type:ignore[operator]
 
     df["fairsharing"] = df["fairsharing"].map(_parse_fairsharing_url, na_action="ignore")
     df = df[df["languages"] != "ja"]  # skip only japanese language database for now
-    del df["languages"]
+    del df["languages"]  # type:ignore[operator]
     # df["languages"] = df["languages"].map(_strip_split, na_action="ignore")
     df["target_keywords"] = df["target_keywords"].map(_strip_split, na_action="ignore")
     df["information_keywords"] = df["information_keywords"].map(_strip_split, na_action="ignore")
     df["pubmeds"] = df["references"].map(_parse_references, na_action="ignore")
     df["description"] = df["description"].map(lambda s: s.replace("\r\n", "\n"), na_action="ignore")
 
-    del df["references"]
+    del df["references"]  # type:ignore[operator]
     # TODO ground database maintenance with ROR?
     rv: dict[str, dict[str, Any]] = {}
     for _, row in df.iterrows():