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

bioregistry/external/aberowl/processed.json

@@ -157,10 +157,11 @@
   },
   "AFO": {
     "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"
   },
   "AFPO": {
     "description": "AfPO is a tool which enables to annotate the African individuals, and brings together knowledge accumulated about existing populations with their genetic fingerprint in a standardized format.",
@@ -401,7 +402,7 @@
   },
   "APO": {
     "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"
@@ -653,11 +654,11 @@
     "version": "2022-12-23"
   },
   "BERVO": {
-    "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"
   },
   "BFLC": {
     "description": "An experimental extension to BIBFRAME 2.0 primarily for use by the Library of Congress, but with additions also applicable for other users",
@@ -1522,18 +1523,18 @@
   },
   "CL": {
     "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"
   },
   "CL-SIMPLE": {
     "description": "Cell Ontology treated as a simple existential graph of the terms defined in an ontology, An ontology of cell types.",
-    "download_owl": "http://aber-owl.net/media/ontologies/CL-SIMPLE/24/cl-simple.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/CL-SIMPLE/25/cl-simple.owl",
     "homepage": "https://cell-ontology.github.io/",
     "name": "Cell Ontology Simple",
     "prefix": "CL-SIMPLE",
-    "version": "2025-11-25"
+    "version": "2025-12-17"
   },
   "CLAO": {
     "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
@@ -2333,7 +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"
@@ -2391,7 +2392,7 @@
   },
   "DRON": {
     "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"
@@ -2619,10 +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.",
@@ -4294,8 +4295,7 @@
   "HRAVS": {
     "description": "A collection of curated and standardized values used by the HuBMAP (Human BioMolecular Atlas Program) and SenNet (Cellular Senescence Network) metadata records to ensure uniformity in the description of samples and single-cell data produced by the consortium.",
     "name": "HuBMAP Research Attributes Value Set",
-    "prefix": "HRAVS",
-    "version": "2.14.3"
+    "prefix": "HRAVS"
   },
   "HRDO": {
     "description": "This resource was designed during a PhD in medical informatics (funded by INSERM, 2010-2012). Its components are (i) a core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and (ii) an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). </ br> Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr).  Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. This ontology is now available on Bioportal.",
@@ -5332,11 +5332,12 @@
     "prefix": "LEPAO"
   },
   "LHO": {
-    "description": "The Live Stock Health Ontology (LHO) is an extension of the DECIDE ontology. LHO follows OBO Foundry guidelines and contains information related to the health and well-being of livestock animal species such as cattle. Furthermore, it represents the explicit structured and standardized framework for specific domain knowledge and data integration of livestock species. During the development process, knowledge can be retrieved from domain experts, and after the retrieving process, the first prototype is designed for reasoning and planning of data related to cattle. Moreover, LHO contains information regarding farms Identifications, their samples, geolocation, breed, diagnostic tests, Pathogen identifications, and Pathogen results for specific bacteria such as Histophilus somni (HS), Mannheimia haemolytica (MH), Pasteurella multocida (PM), Bovine coronavirus (BCV) bacterial mycoplasma and aerobic culture results for the respiratory track in cattle. This information is represented in the form of concepts of classes, subclasses, and their relationship in the form of object and data properties.",
-    "download_owl": "http://aber-owl.net/media/ontologies/LHO/1/lho.owl",
+    "description": "The Livestock Health Ontology (LHO) extends the DECIDE ontology specifically designed for salmon usecase. LHO contains information on the health and well-being of livestock animal species such as cattle, pigs, and poultry. Furthermore, it represents the explicit structured and standardized framework for specific domain knowledge and data integration of livestock species. During the development process, knowledge can be retrieved from domain experts, and after the retrieving process, the prototype is designed for reasoning and planning of data related to cattle, pigs, and poultry. Moreover, LHO contains information regarding farms Identifications, their samples, geolocation, breed, diagnostic tests, Pathogen identifications, and Pathogen results for specific bacteria such as Histophilus Somni (HS), Mannheimia Haemolytica (MH), Pasteurella Multocida (PM), Bovine Coronavirus (BCV) bacterial mycoplasma and aerobic culture results for the respiratory diseases in cattle. This information is represented as concepts of classes, subclasses, and their relationship in the form of object and data properties. For pigs, it includes FarmType, age, weight, and pathogens like PRRS, SwineInfluenza, and M_Hyponemoniea. In poultry, LHO incorporates FarmType, with specific pathogen names such as Infectious Bronchitis (IB), providing a concise overview of health aspects across livestock species. ), Salmon case study demonstrates the semantic modeling and integration of aquaculture-specific attributes such as hasMortality, hasActualBiomass, hasWaterType, and hasLocalAuthority. The data supports epidemiological analysis of fish health by mapping samples and measurements to environmental and production factors.",
+    "download_owl": "http://aber-owl.net/media/ontologies/LHO/9/lho.owl",
+    "homepage": "https://bioportal.bioontology.org/ontologies/LHO",
     "name": "LivestockHealthOntology",
     "prefix": "LHO",
-    "version": "1.0.0"
+    "version": "V1.4"
   },
   "LICO": {
     "description": "Liver Case Ontology (LiCO) is a case-centric ontology for liver patient cases called lico (Liver Case Ontology) that integrates several ontologies and lexicons developed for sub-disciplines of medicine such as RadLex (Radiology Lexicon), SNOMED CT (Systematized Nomenclature of Medicine, Clinical Terms), LOINC (The Logical Observation Identifier Names and Codes). It is an extension of ONLIRA (Ontology of the Liver for Radiology) that represents the liver and lesions from a radiological perspective.",
@@ -6053,7 +6054,7 @@
   },
   "MMO": {
     "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"
@@ -6176,7 +6177,7 @@
   },
   "MP": {
     "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"
@@ -7265,11 +7266,11 @@
     "version": "Vision Release: 1.0.20"
   },
   "OLAS": {
-    "description": "The Ontology of Laboratory Animal Science (OLAS) is established as a community-based biomedical ontology in the field of laboratory animal science, with the aim to ontologically represent entities and the relations among the entities related to laboratory animal science.",
-    "download_owl": "http://aber-owl.net/media/ontologies/OLAS/2/olas.owl",
+    "description": "The Ontology of Laboratory Animal Science (OLAS) is established as a community-based biomedical ontology in the field of laboratory animal science, with the aim to ontologically represent entities and the relations among the entities related to laboratory animal science., OLAS is a biomedical ontology in the area of laboratory animal science.",
+    "download_owl": "http://aber-owl.net/media/ontologies/OLAS/3/olas.owl",
     "name": "Ontology of Laboratory Animal Science",
     "prefix": "OLAS",
-    "version": "2025-05-08"
+    "version": "2025-12-22"
   },
   "OLATDV": {
     "description": "Life cycle stages for Medaka",
@@ -8178,10 +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",
@@ -8267,12 +8268,12 @@
     "prefix": "PLANP"
   },
   "PLANTSO": {
-    "description": "This ontology describes biotic and abiotic stresses that a plant may encounter.",
-    "download_owl": "http://aber-owl.net/media/ontologies/PLANTSO/3/plantso.owl",
+    "description": "This ontology describes biotic and abiotic stresses that a plant may encounter., An ontology describing biotic and abiotic plant stresses.",
+    "download_owl": "http://aber-owl.net/media/ontologies/PLANTSO/4/plantso.owl",
     "homepage": "https://github.com/Planteome/plant-stress-ontology",
     "name": "Plant Stress Ontology",
     "prefix": "PLANTSO",
-    "version": "2023-11-14"
+    "version": "2025-12-16"
   },
   "PLIO": {
     "description": "The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references.",
@@ -8521,7 +8522,7 @@
   },
   "PSO": {
     "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"
@@ -8578,7 +8579,7 @@
   },
   "PW": {
     "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"
@@ -8914,7 +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"
   },
@@ -10326,10 +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/196/vfb_drivers.owl",
+    "download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/198/vfb_drivers.owl",
     "name": "vfb_drivers",
     "prefix": "VFB_DRIVERS",
-    "version": "2025-12-12"
+    "version": "2025-12-29"
   },
   "VHO": {
     "description": "Ontology of terms used for annotating data in Virtual Fly Brain, including anatomical templates.",

bioregistry/external/bartoc/processed.json

@@ -333,7 +333,7 @@
     "description": "The Hornbostel-Sachs system is a classification system for musical instruments, published in 1914 by Erich Moritz von Hornbostel and Curt Sachs in the Zeitschrift fur Ethnologie under the title Systematik der Musikinstrumente Classification of musical instruments (...) The Hornbostel-Sachs system has a hierarchical structure, each category corresponds to a number, with a number being added in each detail step, so that the number of digits increases with increasing concretization Of the number, while further characters (-,:,], +) allow the notation of special meanings.",
     "homepage": "http://www.oberlin.edu/faculty/rknight/Organology/H-S-1914-German.pdf",
     "license": "CC0-1.0",
-    "name": "Hornbostel-Sachs-systematics",
+    "name": "Hornbostel-Sachs Classification",
     "prefix": "1048",
     "wikidata_database": "Q496327"
   },
@@ -13640,7 +13640,7 @@
     "prefix": "20086"
   },
   "20087": {
-    "description": "- To support the policy, the Ministry of Culture decided to unify the promotion policy of the content industry following the reorganization of the government in 2008.\n- Referring to international standards prepared by the OECD (Content Media Industry Classification) and UNESCO (2009 UNESCO Framework for Cultural Statistics) and reflecting the characteristics of domestic industries\n- Includes music, film and video, animation industry, broadcasting industry, game industry, performance industry, craft and design industry, advertising industry, information service industry, intellectual property management, etc.",
+    "description": "- To support the policy, the Ministry of Culture decided to unify the promotion policy of the content industry following the reorganization of the government in 2008.\n- Referring to international standards prepared by the OECD (Content Media Industry Classification) and UNESCO (2009 UNESCO Framework for Cultural Statistics) and reflecting the characteristics of domestic industries\n- It consists of the publishing, comics, music, film, game, animation, broadcasting, advertising, character, knowledge information, content solutions, and performing arts industries.\n- With the second revision in December 2024, future growth industries such as webtoons and online video services (OTT, etc.) were comprehensively included.",
     "homepage": "https://kssc.mods.go.kr:8443/ksscNew_web/kssc/common/ClassificationContent.do?gubun=1&strCategoryNameCode=006&categoryMenu=007&addGubun=no",
     "license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
     "name": "Contents Industry Classification",
@@ -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"
@@ -21748,7 +21748,7 @@
     "description": "Scope: 62 main groups, with about 9000 items down to the fourth hierarchy level.",
     "homepage": "https://museumsvokabular.de/node/6",
     "license": "CC BY-NC-SA 3.0",
-    "name": "Coarse systematics",
+    "name": "General Classification for Museums",
     "prefix": "452"
   },
   "453": {
@@ -22039,7 +22039,7 @@
     "description": "A typology for museums and collections: 12 basic shapes of vessels as well as a hierarchy of these types of forms, the forms are represented by extensive drawings and photographs, each of which is presented in alphabetical order with numerous concrete object names Phrases and each illustrated by a photo.",
     "homepage": "https://museumsvokabular.de/node/6",
     "license": "CC BY-NC-SA 3.0",
-    "name": "Vessels and forms",
+    "name": "Typology of Vessels",
     "prefix": "491"
   },
   "492": {
@@ -22086,7 +22086,7 @@
     "description": "Scope: 4 main groups with subdivision up to the 5th hierarchical level.",
     "homepage": "https://museumsvokabular.de/node/6",
     "license": "CC BY-NC-SA 3.0",
-    "name": "Thesaurus for farm equipment, field orders - Agricultural transport - Utility tools (woodworking)",
+    "name": "Thesaurus of Agricultural Tools",
     "prefix": "497"
   },
   "498": {

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": {
@@ -2032,7 +2035,7 @@
     "license": "CC-BY-4.0",
     "name": "Multi-scale Multi-step ontology",
     "prefix": "MS2O",
-    "version": "0.2000000000000000111"
+    "version": "0.2"
   },
   "NALT": {
     "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/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",
@@ -3028,12 +3033,12 @@
       "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",
     "publications": [
@@ -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"
     ]
   },
@@ -6928,7 +6934,7 @@
   },
   "FAIRsharing.TrcBD2": {
     "description": "Controlled vocabulary used for indexing bibliographical records dealing with chemistry in the PASCAL database (1972-2015). It is aligned with the terms of the ChEBI (Chemical Entities of Biological Interest), RXNO (name reaction ontology), MOP (molecular process ontology), REX (Physico-chemical process), FIX (Physico-chemical methods and properties), ontologies and the terms of the IUPAC Gold Book. This resource contains 9577 entries in 2 languages (English and French) grouped under 25 collections.",
-    "homepage": "https://loterre.istex.fr/37T/en/",
+    "homepage": "https://doi.org/10.13143/lotr.4642",
     "license": "CC-BY-4.0",
     "name": "Chemistry vocabulary",
     "subjects": [
@@ -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"
     ],
@@ -10413,7 +10426,8 @@
   "FAIRsharing.dqnfkg": {
     "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",
     "publications": [
       {
@@ -10496,12 +10510,13 @@
   },
   "FAIRsharing.dxcjn5": {
     "abbreviation": "GECO",
-    "description": "Agroecology knowledge management is an application ontology for the description and organization of knowledge to design innovative crop systems.",
+    "description": "Agroecology knowledge management is an application ontology for the description and organization of knowledge to design innovative crop systems. The GECO ontology is used to manage the knowledge base, forum and web interface of the GECO platform.",
     "domains": [
       "Cropping systems"
     ],
-    "homepage": "https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/1.4822495904463706E12",
+    "homepage": "https://agroportal.lirmm.fr/ontologies/GECO",
     "license": "CC-BY-4.0",
+    "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbnNIIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--a5a9f26b29575e1ef50fd7a18bcb745ae26735e3/layout_set_logo.png?disposition=inline",
     "name": "Agroecology Knowledge Management",
     "subjects": [
       "Farming Systems Research",
@@ -12572,13 +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",
@@ -12816,14 +12831,15 @@
       "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",
     "publications": [
       {
@@ -16227,7 +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",
@@ -16235,6 +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": [
       {
@@ -17116,6 +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": [
       {
@@ -17625,7 +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": [
@@ -17634,6 +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/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():