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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | controlled vocabulary, data or information resource, database, ontology | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/, https://bio.tools/disease_ontology, http://purl.obolibrary.org/obo/doid.obo, | http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | SciCrunch Registry | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-10-17 01:24:42 | 5 | |||
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Gazetteer Resource Report Resource Website 1+ mentions |
Gazetteer (RRID:SCR_000473) | GAZ | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo, owl |
is listed by: BioPortal is listed by: OBO has parent organization: Genomic Standards Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157412 | http://purl.obolibrary.org/obo/gaz.owl, http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/gaz.obo | http://gensc.org/gc_wiki/index.php/GAZ_Project | SCR_000473 | SciCrunch Registry | 2026-10-17 01:24:41 | 1 | ||||||
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Phylogenetic Ontology Resource Report Resource Website |
Phylogenetic Ontology (RRID:SCR_000912) | PHYLONT | controlled vocabulary, data or information resource, ontology | Ontology for Phylogenetic Analysis | owl | is listed by: BioPortal | nlx_157550 | SCR_000912 | SciCrunch Registry | 2026-10-17 01:24:54 | 0 | |||||||||
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Amphibian Taxonomy Ontology Resource Report Resource Website |
Amphibian Taxonomy Ontology (RRID:SCR_000906) | ATO | controlled vocabulary, data or information resource, ontology | A taxonomy of Amphibia | obo | is listed by: BioPortal | nlx_157317 | SCR_000906 | SciCrunch Registry | 2026-10-17 01:24:48 | 0 | |||||||||
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Anatomic Pathology Lexicon Resource Report Resource Website |
Anatomic Pathology Lexicon (RRID:SCR_000907) | PATHLEX | controlled vocabulary, data or information resource, ontology | A comprehensive lexicon - a unified language of anatomic pathology terms - for standardized indexing and retrieval of anatomic pathology information resources. | owl | is listed by: BioPortal | nlx_157318 | SCR_000907 | SciCrunch Registry | 2026-10-17 01:24:54 | 0 | |||||||||
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HIV ontology Resource Report Resource Website |
HIV ontology (RRID:SCR_000908) | HIV | controlled vocabulary, data or information resource, ontology | Ontology that encompasses all knowledge about HIV | obo | is listed by: BioPortal | HIV | nlx_157422 | SCR_000908 | SciCrunch Registry | 2026-10-17 01:24:45 | 0 | ||||||||
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Bleeding History Phenotype Ontology Resource Report Resource Website |
Bleeding History Phenotype Ontology (RRID:SCR_001165) | BHO | controlled vocabulary, data or information resource, ontology | An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders. | owl | is listed by: BioPortal | Hemorrhagic disorder | nlx_157338 | SCR_001165 | SciCrunch Registry | 2026-10-17 01:24:53 | 0 | ||||||||
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Body System Terms from ICD11 Resource Report Resource Website |
Body System Terms from ICD11 (RRID:SCR_001252) | ICD11-BODYSYSTEM | controlled vocabulary, data or information resource, ontology | Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision | owl | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157339 | SCR_001252 | SciCrunch Registry | 2026-10-17 01:24:55 | 0 | ||||||||
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Time Event Ontology Resource Report Resource Website |
Time Event Ontology (RRID:SCR_000310) | TEO | controlled vocabulary, data or information resource, ontology | Ontology for representing events, time, and their relationships. | owl | is listed by: BioPortal | nlx_157610 | SCR_000310 | SciCrunch Registry | 2026-10-17 01:24:37 | 0 | |||||||||
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Variation Ontology Resource Report Resource Website |
Variation Ontology (RRID:SCR_000311) | VARIO | controlled vocabulary, data or information resource, ontology | An ontology for standardized, systematic description of effects, consequences and mechanisms of variations. | obo | is listed by: BioPortal | nlx_157622 | SCR_000311 | SciCrunch Registry | 2026-10-17 01:24:40 | 0 | |||||||||
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Semantic DICOM Ontology Resource Report Resource Website |
Semantic DICOM Ontology (RRID:SCR_000309) | SEDI | controlled vocabulary, data or information resource, ontology | An ontology for DICOM as used in the SeDI project. | owl | is listed by: BioPortal | nlx_157583 | SCR_000309 | SciCrunch Registry | 2026-10-17 01:24:40 | 0 | |||||||||
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Porifera Ontology Resource Report Resource Website 1+ mentions |
Porifera Ontology (RRID:SCR_000134) | PORO | controlled vocabulary, data or information resource, ontology | An ontology covering the anatomy of Porifera (sponges). | owl, anatomy |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is listed by: Ontobee is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157558 | https://code.google.com/p/porifera-ontology/, http://purl.bioontology.org/ontology/PORO, http://purl.obolibrary.org/obo/poro.owl | http://purl.obolibrary.org/obo/poro | SCR_000134 | SciCrunch Registry | 2026-10-17 01:24:34 | 1 | ||||||
|
Xenopus Anatomy Ontology Resource Report Resource Website 1+ mentions |
Xenopus Anatomy Ontology (RRID:SCR_004337) | XAO | controlled vocabulary, data or information resource, ontology | A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis), organized in a graphical structure. Tissues are shown as being part of other tissues and the timing of their development is indicated by start and end stages. The lineage of tissues is represented by develops from relationships between different tissues at different developmental stages. Many items have been classified according to the Common Anatomy Reference Ontology. The Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. They encourage community recommendations for updates and improvements to the ontology. | obo, anatomy, development |
is listed by: BioPortal is listed by: OBO is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: Xenbase |
AHFMR Senior Scholar award ; NICHD R01HD045776-03 |
PMID:18817563 | The community can contribute to this resource | nlx_35222 | https://xenopus-anatomy-ontology.googlecode.com/svn/trunk/current-release/xenopus_anatomy.obo, http://purl.bioontology.org/ontology/XAO, http://obofoundry.org/cgi-bin/detail.cgi?id=xenopus_anatomy | SCR_004337 | SciCrunch Registry | Xenopus anatomy and development ontology | 2026-10-17 01:26:11 | 9 | ||||
|
SysMO JERM Ontology of Systems Biology for Micro-Organisms Resource Report Resource Website |
SysMO JERM Ontology of Systems Biology for Micro-Organisms (RRID:SCR_004569) | JERM | controlled vocabulary, data or information resource, ontology | An ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/ | owl |
is listed by: BioPortal has parent organization: SysMO-DB |
nlx_157602 | SCR_004569 | SciCrunch Registry | 2026-10-17 01:26:13 | 0 | |||||||||
|
PR Resource Report Resource Website |
PR (RRID:SCR_004964) | PR | controlled vocabulary, data or information resource, ontology | An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563). | database, obo, protein |
is listed by: BioPortal has parent organization: Protein Information Resource has parent organization: Georgetown University; Washington D.C.; USA |
NIH ; NIGMS GM080646-01 |
nlx_92849 | SCR_004964 | SciCrunch Registry | PRO, Protein Ontology | 2026-10-17 01:26:10 | 0 | |||||||
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Cereal Plant Development Ontology Resource Report Resource Website |
Cereal Plant Development Ontology (RRID:SCR_005095) | GRO-CPD | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology. | obo |
is listed by: BioPortal is related to: Plant Ontology has parent organization: Gramene |
nlx_157358 | http://www.gramene.org/plant_ontology/ | SCR_005095 | SciCrunch Registry | 2026-10-17 01:26:10 | 0 | ||||||||
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NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | data access protocol, production service resource, service resource, software resource, web service | A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. | ontology, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: STOP has parent organization: BioPortal has parent organization: National Centers for Biomedical Computing has parent organization: Stanford University; Stanford; California |
NHGRI U54 HG004028 | PMID:19483092 | biotools:bioportal, nlx_144389, OMICS_01172 | https://bio.tools/bioportal | SCR_005329 | SciCrunch Registry | Open Biomedical Annotator, NCBO BioPortal Annotator | 2026-10-17 01:26:21 | 6 | |||||
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Computer Assisted Brain Injury Rehabilitation Ontology Resource Report Resource Website |
Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) | CABRO | controlled vocabulary, data or information resource, ontology | A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living. | owl | is listed by: BioPortal | Brain trauma | nlx_157373 | SCR_005288 | SciCrunch Registry | 2026-10-17 01:26:14 | 0 | ||||||||
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Stanford Center for Biomedical Informatics Research Resource Report Resource Website |
Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) | BMIR | data or information resource, laboratory portal, organization portal, portal | Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences. | biomedicine, informatics |
has parent organization: Stanford University; Stanford; California is parent organization of: CLENCH is parent organization of: BioPortal is parent organization of: Center for Expanded Data Annotation and Retrieval is parent organization of: Protege is parent organization of: WebProtege |
nlx_149147 | SCR_005698 | SciCrunch Registry | Stanford Medical Informatics | 2026-10-17 01:26:18 | 0 | ||||||||
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Cell Line Ontology Resource Report Resource Website 1+ mentions |
Cell Line Ontology (RRID:SCR_005840) | CLO | controlled vocabulary, data or information resource, ontology | A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan. | cell line, owl, ontology, standardization, information integration |
is listed by: BioPortal is listed by: OBO is related to: Cell Line Knowledge Base has parent organization: University of Michigan Medical School; Michigan; USA |
The community can contribute to this resource | nlx_149363 | http://bioportal.bioontology.org/ontologies/1245, http://purl.obolibrary.org/obo/clo.owl | SCR_005840 | SciCrunch Registry | 2026-10-17 01:26:28 | 2 |
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