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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-11-07 11:53:55 | 1 | ||||||
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BIRNLex Resource Report Resource Website |
BIRNLex (RRID:SCR_007326) | controlled vocabulary, data or information resource, ontology | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Lexicon that provides entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. These sources may include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer''s disease or schizophrenia. The BIRNLex is a specialized vocabulary utilized by BIRN scientists in the context of their research, including common terms for neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance required for large-scale data integration across disparate experimental studies.The BIRNLex offers well defined terms from several domains of importance to neuroimaging across scales. | controlled vocabulary, owl |
is listed by: BioPortal has parent organization: Drexel University College of Medicine; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00199 | http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/ | SCR_007326 | SciCrunch Registry | BIRNLex | 2026-11-07 11:56:12 | 0 | |||||||
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Computational Neuroscience Ontology Resource Report Resource Website |
Computational Neuroscience Ontology (RRID:SCR_007289) | CNO | controlled vocabulary, data or information resource, ontology | A controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations. | owl | is listed by: BioPortal | Creative Commons Attribution License, v3 Unported | nlx_157372 | SCR_007289 | SciCrunch Registry | 2026-11-07 11:56:11 | 0 | ||||||||
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Computer-Based Patient Record Ontology Resource Report Resource Website |
Computer-Based Patient Record Ontology (RRID:SCR_007540) | CPRO | controlled vocabulary, data or information resource, ontology | A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR) | owl | is listed by: BioPortal | nlx_157375 | https://code.google.com/p/cpr-ontology/ | SCR_007540 | SciCrunch Registry | 2026-11-07 11:56:17 | 0 | ||||||||
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Solanaceae Phenotype Ontology Resource Report Resource Website |
Solanaceae Phenotype Ontology (RRID:SCR_007832) | SPTO | controlled vocabulary, data or information resource, ontology | Ontology for Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance. | obo | is listed by: BioPortal | nlx_157592 | SCR_007832 | SciCrunch Registry | 2026-11-07 11:56:26 | 0 | |||||||||
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Soy Ontology Resource Report Resource Website |
Soy Ontology (RRID:SCR_007847) | SOY | controlled vocabulary, data or information resource, ontology | Growth, trait and development ontology for soybean | obo |
is listed by: BioPortal has parent organization: SoyBase |
nlx_157593 | SCR_007847 | SciCrunch Registry | 2026-11-07 11:56:26 | 0 | |||||||||
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Healthcare Common Procedure Coding System Resource Report Resource Website |
Healthcare Common Procedure Coding System (RRID:SCR_007598) | HCPCS | controlled vocabulary, data or information resource, ontology | Ontology for the healthcare common procedure coding system. | umls | is listed by: BioPortal | nlx_157426 | SCR_007598 | SciCrunch Registry | 2026-11-07 11:56:20 | 0 | |||||||||
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Drug Interaction Knowledge Base Ontology Resource Report Resource Website |
Drug Interaction Knowledge Base Ontology (RRID:SCR_007591) | DIKB | controlled vocabulary, data or information resource, ontology | An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence. | owl | is listed by: BioPortal | PMID:19435613 | nlx_157392 | SCR_007591 | SciCrunch Registry | 2026-11-07 11:56:17 | 0 | ||||||||
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Congenital Heart Defects Ontology Resource Report Resource Website 50+ mentions |
Congenital Heart Defects Ontology (RRID:SCR_007584) | CHD | controlled vocabulary, data or information resource, ontology | An ontology that describes the Congenital Heart Defects data. | owl | is listed by: BioPortal | Congenital Heart Defect | nlx_157376 | SCR_007584 | SciCrunch Registry | 2026-11-07 11:56:26 | 61 | ||||||||
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Surgical Secondary Events Resource Report Resource Website |
Surgical Secondary Events (RRID:SCR_007894) | SSE | controlled vocabulary, data or information resource, ontology | Memorial Sloan-Kettering Cancer Center''s ontology of surgical secondary events (adverse events). | owl | is listed by: BioPortal | SCR_007894 | SciCrunch Registry | 2026-11-07 11:56:26 | 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 | 2026-11-07 11:55:34 | 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 | 2026-11-07 11:55:55 | 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 | 2026-11-07 11:56:03 | 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 | 2026-11-07 11:55:44 | 2 | |||||||
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Read Codes Clinical Terms Version 3 Resource Report Resource Website 1+ mentions |
Read Codes Clinical Terms Version 3 (RRID:SCR_006055) | RCD | controlled vocabulary, data or information resource, ontology | Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre | umls | is listed by: BioPortal | nlx_157570 | SCR_006055 | SciCrunch Registry | Read Codes CTV3, Read Codes Clinical Terms Version 3 (CTV3) | 2026-11-07 11:55:45 | 1 | ||||||||
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Randomized Controlled Trials Ontology Resource Report Resource Website |
Randomized Controlled Trials Ontology (RRID:SCR_005992) | RCTONT | controlled vocabulary, data or information resource, ontology | Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis. | owl | is listed by: BioPortal | nlx_157568 | SCR_005992 | SciCrunch Registry | 2026-11-07 11:56:03 | 0 | |||||||||
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Regulation of Transcription Ontology Resource Report Resource Website |
Regulation of Transcription Ontology (RRID:SCR_006238) | RETO | controlled vocabulary, data or information resource, ontology | An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations. | obo | is listed by: BioPortal | nlx_157573 | SCR_006238 | SciCrunch Registry | 2026-11-07 11:56:11 | 0 | |||||||||
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Ontology for Biomedical Investigations Resource Report Resource Website 10+ mentions |
Ontology for Biomedical Investigations (RRID:SCR_006266) | OBI | controlled vocabulary, data or information resource, ontology | An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project. | life-science, clinical, investigation, biomedical, protocol, instrumentation, experiment, biology, owl, molecular, cellular, organismal, multi-organismal |
is used by: Information Artifact Ontology is used by: Beta Cell Genomics Ontology is listed by: FORCE11 is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology is related to: Chemical Methods Ontology is related to: Genomic Standards Consortium |
PMID:20626927 | Creative Commons Attribution License v3 | nif-0000-06698 | http://purl.obofoundry.org/obo/obi.owl, http://purl.obofoundry.org/obo/obi, https://www.force11.org/node/4700 | SCR_006266 | SciCrunch Registry | OBI Ontology | 2026-11-07 11:55:51 | 21 | |||||
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OMIM Resource Report Resource Website 5000+ mentions |
OMIM (RRID:SCR_006437) | OMIM, MIM | catalog, data or information resource, database | Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources. | gene, genetics, phenotype, genotype, genetic loci, mutation, clinical, trait, disorder, umls, ontology, gold standard, FASEB list |
is used by: Human Phenotype Ontology is used by: NIF Data Federation is used by: MitoMiner is used by: Schizo-Pi is used by: GEMINI is used by: MARRVEL is used by: HmtPhenome is listed by: BioPortal is listed by: OMICtools is related to: HomoloGene is related to: TopoSNP is related to: phenomeNET is related to: Integrated Gene-Disease Interaction is related to: OMIA - Online Mendelian Inheritance in Animals is related to: Europhenome Mouse Phenotyping Resource is related to: Homophila is related to: Biomine is related to: MalaCards is related to: PhenoTips is related to: KOBAS is related to: Integrated Manually Extracted Annotation is related to: aGEM is related to: biomaRt has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA has parent organization: NCBI works with: Human Mouse Disease Connection works with: Database of genes related to Repeat Expansion Diseases |
Genetic disorder, Mendelian disorder, Developmental disorder | PMID:22477700 PMID:22470145 PMID:21472891 PMID:19728286 PMID:18842627 PMID:18428346 PMID:17642958 PMID:17357067 PMID:15608251 PMID:15360913 PMID:11752252 PMID:10845565 PMID:10612823 PMID:9805561 PMID:7937048 PMID:1867277 |
Restricted | nif-0000-03216, r3d100010416, OMICS_00278 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim, http://www.ncbi.nlm.nih.gov/Omim/, http://purl.bioontology.org/ontology/OMIM, https://doi.org/10.17616/R3188W | SCR_006437 | SciCrunch Registry | Online Mendelian Inheritance in Man, OMIM - Online Mendelian Inheritance in Man, MIM, The Online Mendelian Inheritance in Man Morbid Map | 2026-11-07 11:56:13 | 7365 | ||||
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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 | 2026-11-07 11:55:19 | 9 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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