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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | Xenopus anatomy and development ontology | 2026-09-12 12:56:11 | 9 | ||||
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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 | 2026-09-12 12:56:14 | 0 | |||||||||
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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 | PRO, Protein Ontology | 2026-09-12 12:56:19 | 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 | 2026-09-12 12:56:21 | 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 | Open Biomedical Annotator, NCBO BioPortal Annotator | 2026-09-12 12:56:24 | 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 | 2026-09-12 12:56:24 | 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 | Stanford Medical Informatics | 2026-09-12 12:56:30 | 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 | 2026-09-12 12:56:32 | 2 | |||||||
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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 | 2026-09-12 12:55:06 | 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 | 2026-09-12 12:55:07 | 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 | 2026-09-12 12:55:06 | 0 | |||||||||
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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 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-09-12 12:55:10 | 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 | 2026-09-12 12:55:10 | 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 | 2026-09-12 12:55:16 | 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 | 2026-09-12 12:55:16 | 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 | 2026-09-12 12:55:16 | 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 | 2026-09-12 12:55:16 | 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 | 2026-09-12 12:55:20 | 0 | ||||||||
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Gene Ontology Resource Report Resource Website 10000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | consortium, data or information resource, knowledge environment resource, organization portal, portal, project portal | Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases. | gene, product, annotation, molecular, function, cellular, biological, role, database, query, obo, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: GreenPhylDB is used by: LIPID MAPS Proteome Database is used by: Aging Portal is used by: ChannelPedia is used by: Open PHACTS is used by: CoPub is used by: PhenoGO is used by: Database for Annotation Visualization and Integrated Discovery is used by: MitoMiner is used by: dcGO is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: barleyGO is used by: SynGO is used by: Functional Annotation is used by: SwissLipids is listed by: BioPortal is listed by: OBO is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: Mouse Genome Informatics: The Gene Ontology Project is related to: GenNav is related to: SynaptomeDB is related to: High-Throughput GoMiner is related to: Onto-Design is related to: OnEx - Ontology Evolution Explorer is related to: Avadis is related to: GONUTS is related to: PiNGO is related to: Automated Microarray Pipeline is related to: categoryCompare is related to: globaltest is related to: Semantic Measures Library is related to: WegoLoc is related to: AnimalTFDB is related to: MEME Suite - Motif-based sequence analysis tools is related to: Arabidopsis Hormone Database is related to: DAVID is related to: Arabidopsis thaliana Protein Interactome Database is related to: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is related to: pSTIING is related to: GoMiner is related to: FunSimMat is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Centre for Modeling Human Disease Gene Trap Resource is related to: Patterns of Gene Expression in Drosophila Embryogenesis is related to: Babelomics is related to: BioPerl is related to: GeneCruiser is related to: GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool is related to: GOToolBox Functional Investigation of Gene Datasets is related to: Cotton EST Database is related to: MouseNET is related to: PLANTTFDB is related to: T-profiler is related to: Physico-Chemical Process is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: GOCat is related to: Quantitative Enrichment of Sequence Tags is related to: Neural-Immune Gene Ontology is related to: INMEX is related to: StRAnGER is related to: QuickGO is related to: Repository of molecular brain neoplasia data is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PANTHER is related to: Short Time-series Expression Miner (STEM) is related to: DATFAP is related to: GORetriever is related to: Gene Ontology Browsing Utility (GOBU) is related to: GeneTools is related to: GOSlimViewer is related to: go-moose is related to: Network Ontology Analysis is related to: Onto-Compare is related to: Onto-Express is related to: OntoVisT is related to: STRAP is related to: CGAP GO Browser is related to: COBrA is related to: Gene Class Expression is related to: GeneInfoViz is related to: GOfetcher is related to: GoFish is related to: GOProfiler is related to: GOanna is related to: Manatee is related to: Pandora - Protein ANnotation Diagram ORiented Analysis is related to: TAIR Keyword Browser is related to: Wandora is related to: GOTaxExplorer is related to: Onto-Miner is related to: Onto-Translate is related to: ToppGene Suite is related to: DBD - Slim Gene Ontology is related to: ONTO-PERL is related to: Blip: Biomedical Logic Programming is related to: OWL API is related to: CLENCH is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: CateGOrizer is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products is related to: ProteInOn is related to: GeneMerge is related to: GraphWeb is related to: ClueGO is related to: CLASSIFI - Cluster Assignment for Biological Inference is related to: GOHyperGAll is related to: FuncAssociate: The Gene Set Functionator is related to: GOdist is related to: FuncExpression is related to: FunCluster is related to: FIVA - Functional Information Viewer and Analyzer is related to: GARBAN is related to: GOEx - Gene Ontology Explorer is related to: SGD Gene Ontology Slim Mapper is related to: GOArray is related to: SNPsandGO is related to: GoSurfer is related to: GOtcha is related to: MAPPFinder is related to: GoAnnotator is related to: MetaGeneProfiler is related to: OntoGate is related to: ProfCom - Profiling of complex functionality is related to: SerbGO is related to: SOURCE is related to: Ontologizer is related to: THEA - Tools for High-throughput Experiments Analysis is related to: Generic GO Term Mapper is related to: GREAT: Genomic Regions Enrichment of Annotations Tool is related to: GoBean - a Java application for Gene Ontology enrichment analysis is related to: TXTGate is related to: GO-Module is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools is related to: MalaCards is related to: FSST - Functional Similarity Search Tool is related to: Expression Profiler is related to: GOChase is related to: GoPubMed is related to: Whatizit is related to: REViGO is related to: WEGO - Web Gene Ontology Annotation Plot is related to: Blast2GO is related to: InterProScan is related to: PubSearch is related to: TrED is related to: CharProtDB: Characterized Protein Database is related to: VirHostNet: Virus-Host Network is related to: Pathbase is related to: GO Online SQL Environment (GOOSE) is related to: Neurobehavior Ontology is related to: InterSpecies Analysing Application using Containers is related to: KOBAS is related to: ConceptWiki is related to: GeneTerm Linker is related to: Bioconductor is related to: ErmineJ is related to: Gene Ontology For Functional Analysis (GOFFA) is related to: MGI GO Browser is related to: Comparative Toxicogenomics Database (CTD) is related to: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is related to: Ontology Lookup Service is related to: LexGrid is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: g:Profiler is related to: OwlSim is related to: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool is related to: YeTFaSCo is related to: FastSemSim is related to: RamiGO is related to: AutismKB is related to: GeneCodis is related to: FunSpec is related to: FunNet - Transcriptional Networks Analysis is related to: PhenoM - Phenomics of yeast Mutants is related to: agriGO is related to: GOblet is related to: DynGO is related to: SeqExpress is related to: ProbeExplorer is related to: ECgene: Gene Modeling with Alternative Splicing is related to: Organelle DB is related to: Gemma is related to: Candidate Genes to Inherited Diseases is related to: Proteome Analyst PA-GOSUB is related to: Network Analysis, Visualization and Graphing TORonto is related to: GOstat is related to: Onto-Express To Go (OE2GO) is related to: Tk-GO is related to: EGAN: Exploratory Gene Association Networks is related to: Spotfire is related to: GOMO - Gene Ontology for Motifs is related to: GFINDer: Genome Function INtegrated Discoverer is related to: Generic GO Term Finder is related to: Agile Protein Interactomes DataServer is related to: AgingDB is related to: UBERON is related to: Algal Functional Annotation Tool is related to: gsGator is related to: Flash Gviewer is related to: Cerebellar Development Transcriptome Database is related to: PlantNATsDB - Plant Natural Antisense Transcripts DataBase is related to: EASE: the Expression Analysis Systematic Explorer is related to: PiGenome is related to: L2L Microarray Analysis Tool is related to: MeGO is related to: CELDA Ontology is related to: Diabetes Disease Portal is related to: MatrixDB is related to: Kidney and Urinary Pathway Knowledge Base is related to: MouseCyc is related to: Candida Genome Database is related to: Honey Bee Brain EST Project is related to: ECO is related to: FlyMine is related to: Gramene is related to: 3D-Interologs is related to: Biomine is related to: UniProtKB is related to: NCBI BioSystems Database is related to: EBIMed is related to: Coremine Medical is related to: EMAGE Gene Expression Database is related to: GeneMANIA is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: GeneTrail is related to: Magic is related to: Mouse Genome Informatics (MGI) is related to: FlyBase is related to: InterPro is related to: InnateDB is related to: canSAR is related to: HPRD - Human Protein Reference Database is related to: CRCView is related to: Integrated Manually Extracted Annotation is related to: LegumeIP is related to: Renal Disease Portal is related to: PhenoGO is related to: DOAF is related to: OBO is related to: biomaRt is related to: OncoboxPD is parent organization of: AmiGO is parent organization of: GOlr is parent organization of: RefGenome is parent organization of: OBO-Edit is parent organization of: OWLTools is parent organization of: Gene Ontology Tools is parent organization of: Gene Ontology Extension is parent organization of: SO is parent organization of: go-db-perl is parent organization of: go-perl works with: topGO works with: DIANA-mirPath works with: GOnet is organization facet of: Alliance of Genome Resources |
European Union QLRI-CT-2001-00015; European Union QLRI-CT-2001-0098; NHGRI P41 HG002273 |
PMID:23161678 PMID:10802651 |
Free, Freely available, Available for download | biotools:go, OMICS_02278, nif-0000-02915 | http://bioportal.bioontology.org/ontologies/GO, https://bio.tools/go | SCR_002811 | the Gene Ontology, GO, Gene Ontology Resource, Gene Ontology | 2026-09-12 12:55:46 | 12993 | ||||
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Ascomycete Phenotype Ontology Resource Report Resource Website |
Ascomycete Phenotype Ontology (RRID:SCR_003254) | APO | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary for the phenotypes of Ascomycete fungi. | obo, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: SGD |
Free, Freely available | nlx_157321 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo | SCR_003254 | 2026-09-12 12:55:54 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
