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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ontology of Medically Related Social Entities Resource Report Resource Website |
Ontology of Medically Related Social Entities (RRID:SCR_003439) | OMRSE | controlled vocabulary, data or information resource, ontology | An ontology covering the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital, etc.) | owl, medicine, health care, demographic |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157534 | http://purl.bioontology.org/ontology/OMRSE, http://purl.obolibrary.org/obo/omrse.owl | SCR_003439 | 2026-09-05 06:25:03 | 0 | |||||||
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Medical Dictionary for Regulatory Activities Resource Report Resource Website 1+ mentions |
Medical Dictionary for Regulatory Activities (RRID:SCR_003751) | MEDDRA | controlled vocabulary, data or information resource, ontology | Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA) | umls | is listed by: BioPortal | nlx_157471 | SCR_003751 | 2026-09-05 06:25:07 | 4 | |||||||||
|
Experimental Factor Ontology Resource Report Resource Website 10+ mentions |
Experimental Factor Ontology (RRID:SCR_003574) | EFO | controlled vocabulary, data or information resource, ontology | An application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome. | gene expression, owl, experimental factor, disease, cell line, cell type, anatomy, gold standard |
is listed by: BioPortal is related to: ArrayExpress is related to: ArrayExpress is related to: Gene Expression Atlas has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory ; European Union FELICS contract 021902; European Union EMERALD LSHG-CT-2006-037686; European Union Gen2Phen contract 200754 |
PMID:20200009 | The community can contribute to this resource | nlx_11363 | SCR_003574 | 2026-09-05 06:25:05 | 19 | ||||||
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Medical Diagnostic Categories - Diagnosis Related Groups Resource Report Resource Website |
Medical Diagnostic Categories - Diagnosis Related Groups (RRID:SCR_003725) | MDCDRG | controlled vocabulary, data or information resource, ontology | Ontology of Medical Diagnostic Categories-Diagnosis Related Groups | owl | is listed by: BioPortal | nlx_157470 | SCR_003725 | 2026-09-05 06:25:07 | 0 | |||||||||
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Mosquito Insecticide Resistance Ontology Resource Report Resource Website |
Mosquito Insecticide Resistance Ontology (RRID:SCR_003864) | MIRO | controlled vocabulary, data or information resource, ontology | Application ontology for entities related to insecticide resistance in mosquitos | obo | is listed by: BioPortal | nlx_157486 | SCR_003864 | 2026-09-05 06:25:10 | 0 | |||||||||
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Mouse Gross Anatomy and Development Ontology Resource Report Resource Website |
Mouse Gross Anatomy and Development Ontology (RRID:SCR_003891) | EMAP | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). | obo | is listed by: BioPortal | nlx_157488 | SCR_003891 | 2026-09-05 06:25:10 | 0 | |||||||||
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Minimal Standard Terminology of Digestive Endoscopy - French Resource Report Resource Website |
Minimal Standard Terminology of Digestive Endoscopy - French (RRID:SCR_003830) | MSTDE-FRE | controlled vocabulary, data or information resource, ontology | Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001 | umls | is listed by: BioPortal | nlx_157484 | SCR_003830 | Minimal Standard Terminology of Digestive Endoscopy French | 2026-09-05 06:25:09 | 0 | ||||||||
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Systematized Nomenclature of Medicine - Clinical Terms Resource Report Resource Website 1+ mentions |
Systematized Nomenclature of Medicine - Clinical Terms (RRID:SCR_003915) | SNOMEDCT | controlled vocabulary, data or information resource, ontology | Ontology of SNOMED (Systematized Nomenclature of Medicine) clinical terms. | umls | is listed by: BioPortal | nlx_157603 | SCR_003915 | 2026-09-05 06:25:11 | 2 | |||||||||
|
Mouse Pathology Ontology Resource Report Resource Website |
Mouse Pathology Ontology (RRID:SCR_003950) | MPATH | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes | obo |
is listed by: BioPortal has parent organization: Pathbase |
nlx_157489 | SCR_003950 | 2026-09-05 06:25:11 | 0 | |||||||||
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NHS Quality Indicators Resource Report Resource Website 1+ mentions |
NHS Quality Indicators (RRID:SCR_004005) | NHSQI2009 | controlled vocabulary, data or information resource, ontology | Ontology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable. | protege | is listed by: BioPortal | nlx_157491 | SCR_004005 | 2026-09-05 06:25:12 | 1 | |||||||||
|
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 | 2026-09-05 06:25:27 | 0 | |||||||
|
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 | 2026-09-05 06:25:29 | 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 | 2026-09-05 06:25:33 | 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 | 2026-09-05 06:25:33 | 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 | 2026-09-05 06:24:14 | 1 | ||||||
|
Biositemaps Resource Report Resource Website 1+ mentions |
Biositemaps (RRID:SCR_001976) | Biositemaps | service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites. | broadcast, data federation, defined rdf schema, infrastructure, meta-data, rdf, retrieve, biomedical, biositemap, sitemap |
lists: Adaptively Sampled Particle Fluids lists: DicomWorks lists: MEDx lists: Medical Image Processing and Visualization lists: Surface-Based Atlases lists: RESNET lists: SurfRelax lists: FEATURE lists: Cardiovascular Model Repository lists: Simtk.org lists: ConTrack lists: Allopathfinder lists: Molecular Simulation Trajectories Archive of a Villin Variant lists: BioPortal lists: SumsDB lists: NeuronDB lists: BrainInfo lists: Protege lists: i2b2 Cross-Institutional Clinical Translational Research project lists: GeneChip Operating Software lists: Honig Lab lists: Proteomics Identifications (PRIDE) lists: ASAP: the Alternative Splicing Annotation Project lists: MiMI Plugin for Cytoscape lists: Substructure Index-based Approximate Graph Alignment lists: Proteome Commons Tranche repository lists: caTIES - Cancer Text Information Extraction System lists: REDCap lists: miniTUBA lists: Einstein-Montefiore ICTR Research Informatics Core lists: T-profiler lists: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse lists: GCG/SeqWeb lists: Solstice lists: California National Primate Research Center lists: BioGPS: The Gene Portal Hub lists: Blox lists: Subcellular Location Image Finder lists: PeptideAtlas lists: Clair library lists: Lyngby lists: SimTKCore lists: Velos lists: Ingenuity Pathway Analysis lists: Philips lists: Talktech lists: SUN Interface Engine lists: Quadramed - Medicus, Quantim lists: Wisconsin National Primate Research Center lists: i2b2 Research Data Warehouse lists: Merge Healthcare Incorporated lists: Clinical Trial Management Application lists: Cerner Millenium lists: Open Clinical Report Repository lists: Quovadx, Inc. lists: VectorValuedHistogramNormalizer lists: Morphometry BIRN lists: Talairach Daemon lists: LONI Visualization Tool lists: LONI Debabeler lists: LONI Pipeline Processing Environment lists: Brede Wiki lists: medInria lists: FreeSurfer lists: ITK-SNAP lists: VoxBo lists: Ensembl lists: MRIcron lists: Synchronized Histological Image Viewing Architecture lists: LONI ShapeViewer lists: LONI ShapeTools lists: FFT Library lists: NUTMEG lists: bioDBcore lists: Mutant Mouse Resource and Research Center lists: Brainscape lists: MindSeer lists: University of Southern California LONI Software lists: Statistics Online Computational Resource lists: NIH MRI Study of Normal Brain Development lists: Ontology Development and Information Extraction lists: Mindtouch DekiWiki lists: National Mesothelioma Virtual Bank lists: MGH-USC Human Connectome Project lists: Fusion ICA Toolbox lists: Biomedical Resource Ontology lists: Biomedical Informatics Research Network lists: 3D Slicer lists: Analysis of Functional NeuroImages lists: Automated Image Registration lists: TOADS-CRUISE Brain Segmentation Tools lists: BrainImage Software lists: Brede Toolbox lists: Whole Brain Catalog lists: Low Resolution Electromagnetic Tomography lists: Cambridge Brain Activation lists: ModelDB lists: fMRI Data Center lists: EEGLAB lists: 3DViewnix lists: MIPAV: Medical Image Processing and Visualization lists: NeuroLens lists: WFU PickAtlas lists: Protein Subcellular Location Image Database lists: STRIDE Virtual Biospecimen Bank lists: BrainVoyager is related to: Biomedical Resource Ontology is related to: Software Distribution Sets is related to: REX is related to: Rat Genome Database (RGD) has parent organization: National Centers for Biomedical Computing has parent organization: National Institutes of Health is parent organization of: Resource Discovery System |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10583 | SCR_001976 | 2026-09-05 06:32:25 | 1 | ||||||||
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RightField Resource Report Resource Website 1+ mentions |
RightField (RRID:SCR_002649) | RightField | software application, software resource | An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies. | annotation, semantic, ontology, term selection, excel, java, bio.tools |
is listed by: BioPortal is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: SEEK is related to: Workflow4Ever has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:21622664 | Free, Available for download, Freely available | biotools:rightfield, nlx_156077 | https://bio.tools/rightfield | SCR_002649 | 2026-09-05 06:32:28 | 3 | ||||||
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Animal Natural History and Life History Ontology Resource Report Resource Website 1+ mentions |
Animal Natural History and Life History Ontology (RRID:SCR_010292) | ADW | controlled vocabulary, data or information resource, ontology | An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. | owl |
is listed by: BioPortal has parent organization: University of Michigan; Ann Arbor; USA |
nlx_157319 | SCR_010292 | 2026-09-05 06:30:19 | 1 | |||||||||
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Coding Symbols for a Thesaurus of Adverse Reaction Terms Resource Report Resource Website |
Coding Symbols for a Thesaurus of Adverse Reaction Terms (RRID:SCR_010294) | COSTART | controlled vocabulary, data or information resource, ontology | Ontology for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. It is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999. | umls | is listed by: BioPortal | nlx_157367 | SCR_010294 | 2026-09-05 06:30:19 | 0 | |||||||||
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NCBITaxon Resource Report Resource Website 1+ mentions |
NCBITaxon (RRID:SCR_000479) | NCBITAXON | controlled vocabulary, data or information resource, ontology | Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl. | owl |
is listed by: BioPortal has parent organization: NCBI Taxonomy |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157490 | SCR_000479 | National Center for Biotechnology Information Organismal Classification, National Center for Biotechnology Information (NCBI) Organismal Classification, NCBI Organismal Classification | 2026-09-05 06:30:19 | 4 |
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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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