Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | controlled vocabulary, data or information resource, ontology | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-07-28 09:40:58 | 44 | |||||
|
Open Biological and Biomedical Ontologies Relationship Types Resource Report Resource Website 50+ mentions |
Open Biological and Biomedical Ontologies Relationship Types (RRID:SCR_004409) | OBOREL | controlled vocabulary, data or information resource, ontology | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Ontology that defines core relations used in all OBO ontologies. Obsolete. Replaced with RO. | obo | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157539 | SCR_004409 | 2026-07-28 09:40:59 | 62 | ||||||||
|
MPO Resource Report Resource Website 10+ mentions |
MPO (RRID:SCR_004855) | MPO, MP | controlled vocabulary, data or information resource, ontology | Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome. | mus, phenotype, obo |
is used by: NIF Data Federation is listed by: BioPortal is related to: Rat Genome Database (RGD) is related to: MouseBook is related to: Neurocarta is related to: phenomeNET has parent organization: OBO has parent organization: Mouse Genome Informatics (MGI) |
PMID:17989687 | The community can contribute to this resource | nlx_83784 | http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype, http://purl.bioontology.org/ontology/MP | SCR_004855 | Mammalian Phenotype Ontology | 2026-07-28 09:41:10 | 19 | |||||
|
PATO Resource Report Resource Website 10+ mentions |
PATO (RRID:SCR_004782) | PATO | controlled vocabulary, data or information resource, ontology | Ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model). | plant trait, mammalian, phenotype, obo, quality, phenotypic quality |
is used by: Morpholino Database is listed by: BioPortal has parent organization: OBO |
nlx_77534 | http://obofoundry.org/wiki/index.php/PATO:Main_Page | SCR_004782 | PATO - Phenotypic Quality Ontology, Phenotype and Trait Ontology, Phenotypic Quality Ontology | 2026-07-28 09:41:09 | 29 | |||||||
|
BFO Resource Report Resource Website 1+ mentions |
BFO (RRID:SCR_004818) | BFO | controlled vocabulary, data or information resource, ontology | A small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences. | owl, gold standard |
is used by: Beta Cell Genomics Ontology is listed by: BioPortal has parent organization: IFOMIS |
Volkswagen Foundation | nlx_80606 | http://bioportal.bioontology.org/ontologies/BFO | SCR_004818 | Basic Formal Ontology | 2026-07-28 09:41:05 | 4 | ||||||
|
Bioinformatics Web Service Ontology Resource Report Resource Website |
Bioinformatics Web Service Ontology (RRID:SCR_004529) | OBIWS | controlled vocabulary, data or information resource, ontology | Ontology that extends the Ontology for Biomedical Investigations (OBI) to support consistent annotation of Bioinformatics Web services. | owl | is listed by: BioPortal | nlx_157332 | http://code.google.com/p/obi-webservice/ | SCR_004529 | 2026-07-28 09:41:01 | 0 | ||||||||
|
PhenomeBLAST Ontology Resource Report Resource Website 1+ mentions |
PhenomeBLAST Ontology (RRID:SCR_005139) | PHENOMEBLAST | controlled vocabulary, data or information resource, ontology | A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases. | owl | is listed by: BioPortal | nlx_157549 | SCR_005139 | 2026-07-28 09:41:10 | 1 | |||||||||
|
NIFSTD Resource Report Resource Website 10+ mentions |
NIFSTD (RRID:SCR_005414) | NIFSTD | controlled vocabulary, data or information resource, ontology | The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. | behavioral activity, behavioral paradigm, brain region, cell, neuron, disease, molecule, nervous system function, subcellular part, resource type, quality, brain, neuroscience, biological process, cellular anatomy, anatomy, subcellular, subcellular anatomy, organism, neurological disorder, neurologic disease, dysfunction, owl |
is listed by: BioPortal is listed by: FORCE11 is related to: NeuroLex is related to: OntoQuest is related to: InterLex has parent organization: Neuroscience Information Framework is parent organization of: NIF Cell Ontology provides: Neuron Phenotype Ontology |
PMID:18975148 PMID:22737162 |
nlx_144512 | http://bioportal.bioontology.org/ontologies/NIFSTD | https://confluence.crbs.ucsd.edu/display/NIF/Ontologies+and+Vocabularies | SCR_005414 | Neuroscience Information Framework Standard Ontology, NIF Ontology, NIF Standard, NIF-Ontology, Neuroscience Information Framework (NIF) Standard Ontology, NIF Standard Ontology, NIFSTD Ontology, NIF Ontologies | 2026-07-28 09:41:14 | 15 | |||||
|
VIVO Resource Report Resource Website 50+ mentions |
VIVO (RRID:SCR_005246) | VIVO | software application, service resource, community building portal, data or information resource, software resource, ontology, controlled vocabulary, portal | Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work. | data sharing, network, semantic web, linked data, rdf, owl, database, people resource |
is listed by: BioPortal is related to: Clinical and Translational Science Awards Consortium is related to: DataStaR is related to: CTSAconnect is related to: CTSA ShareCenter has parent organization: University of Florida; Florida; USA |
NCRR U24 RR029822 | Open unspecified license | nlx_144266 | SCR_005246 | VIVO - enabling national networking of scientists | 2026-07-28 09:41:19 | 50 | ||||||
|
HGNC Resource Report Resource Website 500+ mentions |
HGNC (RRID:SCR_002827) | controlled vocabulary, data or information resource, database | Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs. | gene, owl, gene symbol, phenotype, nomenclature, gene family, gene groups, genomic, proteomic, ortholog, web service, locus, protein coding, genetics, gold standard, bio.tools, FASEB list, GCBR, ELIXIR Core Data Resource, DRKB |
is used by: Nowomics is used by: Cytokine Registry is listed by: BioPortal is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: INFEVERS is related to: VGNC has parent organization: University of Cambridge School of Clinical Medicine; Cambridge; United Kingdom |
NHGRI U24HG003345 | PMID:36243972 PMID:32747822 PMID:34615987 PMID:33152070 |
Free, Freely available | biotools:genenames.org, nif-0000-02955, r3d100010901 | http://bioportal.bioontology.org/ontologies/HUGO, https://bio.tools/genenames.org, https://doi.org/10.17616/R3XC80 | SCR_002827 | HUGO symbols, HGNC Database, HGNC - HUGO Gene Nomenclature Committee, HUGO Gene Nomenclature Committee, Human Genome Organization Gene Symbols | 2026-07-28 09:40:31 | 974 | |||||
|
International Classification for Nursing Practice Resource Report Resource Website |
International Classification for Nursing Practice (RRID:SCR_003099) | ICNP | controlled vocabulary, data or information resource, ontology | Ontology of the international classification for nursing practice. | owl | is listed by: BioPortal | Free, Available for download, Freely available | nlx_157445 | SCR_003099 | 2026-07-28 09:40:43 | 0 | ||||||||
|
Spider Ontology Resource Report Resource Website |
Spider Ontology (RRID:SCR_003117) | SPD | controlled vocabulary, data or information resource, ontology | An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). | obo, anatomy, organismal, behavior, product, spider |
is listed by: BioPortal is listed by: OBO has parent organization: Tree of Life: Phylogeny of Spiders |
Free, Freely available | nlx_157595 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo | SCR_003117 | 2026-07-28 09:40:36 | 0 | |||||||
|
Interaction Ontology Resource Report Resource Website |
Interaction Ontology (RRID:SCR_003055) | IXNO | controlled vocabulary, data or information resource, ontology | Ontology to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD), a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health. | obo |
is listed by: BioPortal has parent organization: Comparative Toxicogenomics Database (CTD) |
Free, Freely available | nlx_157444 | SCR_003055 | 2026-07-28 09:40:36 | 0 | ||||||||
|
Mental Functioning Ontology Resource Report Resource Website 1+ mentions |
Mental Functioning Ontology (RRID:SCR_003245) | MF, MFO | controlled vocabulary, data or information resource, ontology | An ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies. | mental functioning, mental process, cognition, trait, psychology, neuroscience, owl |
is listed by: BioPortal is listed by: Google Code is listed by: OBO is related to: Information Artifact Ontology is related to: Emotion Ontology is related to: Emotion Ontology has parent organization: University at Buffalo; New York; USA |
Free, Freely available | nlx_157305 | http://purl.obolibrary.org/obo/mf.owl | SCR_003245 | mental-functioning-ontology | 2026-07-28 09:40:40 | 1 | ||||||
|
Kinetic Simulation Algorithm Ontology Resource Report Resource Website |
Kinetic Simulation Algorithm Ontology (RRID:SCR_003361) | KISAO | controlled vocabulary, data or information resource, ontology | An ontology that classifies algorithms available for the simulation of models in biology, their characteristics and the parameters required for their use. | owl, algorithm, simulation |
is listed by: BioPortal is listed by: OBO has parent organization: BioModels |
PMID:22027554 | Free, Available for download, Freely available | nlx_157456 | https://bioportal.bioontology.org/ontologies/KISAO | SCR_003361 | 2026-07-28 09:40:46 | 0 | ||||||
|
Emotion Ontology Resource Report Resource Website |
Emotion Ontology (RRID:SCR_003272) | MFOEM | controlled vocabulary, data or information resource, ontology | An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialization of the broader Mental Functioning Ontology. | owl, affect, emotion, mood, appraisal, feeling, health, ontology |
is listed by: Google Code is listed by: OBO is listed by: BioPortal is related to: Mental Functioning Ontology is related to: Mental Functioning Ontology |
Free, Available for download, Freely available | nlx_157396 | https://github.com/jannahastings/emotion-ontology | SCR_003272 | 2026-07-28 09:40:40 | 0 | |||||||
|
Experimental Conditions Ontology Resource Report Resource Website 1+ mentions |
Experimental Conditions Ontology (RRID:SCR_003306) | XCO | controlled vocabulary, data or information resource, ontology | An ontology designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. | obo, clinical, physiology, morphology, measurement |
is listed by: BioPortal is listed by: OBO has parent organization: Medical College of Wisconsin; Wisconsin; USA |
PMID:22654893 | Free, Available for download, Freely available | nlx_157401 | ftp://rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo, http://sourceforge.net/projects/phenoonto/ | SCR_003306 | Experimental condition ontology | 2026-07-28 09:40:46 | 1 | |||||
|
National Center for Biomedical Ontology Resource Report Resource Website 10+ mentions |
National Center for Biomedical Ontology (RRID:SCR_003304) | NCBO | training resource, data or information resource, organization portal, database, portal | Organization that provides biomedical researchers with online tools and a web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of the work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments. | biomedical ontology, biomedical software tools |
is used by: DisGeNET is related to: Protege is related to: National Centers for Biomedical Computing has parent organization: National Centers for Biomedical Computing is parent organization of: BioPortal is parent organization of: PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate Ontologies is parent organization of: Bio-Mixer |
NHGRI U54 HG004028 | PMID:21672956 PMID:23734708 |
Free, Freely available | nif-0000-31891 | SCR_003304 | 2026-07-28 09:40:40 | 27 | ||||||
|
Vertebrate Trait Ontology Resource Report Resource Website |
Vertebrate Trait Ontology (RRID:SCR_003214) | VT | controlled vocabulary, data or information resource, ontology | A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. | trait, morphology, physiology, development, obo |
is listed by: BioPortal is related to: monarch-ontologies is related to: Rat Genome Database (RGD) is related to: Animal QTLdb is related to: Mouse Phenome Database (MPD) has parent organization: SourceForge |
PMID:23937709 | Free, Available for download, Freely available | nlx_156940 | SCR_003214 | VT Ontology | 2026-07-28 09:40:45 | 0 | ||||||
|
Chemical Information Ontology Resource Report Resource Website 1+ mentions |
Chemical Information Ontology (RRID:SCR_003290) | CHEMINF | controlled vocabulary, data or information resource, ontology | An ontology that aims to establish a standard in representing chemical information including chemical structure and the ability to richly describe chemical properties, whether intrinsic or computed. It includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. | owl, biochemistry, chemistry, chemical structure, chemical property, structure, property, molecular |
is listed by: BioPortal is listed by: OBO is listed by: Google Code has parent organization: European Bioinformatics Institute |
PMID:21991315 | Free, Available for download, Freely available | nlx_157362 | http://purl.bioontology.org/ontology/CHEMINF, http://semanticchemistry.googlecode.com/svn/trunk/ontology/cheminf.owl | SCR_003290 | 2026-07-28 09:40:41 | 2 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the PRECISE-TBI Resources search. From here you can search through a compilation of resources used by PRECISE-TBI and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that PRECISE-TBI has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on PRECISE-TBI then you can log in from here to get additional features in PRECISE-TBI such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into PRECISE-TBI you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
