Searching across hundreds of databases
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
LexGrid Resource Report Resource Website 1+ mentions |
LexGrid (RRID:SCR_006627) | LexGrid | software resource | LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, parse, ontology |
is listed by: BioPortal is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: European Bioinformatics Institute has parent organization: National Cancer Institute |
NIH ; Cancer Biomedical Informatics Grid ; NLM LM07319 |
PMID:19261933 | Free for academic use | nlx_149194 | http://www.lexgrid.org/ | SCR_006627 | Lexical Grid | 2025-04-19 06:43:38 | 1 | ||||
|
RightField Resource Report Resource Website 1+ mentions |
RightField (RRID:SCR_002649) | RightField | software resource, software application | 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 | Open unspecified license | biotools:rightfield, nlx_156077 | https://bio.tools/rightfield | SCR_002649 | 2025-05-12 11:04:39 | 3 | ||||||
|
Biositemaps Resource Report Resource Website 1+ mentions |
Biositemaps (RRID:SCR_001976) | Biositemaps | software resource, service 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 | 2025-05-12 11:03:55 | 1 | ||||||||
|
Plant Environmental Conditions Resource Report Resource Website |
Plant Environmental Conditions (RRID:SCR_003460) | PECO, EO | data or information resource, controlled vocabulary | A structured controlled vocabulary for the representation of plant environmental conditions. | obo, environment, gene expression, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: Gramene |
nlx_157554 | http://purl.bioontology.org/ontology/PECO http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/environment_ontology.obo http://www.gramene.org/plant_ontology/index.html#eo |
SCR_003460 | 2025-05-13 11:12:47 | 0 | ||||||||
|
Dictyostelium Discoideum Anatomy Ontology Resource Report Resource Website |
Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) | DDANAT | data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. | obo, anatomy, organismal, cellular |
is listed by: BioPortal is listed by: OBO has parent organization: Dictyostelium discoideum genome database |
nlx_157387 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/dictyostelium/dictyostelium_anatomy.obo | SCR_003309 | Dictyostelium discoideum anatomy | 2025-05-13 11:12:44 | 0 | |||||||
|
FlyBase Controlled Vocabulary Resource Report Resource Website |
FlyBase Controlled Vocabulary (RRID:SCR_003318) | FB-CV, FBcv | data or information resource, controlled vocabulary | A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them. | obo |
is listed by: BioPortal is listed by: OBO has parent organization: FlyBase |
nlx_157408 | http://sourceforge.net/p/fbcv/code-0/HEAD/tree/releases/latest/fbcv-simple.obo?format=raw | SCR_003318 | 2025-05-13 11:12:44 | 0 | ||||||||
|
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 | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:36 | 0 | |||||||||
|
PR Resource Report Resource Website |
PR (RRID:SCR_004964) | PR | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:53 | 0 | |||||||
|
Cereal Plant Development Ontology Resource Report Resource Website |
Cereal Plant Development Ontology (RRID:SCR_005095) | GRO-CPD | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:55 | 0 | ||||||||
|
NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | software resource, service resource, production service resource, web service, data access protocol | 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 | 2025-05-15 10:37:57 | 6 | |||||
|
Computer Assisted Brain Injury Rehabilitation Ontology Resource Report Resource Website |
Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) | CABRO | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:37:57 | 0 | ||||||||
|
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 | 2025-05-15 10:38:04 | 0 | ||||||||
|
Cell Line Ontology Resource Report Resource Website 1+ mentions |
Cell Line Ontology (RRID:SCR_005840) | CLO | data or information resource, controlled vocabulary, 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 | 2025-05-15 10:38:07 | 2 | |||||||
|
Gene Ontology Resource Report Resource Website 5000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | knowledge environment resource, project portal, portal, data or information resource, consortium, organization 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 |
European Union QLRI-CT-2001-0098; European Union QLRI-CT-2001-00015; NHGRI P41 HG002273 |
PMID:23161678 PMID:10802651 |
The community can contribute to this resource, Acknowledgement required | 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 | 2025-05-15 10:36:45 | 9965 | ||||
|
Bioassay Ontology Resource Report Resource Website 1+ mentions |
Bioassay Ontology (RRID:SCR_002638) | BAO | data or information resource, controlled vocabulary, ontology | Ontology to describe and categorize chemical biology and drug screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation. | chemical biology, drug screening, assay, perturbation, high-throughput screening, owl |
is used by: LINCS Information Framework is listed by: BioPortal is parent organization of: G Protein-Coupled Receptor BioAssays Ontology |
nlx_156065 | SCR_002638 | 2025-05-15 10:36:39 | 7 | |||||||||
|
Ascomycete Phenotype Ontology Resource Report Resource Website |
Ascomycete Phenotype Ontology (RRID:SCR_003254) | APO | data or information resource, controlled vocabulary, 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 |
nlx_157321 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo | SCR_003254 | 2025-05-15 10:37:03 | 0 | ||||||||
|
Beta Cell Genomics Ontology Resource Report Resource Website |
Beta Cell Genomics Ontology (RRID:SCR_003259) | OBI BCGO, BCGO | data or information resource, controlled vocabulary, ontology | An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc. | owl, cell type, classification, ontology, beta cell genomics |
uses: BFO uses: Ontology for Biomedical Investigations is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology has parent organization: Beta Cell Biology Consortium |
nlx_157324 | http://purl.bioontology.org/ontology/OBI_BCGO http://purl.obolibrary.org/obo/bcgo.owl |
SCR_003259 | 2025-05-15 10:37:03 | 0 | ||||||||
|
Biological Collections Ontology Resource Report Resource Website |
Biological Collections Ontology (RRID:SCR_003262) | BCO | data or information resource, controlled vocabulary, ontology | Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. | owl, interoperability, biodiversity, museum collection, environmental sample, metagenomic sample, ecological survey |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
PMID:24595056 | nlx_157333 | http://purl.obolibrary.org/obo/bco.owl http://purl.bioontology.org/ontology/BCO |
SCR_003262 | 2025-05-15 10:37:03 | 0 | |||||||
|
Common Anatomy Reference Ontology Resource Report Resource Website |
Common Anatomy Reference Ontology (RRID:SCR_003296) | CARO | data or information resource, controlled vocabulary, ontology | An ontology developed to facilitate interoperability between existing anatomy ontologies for different species, and to provide a template for building new anatomy ontologies. | obo, anatomy, organismal, ontology, interoperability, template |
is used by: Teleost Anatomy Ontology is listed by: BioPortal is listed by: OBO |
nlx_157369 | http://purl.bioontology.org/ontology/CARO http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo |
SCR_003296 | 2025-05-15 10:37:04 | 0 | ||||||||
|
Clinical Measurement Ontology Resource Report Resource Website |
Clinical Measurement Ontology (RRID:SCR_003291) | CMO | data or information resource, controlled vocabulary, ontology | An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. | obo, phenotype, clinical, measurement, morphology, physiology |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO has parent organization: Medical College of Wisconsin; Wisconsin; USA |
PMID:22654893 | nlx_157364 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo |
SCR_003291 | 2025-05-15 10:37:04 | 0 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
