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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, web application, web service, software resource | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-02-17 10:01:09 | 2760 | ||||
|
YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | storage service resource, data or information resource, production service resource, analysis service resource, database, service resource, data analysis service, data repository | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-02-17 10:01:08 | 34 | |||||
|
g:Profiler Resource Report Resource Website 1000+ mentions |
g:Profiler (RRID:SCR_006809) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service, data analysis service | Web server for functional enrichment analysis and conversions of gene lists. Web based tool for functional profiling of gene lists from large scale experiments. Has web interface with powerful visualization. Used for analyzing data from any organism. | gene, high-throughput, genomics, visualization, statistical analysis, slimmer-type tool, term enrichment, protein interaction, functional similarity, analysis, coexpression, gene id, network enrichment analysis, orthology mapping, genomic locus, ontology or annotation visualization, other analysis, ortholog, functional profile, gene list, ontology, pathway, transcription factor, microrna, regulatory motif, protein-protein interaction, biomolecule, gene expression, gene, homology, single nucleotide polymorphism, dna polymorphism, chromosome, network analysis, disease gene, r |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Ensembl is related to: Ensembl Genomes has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group works with: gProfiler2 |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:21646343 PMID:17478515 PMID:31066453 |
Free, Freely available | OMICS_02223, nif-0000-31975 | SCR_006809 | G:Profiler, g:profiler, gProfiler | 2026-02-17 10:00:59 | 2078 | ||||||
|
GOdist Resource Report Resource Website |
GOdist (RRID:SCR_005770) | GOdist | data analysis software, software application, data processing software, software resource | GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | statistical analysis, function, gene, gene expression, gene ontology, matlab, affymetrix, microarray, biological process, molecular function, cellular component, fisher exact test, kolmogorov-smirnov |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
PMID:15550480 | Free for academic use | nlx_149260 | SCR_005770 | 2026-02-17 10:00:48 | 0 | |||||||
|
Ontologizer Resource Report Resource Website 100+ mentions |
Ontologizer (RRID:SCR_005801) | Ontologizer | software application, production service resource, data processing software, analysis service resource, source code, service resource, software resource, data analysis service | The Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods. The tool can be started directly from the web using Java webstart. For graph visualizations, users need to install the GraphViz library. The tool is freely available to all, and source code is available at SourceForge. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, biological data, gene ontology, statistical analysis, fisher exact test, visualization, graph, java, annotation, parent-child, topology |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
DFG SFB 760 | PMID:18511468 PMID:17848398 |
Free for academic use | nlx_149289 | SCR_005801 | The Ontologizer | 2026-02-17 10:00:49 | 122 | |||||
|
THEA - Tools for High-throughput Experiments Analysis Resource Report Resource Website |
THEA - Tools for High-throughput Experiments Analysis (RRID:SCR_005802) | THEA | data analysis software, software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, on documented July 16, 2012. An integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, analysis, ontology, microarray, genomic, annotation, gene ontology, data mining, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Virtual Biology Lab |
French Ministry of Higher Education and Research ; Bioinformatic Program |
PMID:15130932 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149290 | SCR_005802 | Tools for High-throughput Experiments Analysis | 2026-02-17 10:00:57 | 0 | |||||
|
CGAP GO Browser Resource Report Resource Website 1+ mentions |
CGAP GO Browser (RRID:SCR_005676) | CGAP GO Browser | data or information resource, service resource, data set | With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool | gene, biological process, cellular component, molecular function, browser, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Cancer Genome Anatomy Project |
NCI | Free for academic use | nlx_149116 | SCR_005676 | Cancer Genome Anatomy Project GO Browser | 2026-02-17 10:00:57 | 4 | ||||||
|
PubSearch Resource Report Resource Website 1+ mentions |
PubSearch (RRID:SCR_005830) | PubSearch | data or information resource, service resource, database, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotate, editor, literature curation tool, literature, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR has parent organization: Stanford University; Stanford; California |
NHGRI R01HG02728 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149338 | SCR_005830 | 2026-02-17 10:01:01 | 1 | |||||||
|
Onto-Express Resource Report Resource Website 50+ mentions |
Onto-Express (RRID:SCR_005670) | OE | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool | microarray, gene, ontology, gene expression, biochemical function, biological process, cellular role, cellular component, molecular function, chromosome location, java, data-mining, browser, visualization, analysis, statistical analysis, term enrichment, search engine, other analysis, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, custom level of abstraction of the gene ontology, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
Wayne State University School of Medicine; Michigan; USA ; NICHD HD36512 |
PMID:12620386 PMID:11829497 PMID:15215428 |
Free for academic use | nlx_149110 | http://vortex.cs.wayne.edu:8080 | SCR_005670 | Onto-Express (OE) | 2026-02-17 10:00:47 | 85 | ||||
|
MAPPFinder Resource Report Resource Website 10+ mentions |
MAPPFinder (RRID:SCR_005791) | MAPPFinder | data analysis software, software application, data processing software, software resource | MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible | gene, gene ontology, gene association, gene expression, profile, microarray, pathway, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at San Francisco; California; USA has parent organization: Gene Map Annotator and Pathway Profiler |
University of California at San Francisco; California; USA ; San Francisco General Hospital; California; USA ; NHLBI ; NCRR MO1RR00083 |
PMID:12540299 | Free for academic use | nlx_149270 | SCR_005791 | 2026-02-17 10:00:48 | 26 | ||||||
|
GeneTools Resource Report Resource Website 1000+ mentions |
GeneTools (RRID:SCR_005663) | GeneTools | data or information resource, data access protocol, web service, software resource | Web-service providing access to database that brings together information from broad range of resources. Web application for functional annotation and statistical hypothesis testing. Provides tools for analysis of genomic and microarray data. Collection of tools include Bibliographic Information,Databases,Gene Annotation,Gene Regulation, Microarray,Proteins,Sequence Manipulation - Nucleic Acids,Sequence Manipulation - Protein, Systems Biology. | genome-wide analyses, annotation, gene, visualization, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, statistical analysis, term enrichment, browser, search engine, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Norwegian University of Science and Technology; Trondheim; Norway is parent organization of: GeneTools: explore GeneOntology |
National Council on Cardiovascular Diseases ; Norwegian University of Science and Technology ; Norwegian Research Council |
PMID:17062145 | SCR_002911, SCR_007388, nif-0000-00407, nif-0000-30011, nlx_149102 | SCR_005663 | 2026-02-17 10:00:36 | 1752 | |||||||
|
GOArray Resource Report Resource Website 1+ mentions |
GOArray (RRID:SCR_005785) | GOArray | data analysis software, software application, data processing software, software resource | GOArray is a Perl program which inputs a lists of genes annotated as of interest (GOI) or not, and determines if any associated GO terms have an overrepresentation of GOI. A permutation test is optionally used to assess confidence in the results. Output includes multiple visualizations and supplementary information and, for future reference, a summary of the statistical methods used. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, gene, visualization, gene ontology, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Yale School of Medicine; Connecticut; USA |
Free for academic use | nlx_149259 | http://goarray.med.yale.edu/GOArray/ | SCR_005785 | 2026-02-17 10:01:00 | 1 | |||||||
|
GeneInfoViz Resource Report Resource Website |
GeneInfoViz (RRID:SCR_005680) | GeneInfoViz | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool | gene network, gene ontology, visualization, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:15724283 | Free for academic use | nlx_149121 | SCR_005680 | GeneInfoViz: Constructing and Visualizing Gene Relation Networks | 2026-02-17 10:00:56 | 0 | ||||||
|
TrED Resource Report Resource Website 1+ mentions |
TrED (RRID:SCR_005869) | TrED | software application, data or information resource, data processing software, data analysis software, database, software resource | TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes. | expressed sequence tag, transcriptional profile, fungal pathogen, bmu01672, chuv862.00, mya-3108, cdna, pathway, microarray, classification, blast, unisequence, peptide, annotation |
is related to: Gene Ontology is related to: KEGG is related to: GenBank is related to: Pfam |
Ministry of Science and Technology of China 2006AA020504 | PMID:17650345 | nlx_149408 | SCR_005869 | TrED - T. rubrum Expression Database, Trichophyton rubrum Expression Database, Trichophyton rubrum Expression Database (TrED) | 2026-02-17 10:00:49 | 5 | ||||||
|
EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | data analysis software, software application, data processing software, software resource | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-02-17 10:01:25 | 8 | |||||
|
AgingDB Resource Report Resource Website |
AgingDB (RRID:SCR_010226) | AgingDB | storage service resource, data or information resource, database, service resource, data repository | A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments. | oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factor |
is related to: Gene Ontology has parent organization: Pusan National University; Busan; South Korea |
Aging | PMID:23604914 | The community can contribute to this resource | nlx_156773 | http://aging.pharm.pusan.ac.kr/AgingDB/ | SCR_010226 | Aging Database, Aging DB | 2026-02-17 10:01:43 | 0 | ||||
|
Gene Ontology Extension Resource Report Resource Website |
Gene Ontology Extension (RRID:SCR_010327) | GO-EXT | data or information resource, ontology, controlled vocabulary | An extension of the Gene Ontology. | obo |
is listed by: BioPortal has parent organization: Gene Ontology |
nlx_157414 | SCR_010327 | 2026-02-17 10:01:27 | 0 | |||||||||
|
Centre for Modeling Human Disease Gene Trap Resource Resource Report Resource Website 1+ mentions |
Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) | CMHD Gene Trap Resource | material service resource, production service resource, service resource, biomaterial manufacture | Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | embryonic stem cell, polya trap vector, gene trap, insertion, mutagenic polya trap vector, sequence, expression, mutagenesis, gene, mutation, expression profile, phenotype, database, gene expression, vector insertion, expressed sequence tag, blast, clone |
is related to: Gene Ontology is related to: CMMR - Canadian Mouse Mutant Repository is related to: International Gene Trap Consortium has parent organization: CMHD - Centre for Modeling Human Disease |
Canadian Institutes of Health Research ; Genome Canada ; Genome Prairie ; NIH |
PMID:14681480 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02891 | http://www.cmhd.ca/sub/genetrap.asp | SCR_002785 | Centre for Modeling Human Disease (CMHD) Gene Trap Resource | 2026-02-17 09:59:58 | 3 | ||||
|
BioPortal Resource Report Resource Website 100+ mentions |
BioPortal (RRID:SCR_002713) | BioPortal | ontology, repository, storage service resource, data or information resource, controlled vocabulary, service resource, data repository | Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services. | biomedical, thesaurus, ontology mapping, annotation, metadata standard, ontology repository, portal, web service, obo, owl, rdf, rrf protege frame, lexgrid xml |
lists: MeGO lists: Porifera Ontology lists: EnvO lists: Research Network and Patient Registry Inventory Ontology lists: Semantic DICOM Ontology lists: Time Event Ontology lists: Variation Ontology lists: Vertebrate Skeletal Anatomy Ontology lists: Epoch Clinical Trial Ontology lists: Gazetteer lists: Human Disease Ontology lists: Information Artifact Ontology lists: NCBITaxon lists: Amphibian Taxonomy Ontology lists: Anatomic Pathology Lexicon lists: HIV ontology lists: International Classification of Primary Care - 2 PLUS lists: Mathematical Modelling Ontology lists: Nursing Interventions Classification lists: Phylogenetic Ontology lists: Bleeding History Phenotype Ontology lists: Body System Terms from ICD11 lists: Synthetic Biology Open Language Visual Ontology lists: Teleost Anatomy Ontology lists: Teleost Taxonomy Ontology lists: ECO lists: Bioassay Ontology lists: RightField lists: Gene Ontology lists: HGNC lists: Interaction Ontology lists: International Classification for Nursing Practice lists: Spider Ontology lists: Vertebrate Trait Ontology lists: Mental Functioning Ontology lists: Ascomycete Phenotype Ontology lists: Beta Cell Genomics Ontology lists: Biological Collections Ontology lists: Chemical Methods Ontology lists: Chemical Information Ontology lists: Common Anatomy Reference Ontology lists: Experimental Conditions Ontology lists: Dictyostelium Discoideum Anatomy Ontology lists: Fission Yeast Phenotype Ontology lists: Fly Taxonomy lists: FlyBase Controlled Vocabulary lists: Hymenoptera Anatomy Ontology lists: Influenza Ontology lists: Lipid Ontology lists: Kinetic Simulation Algorithm Ontology lists: Malaria Ontology lists: FMA lists: Minimal Anatomical Terminology lists: NEMO Ontology lists: Ontology for Genetic Interval lists: Ontology for Parasite LifeCycle lists: Ontology of Adverse Events lists: Ontology of Medically Related Social Entities lists: Ontology of Vaccine Adverse Events lists: Rat Strain Ontology lists: Plant Environmental Conditions lists: Plant Trait Ontology lists: Population and Community Ontology lists: RNA Ontology lists: Rat Strain Ontology lists: Subcellular Anatomy Ontology lists: Software Ontology lists: Suggested Ontology for Pharmacogenomics lists: Vertebrate Taxonomy Ontology lists: PharmGKB Ontology lists: Physico-Chemical Process lists: International Classification for Patient Safety lists: Adverse Event Reporting Ontology lists: Experimental Factor Ontology lists: Mass Spectrometry Ontology lists: Master Drug Data Base Clinical Drugs lists: Medaka Fish Anatomy and Development Ontology lists: Medical Diagnostic Categories - Diagnosis Related Groups lists: Medical Dictionary for Regulatory Activities lists: Minimal Standard Terminology of Digestive Endoscopy lists: Minimal Standard Terminology of Digestive Endoscopy - French lists: Ontology of Physical Exercises lists: Mosquito Gross Anatomy Ontology lists: Systematized Nomenclature of Medicine - International Version lists: Mosquito Insecticide Resistance Ontology lists: Mouse Experimental Design Ontology lists: Mouse Gross Anatomy and Development Ontology lists: Systematized Nomenclature of Medicine - Clinical Terms lists: Systems Chemical Biology and Chemogenomics Ontology lists: Mouse Pathology Ontology lists: NIF Cell Ontology lists: NHS Quality Indicators lists: Neural-Immune Gene Ontology lists: Ontology of Physics for Biology lists: Cell Type Ontology lists: Xenopus Anatomy Ontology lists: SO lists: Ontology of Pneumology lists: Open Biological and Biomedical Ontologies Relationship Types lists: Biomedical Resource Ontology lists: MGED Ontology lists: Pharmacovigilance Ontology lists: PhenX Phenotypic Terms lists: Bioinformatics Web Service Ontology lists: SysMO JERM Ontology of Systems Biology for Micro-Organisms lists: MeSH lists: PATO lists: BFO lists: MPO lists: PR lists: Cereal Plant Development Ontology lists: PhenomeBLAST Ontology lists: VIVO lists: Computer Assisted Brain Injury Rehabilitation Ontology lists: Computer Retrieval of Information on Scientific Projects Thesaurus lists: NIFSTD lists: Cell Line Ontology lists: Student Health Record Ontology lists: Zebrafish Anatomical Ontology lists: Physical Medicine and Rehabilitation lists: Randomized Controlled Trials Ontology lists: Human Phenotype Ontology lists: Read Codes Clinical Terms Version 3 lists: Reference Sequence Annotation lists: Regulation of Gene Expression Ontolology lists: Neurobehavior Ontology lists: Regulation of Transcription Ontology lists: Reproductive Trait and Phenotype Ontology lists: Skin Physiology Ontology lists: Vaccine Ontology lists: OMIM lists: MedlinePlus lists: Adult Mouse Anatomy Ontology lists: Bone Dysplasia Ontology lists: Bone and Cartilage Tissue Engineering Ontology lists: Botryllus schlosseri anatomy and development ontology lists: EDAM Ontology lists: LexGrid lists: RxNorm lists: Breast Cancer Grading Ontology lists: Breast Tissue Cell Lines Ontology lists: SBO lists: Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology lists: Brucellosis Ontology lists: Sleep Domain Ontology lists: C. elegans Development Vocabulary lists: Physician Data Query lists: C. elegans Gross Anatomy Vocabulary lists: Plant Ontology lists: C. elegans Phenotype Vocabulary lists: CPTAC Proteomics Pipeline Infrastructure Ontology lists: Cancer Research and Management ACGT Master Ontology lists: Cancer Chemoprevention Ontology lists: Cell Behavior Ontology lists: Cereal Plant Gross Anatomy Ontology lists: Cardiac Electrophysiology Ontology lists: Cerebrotendinous Xanthomatosis Ontology lists: Cell Cycle Ontology lists: Cell Culture Ontology lists: Cerrado concepts and plant community dynamics lists: Clinical Signs and Symptoms Ontology lists: Clusters of Orthologous Groups Analysis Ontology lists: Computational Neuroscience Ontology lists: BIRNLex lists: Computer-Based Patient Record Ontology lists: Congenital Heart Defects Ontology lists: Drug Interaction Knowledge Base Ontology lists: Healthcare Common Procedure Coding System lists: Host Pathogen Interactions Ontology lists: Human Dermatological Disease Ontology lists: Solanaceae Phenotype Ontology lists: Soy Ontology lists: Spatial Ontology lists: Surgical Secondary Events lists: eagle-i research resource ontology lists: Biological Pathways Exchange lists: Autism Spectrum Disorder Phenotype Ontology lists: BRENDA Tissue and Enzyme Source Ontology lists: BioTop Ontology lists: Family Health History Ontology lists: International Classification of Diseases Version 9 - Clinical Modification lists: BioModels Ontology lists: Bilingual Ontology of Alzheimer lists: BioPortal Metadata Ontology lists: Biochemical Substructure Ontology lists: Biodiversity Ontology lists: Biological Imaging Methods Ontology lists: International Classification of Functioning Disability and Health lists: Biologie Hors Nomenclature lists: International Classification of Primary Care lists: Biomedical Research Integrated Domain Group Model lists: KB Bio 101 lists: Bionutrition Ontology lists: Artificial Intelligence Rheumatology Consultant System Ontology lists: Leukocyte Surface Marker Ontology lists: Cell Line Ontology by Mahadevan lists: Cellular microscopy phenotype ontology lists: ABA Adult Mouse Brain Ontology lists: AEO lists: African Traditional Medicine Ontology lists: Alzheimer's disease ontology lists: Amino Acid Ontology lists: Amphibian Gross Anatomy Ontology lists: Animal Natural History and Life History Ontology lists: Coding Symbols for a Thesaurus of Adverse Reaction Terms lists: Cognitive Atlas Ontology lists: Common Terminology Criteria for Adverse Events lists: Comparative Data Analysis Ontology lists: Content Archive Resource Exchange Lexicon lists: Crop Ontology lists: Current Procedural Terminalogy Hierarchy lists: Current Procedural Terminology lists: DICOM Controlled Terminology lists: Dataset processing lists: Dengue Fever Ontology lists: Dermatology Lexicon lists: Diagnosis Ontology of Clinical Care Classification lists: Diagnostic Ontology lists: Disease core ontology applied to Rare Diseases lists: Dispedia Core Ontology lists: Drosophila Development Ontology lists: Drosophila Gross Anatomy Ontology lists: EDDA Study Design Terminology lists: Electrocardiography Ontology lists: Eligibility Feature Hierarchy lists: Enzyme Mechanism Ontology lists: Enzyme Reaction Ontology for partial chemical perspectives lists: Epilepsy Ontology lists: Loggerhead Nesting Ontology lists: Fanconi Anemia Ontology lists: Fire Ontology lists: Flora Phenotype Ontology lists: Fungal Gross Anatomy Ontology lists: Human Developmental Anatomy Ontology abstract version 1 lists: G Protein-Coupled Receptor BioAssays Ontology lists: Galen Ontology lists: Gene Expression Ontology lists: Gene Ontology Extension lists: General Formal Ontology lists: General Formal Ontology for Biology lists: Genome Component Ontology lists: Genomic Clinical Decision Support Ontology lists: GeoSpecies Ontology lists: Glycomics Ontology lists: Habronattus Courtship Ontology lists: Health Indicator Ontology lists: Health Level Seven Reference Implementation Model Version 3 lists: Human Developmental Anatomy Ontology abstract version 2 lists: Human Developmental Anatomy Ontology timed version lists: Human Interaction Network Ontology lists: Human Physiology Simulation Ontology lists: Logical Observation Identifier Names and Codes lists: IMGT-ONTOLOGY lists: Image and Data Quality Assessment Ontology lists: Immune Disorder Ontology lists: Infectious Disease Ontology lists: InterNano Nanomanufacturing Taxonomy lists: Interaction Network Ontology lists: International Classification of External Causes of Injuries lists: International Classification of Diseases Version 10 lists: International Classification of Diseases Version 10 - Clinical Modification lists: International Classification of Diseases Version 10 - Procedure Coding System lists: MR dataset acquisition lists: Maize Gross Anatomy Ontology lists: Major Histocompatibility Complex Ontology lists: Medical image simulation lists: Menelas Project Top-Level Ontology lists: Mental State Assessment lists: Metagenome Sample Vocabulary lists: Metagenome and Microbes Environmental Ontology lists: MicroRNA Ontology lists: Microbial Culture Collection Vocabulary lists: Microbial Typing Ontology lists: Minimal Information about any Sequence Controlled Vocabularies lists: Minimal Information about any Sequence Ontology lists: NIF Dysfunction Ontlogy lists: NIF Subcellular Ontology lists: NMR-Instrument Component of Metabolomics Investigations Ontology lists: Name Reaction Ontology lists: NanoParticle Ontology lists: National Cancer Institute Thesaurus lists: National Drug Data File lists: National Drug File - Reference Terminology lists: Natural Products Ontology lists: Neglected Tropical Disease Ontology lists: Neomark Oral Cancer Ontology version 3 lists: Neomark Oral Cancer Ontology version 4 lists: Neural Motor Recovery Ontology lists: NeuroMorpho.Org species ontology lists: NeuroMorpho.Org species ontology old lists: Non-Randomized Controlled Trials Ontology lists: Nursing Care Coordination Ontology lists: Ontological Knowledge Base Model for Cystic Fibrosis lists: Ontology for Drug Discovery Investigations lists: Ontology for General Medical Science lists: Ontology for Genetic Disease Investigations lists: Ontology for Genetic Susceptibility Factor lists: Ontology for MicroRNA Target Prediction lists: Symptom Ontology lists: Ontology for Newborn Screening Follow-up and Translational Research lists: Ontology of Alternative Medicine French lists: Ontology of Biological and Clinical Statistics lists: Ontology of Clinical Research lists: Ontology of Core Data Mining Entities lists: Ontology of Data Mining Investigations lists: Pediatric Terminology lists: Ontology of Experimental Variables and Values lists: Ontology of General Purpose Datatypes lists: Ontology of Geographical Region lists: Ontology of Glucose Metabolism Disorder lists: Ontology of Homology and Related Concepts in Biology lists: Ontology of Language Disorder in Autism lists: Orphanet Rare Disease Ontology lists: Parasite Experiment Ontology lists: Pathogen Transmission Ontology lists: Pathogenic Disease Ontology lists: Pharmacogenomic Relationships Ontology lists: Physico-Chemical Methods and Properties lists: Plant Anatomy lists: Syndromic Surveillance Ontology lists: Plant Structure Development Stage lists: Portfolio Management Application lists: Protein Modification Ontology lists: Protein-Protein Interaction Ontology lists: Proteomics Data and Process Provenance Ontology lists: Provenance Ontology lists: QUDT lists: Quantitative Imaging Biomarker Ontology lists: Radiology Lexicon lists: Robert Hoehndorf Version of MeSH lists: Role Ontology lists: STATistics Ontology lists: Sage Bionetworks Synapse Ontology lists: Sample Processing and Separation Techniques Ontology lists: Santa Barbara Coastal Observation Ontology lists: Semantic Types Ontology lists: Semantic Web for Earth and Environment Technology Ontology lists: Semanticscience Integrated Ontology lists: Single-Nucleotide Polymorphism Ontology lists: Situation-Based Access Control Ontology lists: Taxonomic Rank Vocabulary lists: Taxonomy for Rehabilitation of Knee Conditions lists: Terminological and Ontological Knowledge Resources Ontology lists: Tick Gross Anatomy Ontology lists: Tissue Microarray Ontology lists: Traditional Medicine Constitution Value Set lists: Traditional Medicine Meridian Value Sets lists: Traditional Medicine Other Factors Value Set lists: Traditional Medicine Signs and Symptoms Value Set lists: Translational Medicine Ontology lists: Tribolium Ontology lists: Units Ontology lists: Units of Measurement Ontology lists: Upper-Level Cancer Ontology lists: Vertebrate Homologous Organ Group Ontology lists: Veterans Health Administration National Drug File lists: Vital Sign Ontology lists: WHO Adverse Reaction Terminology lists: Web-Service Interaction Ontology lists: Wheat Trait Ontology lists: XEML Environment Ontology lists: suicideo lists: suicideonto lists: Pseudogene lists: Terminology for the Description of Dynamics lists: Gene Regulation Ontology lists: UBERON lists: CHEBI lists: Cognitive Paradigm Ontology lists: Emotion Ontology lists: Clinical Measurement Ontology lists: Measurement Method Ontology lists: NCI Thesaurus lists: Ontology for Biomedical Investigations lists: Biological Pathways Exchange is listed by: Biositemaps is listed by: FORCE11 is related to: Provisional Cell Ontology has parent organization: National Center for Biomedical Ontology has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Biomedical Informatics Research is parent organization of: NCBO Annotator |
NIGMS U24 GM143402 | PMID:19483092 PMID:21672956 PMID:18999306 |
Free, Available for download, Freely available | nif-0000-23346, r3d100012344 | https://www.force11.org/node/4646 https://doi.org/10.17616/R3J362 |
SCR_002713 | BioPortal Knowledgebase | 2026-02-17 09:59:50 | 328 | ||||
|
3D-Interologs Resource Report Resource Website |
3D-Interologs (RRID:SCR_003101) | 3D-interologs | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins. | interolog, protein-protein interaction, blast, homolog, protein, interaction, function |
is related to: IntAct is related to: UniProt is related to: Gene Ontology has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:21143789 | Resource:OMICtools, Resource:UniProt | nif-0000-00554, OMICS_01896 | https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-S3-S7 | SCR_003101 | 2026-02-17 10:00:04 | 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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
