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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | data repository, data or information resource, database, storage service resource, service resource | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-08-03 09:31:37 | 8 | ||||
|
Cardiovascular Gene Ontology Annotation Initiative Resource Report Resource Website 1+ mentions |
Cardiovascular Gene Ontology Annotation Initiative (RRID:SCR_004795) | CV-GO, BHF-UCL | data or information resource, data set | Full Gene Ontology annotation to genes associated with cardiovascular processes. Every GO annotation made, is attributed to an identified source, such as a publication identifier (PMID), and an indication of the type of evidence which supports the association between the gene product and the GO term. Over 4,000 cardiovascular associated genes have been identified. A variety of tools have been provided to enable cardiovascular scientists to review the annotation of their ''''favorite'''' gene and suggest information that may be missing, inaccurate or incomplete in these annotations. Annotation suggestions can be sent through the feedback form or by email. The Gene Ontology (GO) vocabulary is the established standard for the functional annotation of gene products. By using GO to curate scientific literature and by integrating results from high-quality high-throughput experiments they will create an information-rich resource for the cardiovascular-research community, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research. | cardiovascular process, heart disease, cardiovascular, heart, cardiovascular system, annotation, gene, functional annotation, gene product, gold standard |
is related to: Gene Ontology is related to: IntAct has parent organization: University College London; London; United Kingdom |
British Heart Foundation SP/07/007/23671 | PMID:21419760 PMID:19046747 |
The community can contribute to this resource | nlx_79058 | http://www.ebi.ac.uk/GOA/CVI/ | SCR_004795 | Cardiovascular Gene Ontology, Cardiovascular GO Annotation Initiative | 2026-08-03 09:32:44 | 2 | ||||
|
ONTO-PERL Resource Report Resource Website |
ONTO-PERL (RRID:SCR_005731) | ONTO-PERL | software resource, source code | ONTO-PERL is a collection of Perl modules to handle OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), and a set of test files to ensure the suite''''s implementation quality. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | application programming interface, software library, ontology, analysis, development, biomedical |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: Comprehensive Perl Archive Network has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
European Union FP6 LSHG-CT-2004-512143; European Union FP6 MEST-CT-2004-414632 |
PMID:18245124 | Free for academic use | nlx_149191 | SCR_005731 | 2026-08-03 09:32:46 | 0 | ||||||
|
RefGenome Resource Report Resource Website 1+ mentions |
RefGenome (RRID:SCR_004263) | RefGenome | data or information resource, data set | The GO Consortium coordinates an effort to maximize and optimize the GO annotation of a large and representative set of key genomes, known as ''reference genomes''. The goal of the Reference Genome Annotation project is to completely annotate twelve reference genomes so that those annotations may be used to effectively seed the automatic annotation efforts of other genomes. With more and more genomes being sequenced, we are in the middle of an explosion of genomic information. The limited resources to manually annotate the growing number of sequenced genomes imply that automatic annotation will be the method of choice for many groups. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO''s logical structure and biological content. All GO annotations from this project are included in the gene association files that each group submits to GO. Annotations can also be viewed using the GO search engine and browser AmiGO. Annotated families can be viewed with the homolog set browser. | has parent organization: Gene Ontology | PMID:19578431 | nlx_27840 | SCR_004263 | Reference Genome Annotation Project, Reference Genome Project | 2026-08-03 09:32:38 | 7 | ||||||||
|
GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | data analysis service, service resource, analysis service resource, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results. | annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarray, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:15980570 PMID:15215397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149256, biotools:gfinder | https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538, https://bio.tools/gfinder | SCR_008868 | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-08-03 09:33:58 | 1 | |||||
|
Integrated Manually Extracted Annotation Resource Report Resource Website |
Integrated Manually Extracted Annotation (RRID:SCR_008876) | Integrated MEA, Integrated LinkOut, Manually Extracted Annotation, | data or information resource, database | A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org | biomedical, bibliographic, linkout, literature |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Gene Ontology Tools is related to: BAMS Connectivity is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: BioNumbers is related to: PubMed is related to: Brain Architecture Management System is related to: CellML Model Repository is related to: CHEBI is related to: Comparative Toxicogenomics Database (CTD) is related to: Coriell Cell Repositories is related to: Drug Related Gene Database is related to: DrugBank is related to: Gene Weaver is related to: Internet Brain Volume Database is related to: Cell Centered Database is related to: Brede Database is related to: ModelDB is related to: NeuronDB is related to: NeuroMorpho.Org is related to: Nuclear Receptor Signaling Atlas is related to: Cell Image Library (CIL) is related to: Animal Imaging Database is related to: Olfactory Receptor DataBase is related to: Glomerular Activity Response Archive is related to: CRCNS is related to: OMIM is related to: Rat Genome Database (RGD) is related to: Visiome Platform is related to: NIDA Data Share is related to: bioDBcore is related to: Addgene is related to: Antibody Registry is related to: Beta Cell Biology Consortium is related to: FlyBase is related to: SumsDB is related to: SciCrunch Registry is related to: Mouse Genome Informatics Transgenes is related to: NCBI Taxonomy is related to: OpenNeuro is related to: PeptideAtlas is related to: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat is related to: NIF Registry Automated Crawl Data is related to: AutDB is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: Avian Brain Circuitry Database is related to: Zebrafish Information Network (ZFIN) is related to: GeneDB is related to: WormBase is related to: YPED has parent organization: Integrated |
PMID:20387131 PMID:18975149 |
Data are licensed by their respective owners. Use and distribution is subject to the Terms of Use by the original resource as well as the, Creative Commons Attribution License | nlx_149407 | http://neuinfo.org/nif/nifgwt.html?query=nlx_149407, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_149407-1 | SCR_008876 | Integrated Manually Extracted Annotation View, NIF Integrated LinkOut, NIF Integrated Manually Extracted Annotation, NIF LinkOut | 2026-08-03 09:34:14 | 0 | |||||
|
SwissLipids Resource Report Resource Website 10+ mentions |
SwissLipids (RRID:SCR_019074) | data or information resource, database | Expert curated resource that provides framework for integration of lipid and lipidomic data with biological knowledge and models. Provides curated knowledge of lipid structures and metabolism which is used to generate in silico library of feasible lipid structures. These are arranged in hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. Provides reference namespace for lipidomic data publication, data exploration and hypothesis generation. | Lipid, lipidomic data, curated lipid data, lipid structure, lipid metabolism, mass spectrometry analytical output, refernce namespace, lipidomic data publication, hypothesis generation |
uses: UniProt uses: CHEBI uses: RHEA uses: Gene Ontology |
Swiss Federal Government ; SystemsX.ch |
DOI:10.1093/bioinformatics/btv285 | Free, Freely available | r3d100012603 | https://doi.org/10.17616/R3TZ18 | SCR_019074 | 2026-08-03 09:37:09 | 16 | ||||||
|
Onto-Design Resource Report Resource Website |
Onto-Design (RRID:SCR_000601) | Onto-Design | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool | microarray, gene, biological process, molecular function, cellular component, data-mining, browser, visualization, analysis, design, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, design custom microarrays based on go terms of interest |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149109 | SCR_000601 | 2026-08-03 09:31:05 | 0 | |||||||
|
ECgene: Gene Modeling with Alternative Splicing Resource Report Resource Website 10+ mentions |
ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) | ECgene | data or information resource, database | Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. | est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snp |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:17132829 PMID:15805497 PMID:15608289 |
nif-0000-02780, OMICS_01884 | http://genome.ewha.ac.kr/ECgene/ | SCR_007634 | ECgene - Genome Annotation for Alternative Splicing | 2026-08-03 09:33:27 | 12 | ||||||
|
GORetriever Resource Report Resource Website 10+ mentions |
GORetriever (RRID:SCR_005633) | GORetriever | data analysis service, service resource, analysis service resource, production service resource | GORetriever is used to find all of the GO annotations corresponding to a list of user-supplied protein identifiers. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. Platform: Online tool | gene, annotation, protein, ontology or annotation search engine |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149140 | SCR_005633 | AgBase GORetriever | 2026-08-03 09:32:53 | 13 | |||||
|
FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | data analysis service, service resource, analysis service resource, production service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-08-03 09:32:56 | 36 | |||||
|
MetaGeneProfiler Resource Report Resource Website |
MetaGeneProfiler (RRID:SCR_005794) | MetaGP | data analysis service, service resource, analysis service resource, production service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Meta Gene Profiler (MetaGP) is a web application tool for discovering differentially expressed gene sets (meta genes) from the gene set library registered in our database. Once user submits gene expression profiles which are categorized into subtypes of conditioned experiments, or a list of genes with the valid pvalues, MetaGP assigns the integrated p-value to each gene set by combining the statistical evidences of genes that are obtained from gene-level analysis of significance. The current version supports the nine Affymetrix GeneChip arrays for the three organisms (human, mouse and rat). The significances of GO terms are graphically mapped onto the directed acyclic graph (DAG). The navigation systems of GO hierarchy enable us to summarize the significance of interesting sub-graphs on the web browser. Platform: Online tool | gene, gene expression, differentially expressed, gene ontology, meta gene, gene set, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Institute of Statistical Mathematics; Tokyo; Japan |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149271 | SCR_005794 | Meta Gene Profiler, MetaGeneProfiler on the WEB, Meta Gene Profiler (MetaGP), MetaGeneProfiler on the WEB - Web service for significance test of differentially-expressed Meta Genes | 2026-08-03 09:32:56 | 0 | |||||||
|
OntoVisT Resource Report Resource Website 1+ mentions |
OntoVisT (RRID:SCR_005674) | OntoVisT | service resource, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. Web based ontological visualization tool for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery. | ontology, visualization, web service, gene ontology, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, dag hierarchical form, dag, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: OBO has parent organization: Jawaharlal Nehru University; New Delhi; India |
Council of Scientific and Industrial Research; New Delhi; India ; Jawaharlal Nehru University; New Delhi; India ; Department of Biotechnology |
PMID:21738333 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02274, nlx_149113 | SCR_005674 | OntoVisT: A General purpose Ontological Visualization Tool | 2026-08-03 09:32:54 | 1 | |||||
|
OntoGate Resource Report Resource Website |
OntoGate (RRID:SCR_005795) | OntoGate | data analysis service, service resource, analysis service resource, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2012. OntoGate provides access to GenomeMatrix (GM) entries from Ontology terms and external datasets which have been associated with ontology terms, to find genes from different species in the GM, which have been mapped to the ontology terms. OntoGate includes a BLAST search of amino acid sequences corresponding to annotated genes. Platform: Online tool | gene, ontology, blast, amino acid sequence, annotation, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
PMID:12824422 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149274 | SCR_005795 | 2026-08-03 09:32:47 | 0 | |||||||
|
WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | data analysis service, service resource, analysis service resource, production service resource | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-08-03 09:32:48 | 386 | ||||
|
REViGO Resource Report Resource Website 1000+ mentions |
REViGO (RRID:SCR_005825) | REViGO | data analysis service, service resource, analysis service resource, production service resource | Web server that summarizes lists of Gene Ontology terms by removing redundant terms and visualizing the remaining ones in scatterplots, interactive graphs, treemaps, or tag clouds. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene ontology, visualization, statistical analysis, ontology or annotation visualization |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Rudjer Boskovic Institute; Zagreb; Croatia |
PMID:21789182 PMID:20585573 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02283, nlx_149332 | SCR_005825 | Reduce + Visualize Gene Ontology, REViGO - Reduce Visualize Gene Ontology, REViGO - Reduce & Visualize Gene Ontology, REViGO - Reduce and Visualize Gene Ontology, REViGO - Reduce + Visualize Gene Ontology | 2026-08-03 09:32:56 | 2299 | ||||||
|
Network Ontology Analysis Resource Report Resource Website 1+ mentions |
Network Ontology Analysis (RRID:SCR_005667) | NOA | data analysis service, service resource, analysis service resource, production service resource | Network Ontology Analysis (NOA) (abbreviated to NOA) is a freely available collection of Gene Ontology tools aiming to analyze functions of gene network instead of gene list. Network rewiring facilitates the function changes between conditions even with the same gene list. Therefore, it is necessary to annotate the specific function of networks by considering the fundamental roles of interactions from the viewpoint of systems biology. NOA is such a novel functional enrichment analysis method capable to handle both dynamic and static networks. The application of NOA in biological networks shows that NOA can not only capture changing functions in rewiring networks but also find more relevant and specific functions in traditional static networks. Platform: Online tool | gene, ontology, ontology or annotation browser, statistical analysis, term enrichment, browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Chinese Academy of Sciences; Beijing; China |
Chief Scientist Program of SIBS 2009CSP002; Knowledge Innovation Program of CAS KSCX2-EW-R-01; NSFC 61072149; NSFC 91029301; NSFC 60873205; NSFC 10801131; NSFC 60970091; Shanghai NSF 11ZR1443100 |
PMID:21543451 | Open unspecified license - Free for academic use | nlx_149105 | SCR_005667 | Network Ontology Analysis (NOA) | 2026-08-03 09:32:54 | 7 | |||||
|
SNPsandGO Resource Report Resource Website 50+ mentions |
SNPsandGO (RRID:SCR_005788) | SNPs&GO | data analysis service, service resource, analysis service resource, production service resource | A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans. | prediction, protein, mutation, disease, single nucleotide polymorphism, bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Bologna; Bologna; Italy |
PMID:19514061 | biotools:snps_go, OMICS_02219 | https://bio.tools/snps_go | SCR_005788 | SNPs and GO | 2026-08-03 09:32:56 | 58 | ||||||
|
OBO-Edit Resource Report Resource Website 10+ mentions |
OBO-Edit (RRID:SCR_005668) | OBO-Edit | software resource, source code, software application | OBO-Edit is an open source, platform-independent application written in Java for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes. The UI components are cleanly separated from the data model and data adapters, so these can be reused in other applications. The oboedit foward-chaining reasoner can also be used independently (for example, for traversing ontology graphs). OBO-Edit uses the OBO format flat file. See the GO wiki, http://wiki.geneontology.org/index.php/OBO-Edit:_Getting_the_Source_Code, for instructions on downloading the source code. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, browser, search engine, visualization, editor, software library, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: OBO is related to: Ontology Lookup Service is related to: Phenote: A Phenotype Annotation Tool using Ontologies has parent organization: Gene Ontology |
PMID:17545183 | Open unspecified license - Free for academic use | nlx_149107 | http://org.geneontology.oboedit | SCR_005668 | OBO-Edit: The OBO Ontology Editor | 2026-08-03 09:32:45 | 21 | |||||
|
Yeast Search for Transcriptional Regulators And Consensus Tracking Resource Report Resource Website 100+ mentions |
Yeast Search for Transcriptional Regulators And Consensus Tracking (RRID:SCR_006076) | YEASTRACT | data or information resource, database | A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database. | yeast, gene, regulatory association, transcription factor, target gene, genomic, transcription regulation, transcription, web service, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SGD is related to: Gene Ontology is related to: Regulatory Sequence Analysis Tools |
Fundacao para a Ciencia e a Tecnologia contract Pest-OE/EQB/LA0023/2011_research line: Systems and Synthetic Biology; Fundacao para a Ciencia e a Tecnologia ERA-IB/0002/2010; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-EIA/111239/2009; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-CCO/118522/2010 |
PMID:24170807 PMID:20972212 PMID:18032429 PMID:16381908 |
Free | nif-0000-03652, OMICS_00547, biotools:yeastract | https://bio.tools/yeastract | SCR_006076 | 2026-08-03 09:32:52 | 120 |
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.
