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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | Plant Natural Antisense Transcripts DataBase | 2026-09-03 04:52:16 | 9 | ||||
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L2L Microarray Analysis Tool Resource Report Resource Website 1+ mentions |
L2L Microarray Analysis Tool (RRID:SCR_013440) | L2L | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, data repository, database, production service resource, service resource, software application, software resource, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019. Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible |
microarray, gene expression, adipogenesis, biological, biological process, cancer, cell cycle regulator, cellular component, chromatin, cockayne syndrome, dna damage, growth factor, hormone, human biology, hypoxic response, immune mediator, inflammatory mediator, molecular function, molecular neuroanatomy resource, adipocyte, development, hypoxia, immune, inflammation, metabolism, mitogen, neuro, rna, vascular, transcription, tissue, splicing, mouse, human, rat, source code, statistical analysis, gene, chromatin structure |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Washington; Seattle; USA |
Cockayne syndrome, DNA damage, Other, Aging, Cancer | Cora May Poncin Foundation ; NIGMS GM41624 |
PMID:16168088 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10463 | http://depts.washington.edu/l2l/about.html | SCR_013440 | L2L Microarray Database, L2L Microarray Analysis Tool: A simple tool for discovering the hidden biological significance in microarray expression data, L2L MDB | 2026-09-03 04:52:00 | 1 | |||
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PiGenome Resource Report Resource Website |
PiGenome (RRID:SCR_013394) | PiGenome | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6. | gene expression, genome, sequence, gene, expressed sequence tag, consensus sequence, bac clone, bac end sequence, bac contig, quantitative trait loci, singleton, marker, unigene, chromosome 6, blast, transcript, bacterial artificial chromosome, snp, alignment |
is related to: Gene Ontology has parent organization: National Institute of Animal Science; Gyeonggi-do; South Korea |
National Institute of Animal Science; Gyeonggi-do; Korea ; Korean Rural Development Administration ; Biogreen21 Project 20050301034467 |
PMID:19082661 | nlx_153888 | http://pigenome.nabc.go.kr/ | SCR_013394 | Sus scrofa Genome database, Pig Genome Database, Pigenome database | 2026-09-03 04:51:58 | 0 | |||||
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KOBAS Resource Report Resource Website 5000+ mentions |
KOBAS (RRID:SCR_006350) | KOBAS | analysis service resource, data analysis service, production service resource, service resource, software resource | Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ortholog, pathway, disease, gene, protein, annotation, command line, FASEB list |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: OMIM is related to: Pathway Interaction Database is related to: BioCarta Pathways is related to: Reactome is related to: BioCyc is related to: PANTHER is related to: FunDO is related to: Genetic Association Database is related to: GWAS: Catalog of Published Genome-Wide Association Studies has parent organization: Peking University; Beijing; China |
PMID:21715386 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02228 | SCR_006350 | KEGG Orthology Based Annotation System | 2026-09-03 04:48:57 | 5008 | ||||||
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MGI GO Browser Resource Report Resource Website 1+ mentions |
MGI GO Browser (RRID:SCR_006489) | MGI GO Browser | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | With the MGI GO Browser, you can search for a GO term and view all mouse genes annotated to the term or any subterms. You can also browse the ontologies to view relationships between terms, term definitions, as well as the number of mouse genes annotated to a given term and its subterms. The MGI GO browser directly accesses the GO data in the MGI database, which is updated nightly. Platform: Online tool | gene, ontology, browser, molecular function, biological process, cellular component, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Mouse Genome Informatics (MGI) |
Free for academic use | nlx_149104 | SCR_006489 | 2026-09-03 04:49:02 | 8 | ||||||||
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Gene Ontology For Functional Analysis (GOFFA) Resource Report Resource Website 1+ mentions |
Gene Ontology For Functional Analysis (GOFFA) (RRID:SCR_006484) | GOFFA | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Software tool developed for ArrayTrack that takes a list of genes and identifies terms in Gene Ontology associated with those genes. GOFFA provides tools to view/access the following: GO term hierarchy, full listing of GO terms annotated with the genes associated with a given term, Fisher's exact test p-value providing the probability of identifying that many genes for a given term by chance alone, and relative enrichment factor (E-value) giving the enrichment of a GO term for genes in the submitted list relative to the frequency of genes assigned to that term from the full set of GOFFA annotated genes for a particular species. | gene ontology, proteomic, visualization, fisher's exact test, browser, search engine, term enrichment, text mining, ontology browser, annotation browser, ontology visualization, annotation visualization, database, data warehouse, software, identify term |
is used by: ArrayTrack is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: National Center for Toxicological Research |
PMID:17118145 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149101 | http://edkb.fda.gov/webstart/arraytrack/ | SCR_006484 | Gene Ontology For Functional Analysis | 2026-09-03 04:48:29 | 9 | |||||
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Mouse Genome Informatics: The Gene Ontology Project Resource Report Resource Website 10+ mentions |
Mouse Genome Informatics: The Gene Ontology Project (RRID:SCR_006447) | controlled vocabulary, data or information resource, database | This resource is part of the Gene Ontology Consortium which seeks to provide controlled vocabularies for the description of the molecular function, biological process, and cellular component of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them. GO team members at MGI participate in ontology development, outreach, and functional curation of mouse gene products. The GO vocabularies have a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low level, highly specific terms. This broad range is useful both in annotating genes and in searching for gene information using these terms as search criteria. GO terms are defined, allowing all databases to use the terms consistently and properly. GO annotations in the databases additionally include the publication reference which allowed the association to be made and an evidence statement citing how the association was determined. | function, gene, biological, cellular, component, molecular, process, product |
is affiliated with: Gene Ontology has parent organization: Jackson Laboratory |
NHGRI HG002273 | Available to the research community | nif-0000-10304 | SCR_006447 | Gene Ontology (GO) Project, MGI: GO Project, Gene Ontology Project | 2026-09-03 04:48:30 | 14 | |||||||
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Ontology Lookup Service Resource Report Resource Website 10+ mentions |
Ontology Lookup Service (RRID:SCR_006596) | OLS | data access protocol, data or information resource, database, software resource, source code, web service | Interactive and programmatic interfaces to query, browse and navigate an increasing number of biomedical ontologies and controlled vocabularies. It provides a web service interface to query multiple ontologies from a single location with a unified output format. It can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A weekly MySQL database export file can be downloaded from the EBI public FTP directory. | ontology, ontology or annotation browser, ontology or annotation search engine, gold standard |
lists: Cell Type Ontology is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: OBO-Edit is related to: OBO has parent organization: European Bioinformatics Institute |
BBSRC ; iSPIDER ; European Union FP6 Felics contract 021902 (RII3) |
PMID:18467421 PMID:16507094 |
Apache License, v2, Acknowledgement requested | OMICS_02275, nif-0000-10390, r3d100010413 | https://doi.org/10.17616/R3GS9G | http://www.ebi.ac.uk/ols | SCR_006596 | OLS - Ontology Lookup Service, Ontology Lookup Service (OLS) | 2026-09-03 04:48:50 | 24 | |||
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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 | 2026-09-03 04:48:52 | 1 | ||||
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InnateDB Resource Report Resource Website 500+ mentions |
InnateDB (RRID:SCR_006714) | InnateDB | data or information resource, database | Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice. | gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resource, FASEB list |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: PSICQUIC Registry is related to: Gene Ontology is related to: IntAct has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada works with: IMEx - The International Molecular Exchange Consortium |
Microbial infection, Allergy, Asthma | Michael Smith Foundation for Health Research ; AllerGen 12ASI1; AllerGen 12B&B2; Teagasc RMIS6018; European Union PSIMEx project contract FP7-HEALTH-2007-223411 |
PMID:23180781 PMID:18766178 |
Free, Freely available | nif-0000-20808, r3d100010676 | https://doi.org/10.17616/R36S43 | SCR_006714 | A Knowledge Resource for Innate Immunity Interactions and Pathways, InnateDB: Systems Biology of the Innate Immune Response, InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways | 2026-09-03 04:48:44 | 571 | |||
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canSAR Resource Report Resource Website 50+ mentions |
canSAR (RRID:SCR_006794) | canSAR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data. | molecular target, expression, cell line, compound, molecule, protein, structure, ligand, drug, 3d, genomics, 3d complex, bioactivity, protein affinity, cell line sensitivity, pathway, annotation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BindingDB is related to: Gene Ontology has parent organization: Cancer Research UK |
Cancer | Cancer Research UK C309/A8274 | PMID:22013161 | CanSAR is freely available to all cancer researchers. By using canSAR you are agreeing to the Terms of Use, Https://cansar.icr.ac.uk/cansar/terms-of-use/ | biotools:cansar, nlx_149410 | https://bio.tools/cansar | SCR_006794 | 2026-09-03 04:48:48 | 56 | ||||
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Alliance of Genome Resources Resource Report Resource Website 50+ mentions |
Alliance of Genome Resources (RRID:SCR_015850) | access service resource, consortium, data or information resource, organization portal, portal, service resource | Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN). | gene ontology, human biology, genome, organism model, gene ontology consortium, FASEB list, DRKB |
has organization facet: WormBase has organization facet: Mouse Genome Databases has organization facet: FlyBase has organization facet: Gene Ontology has organization facet: SGD has organization facet: Rat Genome Database (RGD) has organization facet: Zebrafish Information Network (ZFIN) |
NHGRI U41HG02223E; NIH HG010859 |
SCR_015850 | The Alliance | 2026-09-03 04:53:36 | 87 | |||||||||
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GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, service resource, software resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626; NIGMS ; NIH Common Fund |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-09-03 04:55:19 | 7 | |||||||
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Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | 2026-09-03 04:51:26 | 0 | |||||||
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MEME Suite - Motif-based sequence analysis tools Resource Report Resource Website 1000+ mentions |
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) | MEME Suite | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code | Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. | gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list |
lists: DREME is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Glam2 is related to: ANNOgesic is related to: memesuite-lite has parent organization: National Biomedical Computation Resource is parent organization of: GOMO - Gene Ontology for Motifs |
NCRR R01 RR021692 | PMID:19458158 DOI:10.1093/nar/gkl198 |
Free, Freely available | nif-0000-10298, biotools:meme_suite, OMICS_08103 | https://bio.tools/meme_suite | http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ | SCR_001783 | The MEME Suite | 2026-09-03 04:44:56 | 2472 | |||
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AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium. | search, sort, analyze, visualize, data, ontology, gene, annotation, FASEB list |
uses: GOlr is used by: NIF Data Federation is listed by: OMICtools is listed by: Gene Ontology Tools is related to: ASAP is related to: Candida Genome Database is related to: Berkeley Bioinformatics Open-Source Projects is related to: ECO is related to: Zebrafish Information Network (ZFIN) is related to: Gramene is related to: WormBase is related to: NCBI Protein Database is related to: UniProtKB is related to: GeneDB Lmajor is related to: TAIR is related to: SGD is related to: GeneDB Tbrucei is related to: VMD is related to: JCVI CMR is related to: go-db-perl is related to: Mouse Genome Informatics (MGI) is related to: NCBI is related to: FlyBase is related to: GeneDB Pfalciparum is related to: PomBase is related to: Pseudomonas Genome Database is related to: Dictyostelium discoideum genome database is related to: Plant Ontology is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: MeGO is related to: ASPGD is related to: EcoCyc is related to: Reactome is related to: SGN is related to: GO-Module is related to: Songbird Brain Transcriptome Database is related to: Rat Genome Database (RGD) is related to: RamiGO has parent organization: Gene Ontology |
NHGRI P41 HG002273 | PMID:19033274 | Free, Available for download, Freely available | OMICS_02266, nif-0000-20935 | http://sourceforge.net/projects/geneontology/ | SCR_002143 | GO Consortium, AmiGO, AmiGO 2, AmiGene Ontology, Gene Ontology Database, Gene Ontology Consortium, GO Database, The Gene Ontology Consortium | 2026-09-03 04:45:12 | 1285 | ||||
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GoMiner Resource Report Resource Website 100+ mentions |
GoMiner (RRID:SCR_002360) | GoMiner | data processing software, software application, software resource | GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches. | experiment, expression, function, gene, genomics, biological, genomic, microarray, omic, process, gene expression, gene ontology, biological process, biological function, biological component, proteomic, database, FASEB list |
is related to: Gene Ontology is related to: High-Throughput GoMiner has parent organization: Georgia Institute of Technology; Georgia; USA has parent organization: Emory University; Georgia; USA has parent organization: National Cancer Institute |
NCI ; Georgia Institute of Technology; Georgia; USA ; Emory University; Georgia; USA |
PMID:12702209 | nif-0000-21181 | SCR_002360 | 2026-09-03 05:00:33 | 115 | |||||||
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FIVA - Functional Information Viewer and Analyzer Resource Report Resource Website 1+ mentions |
FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) | FIVA | data processing software, software application, software resource | Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: MolGen |
Netherlands Organization for Scientific Research ; industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes ; Center IOP Genomics ; European Union QLK3-CT-2001-01473 |
PMID:17237043 | Free for academic use | nlx_149245 | SCR_005776 | FIVA - Functional Information Viewer Analyzer, Functional Information Viewer and Analyzer (FIVA), Functional Information Viewer and Analyzer | 2026-09-03 04:59:55 | 1 | |||||
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GoBean - a Java application for Gene Ontology enrichment analysis Resource Report Resource Website 10+ mentions |
GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) | GoBean | data processing software, software application, software resource | GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible | java, gene ontology, ontology, gene association, analysis, enrichment, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Gachon University of Medicine and Science; Incheon; South Korea |
PMID:22360891 | Free for academic use | nlx_149296 | http://neon.gachon.ac.kr/GoBean/ | SCR_005808 | 2026-09-03 04:59:38 | 22 | ||||||
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NIF Data Federation Resource Report Resource Website 10+ mentions |
NIF Data Federation (RRID:SCR_004834) | Data Federation | data or information resource, portal, service resource | Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below. | semantics, neuroscience, animal, annotation, antibody, biospecimen, brain activation foci, clinical trial, connectivity, dataset, disease, drug, grant, image, microarray, model, multimedia, negative data, pathway, people, plasmid, registry, software, brain region, cell, gene, molecule, multi-level, nervous system, nervous system function, model |
uses: MNI Podcasts uses: Educational Resources in Neuroscience uses: Mind Hacks uses: BAMS Nested Regions uses: Indeed uses: NINDS Disorder Index uses: Drug Design Data Resource uses: PubMed Health uses: This Week In Science uses: Science Talk uses: BAMS Connectivity uses: Lady Scientist uses: Psychology Corner uses: Wired Science uses: CENtral Science uses: RetractionWatch.com uses: The Guardian: Science Weekly uses: H2SO4Hurts uses: 60-Second Mind uses: PLoS Blogs uses: Clarity resources uses: Open Source Brain uses: Diabetic Complications Consortium uses: Integrated Animals uses: Kawasaki Disease Dataset uses: EEGbase uses: Integrated Models uses: Lifespan Observations Database uses: NIF Web Services uses: NIF Blog uses: ATCC uses: Cerebellar Platform uses: Brain Machine Interface Platform uses: Rafael Yustes Laboratory uses: ASAP uses: NIH VideoCasting uses: NIDA Data Share uses: Neurofed uses: Candida Genome Database uses: Addgene uses: ASPGD uses: Glomerular Activity Response Archive uses: WikiPathways uses: AmiGO uses: NeuroMorpho.Org uses: Cell Centered Database uses: Integrated uses: Community Structure-Activity Resource uses: ClinicalTrials.gov uses: Ensembl uses: GeneNetwork uses: Avian Brain Circuitry Database uses: EcoCyc uses: Entrez Gene uses: Zebrafish Information Network (ZFIN) uses: Arredondo ANT fNIRS dataset1 uses: Grants.gov uses: T3DB uses: Simtk.org uses: PharmGKB uses: DrugBank uses: Aging Genes and Interventions Database uses: Gene Expression Nervous System Atlas uses: SumsDB uses: bioDBcore uses: BioNumbers uses: Gene Ontology uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Gramene uses: Retina Project uses: HomoloGene uses: ArrayExpress uses: Journal of Visualized Experiments uses: Allen Mouse Brain Reference Atlas uses: Gene Weaver uses: Visiome Platform uses: Developmental Therapeutics Program uses: NeuroMab uses: WormBase uses: NeuronDB uses: Integrated Grants uses: studyforrest.org uses: BrainInfo uses: Mouse Phenome Database (MPD) uses: NCBI Taxonomy uses: NCBI Protein Database uses: Psychoactive Drug Screening Program Ki Database uses: Nuclear Receptor Signaling Atlas uses: Brede Database uses: NeuroImaging Tools and Resources Collaboratory (NITRC) uses: Mouse Genome Informatics Transgenes uses: Reactome uses: Cell Image Library (CIL) uses: BAMS Cells uses: Synapse Web uses: Integrated Videos uses: NeuroVault uses: Royal College of Psychiatrists Podcasts uses: WU-Minn HCP 500 Subjects MR and MEG Release uses: Data.gov Science and Research Data Catalog uses: NITRC-IR uses: One Mind Biospecimen Bank Listing uses: Integrated Brain Gene Expression uses: BrainSpan uses: All In The Mind uses: Scientific American Cross-Check uses: PubChem uses: NeuroPod uses: BrainSpan uses: Health.Data.gov uses: Biointeractive uses: UniProtKB uses: Gray Matters uses: dkCOIN uses: Brain Science Podcast uses: NIGMS Human Genetic Cell Repository uses: DISCO uses: GeneDB Lmajor uses: TAIR uses: ScienceNOW uses: Daily Scan uses: SGD uses: Integrated Software uses: BrainPod uses: GeneDB Tbrucei uses: MPO uses: PANTHER uses: Neurology Podcast uses: Integrated Disease uses: VMD uses: UCSF Laboratory for Visual Neuroscience uses: NIMH Chemical Synthesis and Drug Supply Program uses: NIH Neuroscience Microarray Consortium uses: SGN uses: Protocol Online - Your labs reference book uses: Integrated Podcasts uses: OpenNeuro uses: National Academy of Sciences Podcasts uses: Beta Cell Biology Consortium uses: Naturejobs uses: Scientific American Guest Blog uses: jobs.ac.uk uses: New Scientist Jobs uses: Science Careers uses: Access-ScienceJobs.co.uk uses: ScienceBlogs: Life Science uses: ScienceBlogs: Brain and Behavior uses: TheScienceJobs.com uses: Nature Network Blogs uses: The Guardian: Science uses: LabSpaces uses: ScienceBlogs: Medicine and Health uses: Scientific American Observations uses: Scientific American Bering in Mind uses: QUEST uses: Daring Nucleic Adventures - genegeek uses: Oxford Science Blog uses: Sciblogs uses: New York Times - Well uses: SciLogs uses: Cassandras Tears uses: BioPortfolio uses: Now at NEJM uses: 1000 Functional Connectomes Project uses: Integrated Jobs uses: Integrated Blogs uses: JCVI CMR uses: SciCrunch Registry uses: Neuroskeptic uses: CRCNS uses: Expression Atlas of the Marmoset uses: IXI dataset uses: Integrated Auto-Extracted Annotation uses: EU Clinical Trials Register uses: Integrated Clinical Trials uses: Human Brain Atlas uses: goCognitive uses: Law and Neuroscience uses: International Mouse Phenotyping Consortium (IMPC) uses: ClinVar uses: Integrated Gene-Disease Interaction uses: XNAT Central uses: neuroelectro uses: Integrated Nervous System Connectivity uses: Antibody Registry uses: OMIA - Online Mendelian Inheritance in Animals uses: OMIM uses: Science Podcast uses: Mouse Genome Informatics (MGI) uses: Monster uses: NCBI uses: Wired Science Blogs uses: F1000 Posters uses: Neurophilosophy uses: Comparative Toxicogenomics Database (CTD) uses: FlyBase uses: GeneReviews uses: GeneDB Pfalciparum uses: Naturally Selected uses: PomBase uses: Pseudomonas Genome Database uses: The Guardian: Science Videos uses: Orphanet uses: Dictyostelium discoideum genome database uses: PeptideAtlas uses: NeuroSynth uses: neuropathology blog uses: Genomes Unzipped uses: National Institutes of Health Research Portfolio Online Reporting Tool uses: BrainMaps.org uses: It Takes 30 uses: Gait in Parkinson's Disease uses: Physiobank uses: Gait Dynamics in Neuro-Degenerative Disease Data Base uses: American Journal of Psychiatry Podcasts uses: Neurodatabase.org uses: Brain Architecture Management System uses: RanchoBiosciences uses: ModelDB uses: CoCoMac uses: Olfactory Bulb Odor Map DataBase (OdorMapDB) uses: Gene Expression Omnibus uses: Caenorhabditis Genetics Center uses: Labome uses: Open Access Series of Imaging Studies uses: Biological General Repository for Interaction Datasets (BioGRID) uses: Olfactory Receptor DataBase uses: T1DBase uses: Gemma uses: CellML Model Repository uses: ResearchCrossroads uses: Biocompare uses: BioNOT uses: Hays uses: Research Blogging uses: Discover Magazine uses: PolygenicBlog uses: Kawasaki Disease Dataset2 uses: Allen Mouse Brain Connectivity Atlas uses: Integrated Manually Extracted Annotation uses: Roadmap Epigenomics Project uses: Integrated Cell Lines uses: National Mouse Metabolic Phenotyping Centers uses: Mendelspod uses: Integrated Snippets uses: Integrated Datasets uses: Nature Podcast uses: GWAS: Catalog of Published Genome-Wide Association Studies uses: KEGG uses: USC Multimodal Connectivity Database uses: Inside NIA: A Blog for Researchers uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: NIF Registry Automated Crawl Data uses: Genetic Analysis Software uses: anage uses: Intestinal Stem Cell Consortium uses: Animal QTLdb uses: elements of morphology uses: Human Life-Table Database uses: Clinical Genomic Database uses: NIDDK Central Repository uses: MONARCH Initiative uses: Human Phenotype Ontology is used by: SciCrunch is used by: NIDDK Information Network (dkNET) lists: AutDB lists: Drug Related Gene Database lists: Gene Ontology Tools lists: CHEBI is listed by: 3DVC is related to: International Mouse Strain Resource is related to: Internet Brain Volume Database is related to: Resource Identification Portal is related to: Rat Genome Database (RGD) is related to: VISTA Enhancer Browser is related to: NIH Human Pluripotent Stem Cell Registry is related to: Zebrafish International Resource Center is related to: Bloomington Drosophila Stock Center is related to: Journal of Comparative Neurology Antibody database has parent organization: Neuroscience Information Framework |
NIDA ; NIH Blueprint for Neuroscience Research ; U.S. Department of Health and Human Services HHSN27120080035C |
Refer to individual databases | nlx_81822 | http://neuinfo.org/nif/nifgwt.html?query=* | SCR_004834 | Neuroscience Information Framework Data Federation | 2026-09-03 04:59:53 | 28 |
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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.
