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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PiGenome Resource Report Resource Website |
PiGenome (RRID:SCR_013394) | PiGenome | data analysis service, analysis service resource, database, production service resource, service resource, data or information 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 | 2026-02-16 09:48:22 | 0 | |||||
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ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | ontology, data or information resource, controlled vocabulary | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/ http://bioportal.bioontology.org/ontologies/ECO |
SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-02-16 09:45:48 | 19 | |||||
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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 | 2026-02-16 09:45:44 | 115 | |||||||
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Pathway Analysis Tool for Integration and Knowledge Acquisition Resource Report Resource Website 1+ mentions |
Pathway Analysis Tool for Integration and Knowledge Acquisition (RRID:SCR_002100) | PATIKA | pathway analysis software, data or information resource, database | The human pathway database which contains different biological entities and reactions and software tools for analysis. PATIKA Database integrates data from several sources, including Entrez Gene, UniProt, PubChem, GO, IntAct, HPRD, and Reactome. Users can query and access this data using the PATIKAweb query interface. Users can also save their results in XML or export to common picture formats. The BioPAX and SBML exporters can be used as part of this Web service. | human, pathway, reaction, database, pathway analysis software, web service, biological entity, biological reaction |
uses: Entrez Gene uses: UniProt uses: PubChem uses: Gene Ontology uses: IntAct uses: HPRD - Human Protein Reference Database uses: Reactome |
PMID:12117798 PMID:14960461 |
THIS RESOURCE IS NO LONGER IS SERVICE. | nif-0000-20882 | http://www.cs.bilkent.edu.tr/~patikaweb/ | SCR_002100 | Pathway Analysis Tool for Integration and Knowledge Acquisition (PATIKA), PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition | 2026-02-16 09:45:40 | 2 | |||||
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Generic GO Term Mapper Resource Report Resource Website 10+ mentions |
Generic GO Term Mapper (RRID:SCR_005806) | GOTermMapper, GO Term Mapper | software application, data processing software, data analysis service, analysis service resource, software resource, production service resource, service resource | The Generic GO Term Mapper finds the GO terms shared among a list of genes from your organism of choice within a slim ontology, allowing them to be binned into broader categories. The user may optionally provide a custom gene association file or slim ontology, or a custom list of slim terms. The implementation of this Generic GO Term Mapper uses map2slim.pl script written by Chris Mungall at Berkeley Drosophila Genome Project, and some of the modules included in the GO-TermFinder distribution written by Gavin Sherlock and Shuai Weng at Stanford University, made publicly available through the GMOD project. GO Term Mapper serves a different function than the GO Term Finder. GO Term Mapper simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, GO Term Finder finds the GO terms significantly enriched in a submitted list of genes. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, gene association, slim ontology, slimmer-type tool, term enrichment, gene annotation, genomics, ontology, process, function, component, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Generic Model Organism Database Project has parent organization: Princeton University; New Jersey; USA |
Free for academic use | nlx_149294, biotools:go_term_mapper | https://bio.tools/go_term_mapper | SCR_005806 | Generic Gene Ontology Term Mapper, Generic Gene Ontology (GO) Term Mapper | 2026-02-16 09:46:41 | 44 | ||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1 https://bio.tools/source |
SCR_005799 | 2026-02-16 09:46:41 | 69 | |||||
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Gene Class Expression Resource Report Resource Website 1+ mentions |
Gene Class Expression (RRID:SCR_005679) | Gene Class | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. Gene Class Expression allows functional annotation of SAGE data using the Gene Ontology database. This tool performs searches in the GO database for each SAGE tag, making associations in the selected GO category for a level selected in the hierarchy. This system provides user-friendly data navigation and visualization for mapping SAGE data onto the gene ontology structure. This tool also provides graphical visualization of the percentage of SAGE tags in each GO category, along with confidence intervals and hypothesis testing. Platform: Online tool | serial analysis of gene expression, functional annotation, annotation, gene expression, tag classification, gene ontology, gene, ontology, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Sao Paulo; Sao Paulo; Brazil |
Center for Cell-Based Therapy/FAPESP ; CNPq |
PMID:16755502 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149119 | http://gdm.fmrp.usp.br/cgi-bin/gc/upload/upload.pl | SCR_005679 | GC Browser, Gene Classification Browser Tool, Gene Class expression: analysis tool of Gene Ontology terms with gene expression data | 2026-02-16 09:46:31 | 1 | ||||
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Onto-Compare Resource Report Resource Website 1+ mentions |
Onto-Compare (RRID:SCR_005669) | Onto-Compare | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool | microarray, gene, ontology, gene expression, data-mining, browser, visualization, analysis, compare, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, compare commercially available microarrays based on go |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:12664686 PMID:15215428 |
Free for academic use | nlx_149108 | SCR_005669 | 2026-02-16 09:46:31 | 1 | |||||||
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Pathbase Resource Report Resource Website 10+ mentions |
Pathbase (RRID:SCR_006141) | Pathbase | web service, controlled vocabulary, image repository, data access protocol, image collection, data repository, database, storage service resource, software resource, ontology, service resource, data or information resource | Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) | histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: Mouse Pathology Ontology |
Lesion, Mutant mouse strain, Inbred mouse strain | North American Hair Research Society ; Ellison Medical Foundation ; European Union QLRI-1999-00320; European Union LSHG-CT-2006-037188; NCI CA089713; NCRR RR17436; NIH AR49288 |
PMID:20587689 PMID:15623888 PMID:14681470 |
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. | biotools:pathbase, nlx_151637 | https://bio.tools/pathbase | SCR_006141 | Pathbase - European mutant mouse pathology database | 2026-02-16 09:46:38 | 11 | |||
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Neurobehavior Ontology Resource Report Resource Website 1+ mentions |
Neurobehavior Ontology (RRID:SCR_006201) | NBO | ontology, data or information resource, controlled vocabulary | An ontology consisting of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending the GO process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms. The prime application of NBO is to provide the vocabulary that is required to integrate behavior observations within and across species. It is currently being applied by several model organism communities as well as in the description of human behavior-related disease phenotypes. The main ontology is available in both the OBO Flatfile Format and the Web Ontology Language (OWL). | obo, neurobehavior, behavior, phenotype, behavioral process, biology, animal, normal, abnormal, owl, genetics |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Gene Ontology |
New BSD License, (Code) | nlx_151745 | http://purl.bioontology.org/ontology/NBO http://behavior-ontology.googlecode.com/svn/trunk/behavior.owl http://bioportal.bioontology.org/ontologies/1621 |
SCR_006201 | Neurobehavior Ontology (NBO), Neuro Behavior Ontology, behavior-ontology, Behavioral Ontology | 2026-02-16 09:46:39 | 2 | ||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | controlled vocabulary, data analysis service, analysis service resource, ontology, service resource, data or information resource, production service resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-02-16 09:49:13 | 134 | |||||||
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GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | 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 |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-16 09:49:37 | 3 | |||||||
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Gene Ontology Browsing Utility (GOBU) Resource Report Resource Website |
Gene Ontology Browsing Utility (GOBU) (RRID:SCR_005662) | GOBU | source code, software resource | Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, gene, browser, computation, visualization, software library, statistical analysis, term enrichment, ontology or annotation browser, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Academia Sinica; Taipei; Taiwan |
Open unspecified license - Free for academic use | nlx_149098 | SCR_005662 | Gene Ontology Browsing Utility | 2026-02-15 09:19:09 | 0 | |||||||
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OWL API Resource Report Resource Website 10+ mentions |
OWL API (RRID:SCR_005734) | OWL API | source code, software resource | The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, owl, api, java, software library, parser, writer |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: SourceForge |
Open unspecified license - Free for academic use; available under either the LGPL or Apache Licenses | nlx_149195 | SCR_005734 | The OWL API, OWLAPI | 2026-02-15 09:19:02 | 15 | |||||||
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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 | software application, data processing software, data analysis software, data analysis service, analysis service resource, software resource, database, source code, production service resource, service resource, data or information resource | 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 | 2026-02-16 09:45:37 | 2091 | |||
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AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | data analysis service, analysis service resource, database, production service resource, service resource, data or information 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 | nif-0000-20935, OMICS_02266 | 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 | 2026-02-16 09:45:41 | 1242 | ||||
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Aging Portal Resource Report Resource Website |
Aging Portal (RRID:SCR_000496) | Aging | database, topical portal, catalog, portal, data or information resource | Portal devoted to aging relevant scientific data and resources. | late adult human, senescence |
uses: Aging Genes and Interventions Database uses: anage uses: Human Life-Table Database uses: Gene Ontology uses: Grants.gov uses: Integrated Blogs uses: Integrated Clinical Trials uses: Integrated Videos uses: Integrated Grants uses: Lifespan Observations Database uses: One Mind Biospecimen Bank Listing uses: Gait in Parkinson's Disease uses: SciCrunch Registry has parent organization: SciCrunch |
Aging | NIA 1R03AG043018-01 | Restricted | nlx_158366 | SCR_000496 | 2026-02-16 09:45:16 | 0 | ||||||
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GONUTS Resource Report Resource Website 1+ mentions |
GONUTS (RRID:SCR_000653) | GONUTS | wiki, data or information resource, database, narrative resource | A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase... | ontology or annotation browser, ontology or annotation search engine, ontology or annotation editor, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: EcoliHub |
NIGMS 1U24 GM077905-01; NIGMS U24 GM088849 |
PMID:22110029 | Free for academic use, The community can contribute to this resource | OMICS_02268, nlx_30164 | SCR_000653 | Gene Ontology Normal Usage Tracking System, GONUTS wiki | 2026-02-16 09:45:18 | 1 | |||||
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Semantic Measures Library Resource Report Resource Website |
Semantic Measures Library (RRID:SCR_001383) | SML | software resource, software toolkit, software library | Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology). | semantic measure, semantic similarity, semantic relatedness, functional similarity, gene ontology, annotation, parse, gene, disease ontology, mesh, rdf, owl, umls, snomed-ct, java, semantic, command line |
is listed by: FORCE11 is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Ecole des Mines d'Ales; Ales; France |
Ecole des Mines d'Ales; Ales; France ; LGI2P Research Center |
PMID:24108186 | Free, Available for download, Freely available | nlx_152555 | http://www.semantic-measures-library.org | SCR_001383 | SML-Toolkit, Semantic Measures Library and ToolKit, Semantic Measures Library & ToolKit | 2026-02-16 09:45:28 | 0 | ||||
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Automated Microarray Pipeline Resource Report Resource Website |
Automated Microarray Pipeline (RRID:SCR_001219) | AMP | production service resource, service resource, data analysis service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis. | microarray, normalization |
is listed by: OMICtools is related to: Gene Ontology has parent organization: TM4 |
NLM R01-LM008795 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02125 | http://www.tm4.org/amp.html | SCR_001219 | TM4 AMP, AMP: Automated Microarray Pipeline, AMP (TM4 Microarray Software Suite), TM4 Microarray Software Suite: Automated Microarray Pipeline, TM4 Microarray Software Suite: AMP | 2026-02-16 09:45:26 | 0 |
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Welcome to the nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms 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 nidm-terms then you can log in from here to get additional features in nidm-terms 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 nidm-terms 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.
