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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-12 01:02:19 | 17 | ||||||
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EASE: the Expression Analysis Systematic Explorer Resource Report Resource Website 50+ mentions |
EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) | EASE | data processing software, software application, software resource | Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible | gene, microarray, genome, gene ontology, statistical analysis, enrichment analysis, FASEB list |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Database for Annotation Visualization and Integrated Discovery |
NIAID | PMID:12734009 PMID:19131956 PMID:19033363 |
Free for academic use | nlx_149218 | SCR_013361 | Expression Analysis Systematic Explorer | 2026-09-12 01:01:01 | 94 | |||||
|
Avadis Resource Report Resource Website 1+ mentions Rating or validation data |
Avadis (RRID:SCR_000644) | Avadis | software library, software resource, software toolkit | Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible, | pathway network views, genome browsers, chemical structure views, pipe-line views, next-generation sequencing data, integrated platform, view ontology hierarchies, statistical mining and modelling, collection of data, text mining algorithms collection, data visualization libraries, |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01120, nlx_149208 | http://www.strandls.com/Avadis | SCR_000644 | Access Visualize Analyze Discover, Avadis NGS | 2026-09-12 01:00:51 | 2 | ||||||
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biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, data processing software, software application, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-09-12 12:59:10 | 2879 | ||||||
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DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
Development Grants For Research Institutions – KRIPIS ; European Regional Development Fund ; European Social Fund ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; John S. Latsis Public Benefit Foundation |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/, http://www.microrna.gr/miRPathv3, https://bio.tools/diana-mirpath | http://www.microrna.gr/miRPathv2 | SCR_017354 | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-09-12 12:58:52 | 424 | ||||
|
Functional Annotation Resource Report Resource Website 1+ mentions |
Functional Annotation (RRID:SCR_017519) | service resource | MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO). | MGI, GO, functional, annotation, mouse, gene, product, Gene Ontology |
uses: Gene Ontology has parent organization: Mouse Genome Informatics (MGI) |
Free, Freely available | SCR_017519 | 2026-09-12 12:58:53 | 4 | ||||||||||
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LIPID MAPS Proteome Database Resource Report Resource Website 1+ mentions |
LIPID MAPS Proteome Database (RRID:SCR_003062) | LMPD | data or information resource, database | Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio. | gene, protein, lipid, metabolism, metabolomics |
uses: Gene Ontology uses: KEGG uses: UniProt uses: Entrez Gene uses: ENZYME has parent organization: LIPID Metabolites And Pathways Strategy |
NIGMS | PMID:16381922 | Free, Freely available | nif-0000-03085 | http://www.lipidmaps.org/data/proteome/index.cgi | SCR_003062 | LIPID MAPS Proteome Database (LMPD) | 2026-09-12 01:01:27 | 3 | ||||
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Integrated Molecular Interaction Database Resource Report Resource Website 1+ mentions |
Integrated Molecular Interaction Database (RRID:SCR_003546) | IMID | data or information resource, database | Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database. | pathway, disease, gene ontology, specie, interaction, molecular, protein-protein interaction, gene/protein regulation, protein-small molecule interaction, gene, protein, regulation |
is related to: Gene Ontology is related to: Entrez Gene is related to: Pathway Commons is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Search Tool for Interactions of Chemicals is related to: KEGG is related to: Pathway Interaction Database is related to: Reactome is related to: PharmGKB has parent organization: Florida State University; Florida; USA |
PMID:22238258 | nlx_157667 | SCR_003546 | 2026-09-12 01:01:29 | 1 | ||||||||
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Cotton EST Database Resource Report Resource Website 10+ mentions |
Cotton EST Database (RRID:SCR_003301) | Cotton EST Database | data or information resource, database | Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information. | expressed sequence tag, contig, indel mutant, single nucleotide polymorphism, transcription factor, protein kinase, gene, mirna, blast, est-simple sequence repeat, simple sequence repeat, pathway, function |
is related to: Gene Ontology is related to: KEGG has parent organization: East Carolina University; Carolina; USA |
PMID:22087239 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100011232 | https://doi.org/10.17616/R3X63C | http://www.leonxie.com/ | SCR_003301 | 2026-09-12 01:01:28 | 10 | |||||
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Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | analysis service resource, data analysis service, production service resource, service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/, http://www.gepas.org/, http://babelomics3.bioinfo.cipf.es | http://www.babelomics.org | SCR_002969 | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-09-12 01:01:27 | 138 | |||
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GORetriever Resource Report Resource Website 10+ mentions |
GORetriever (RRID:SCR_005633) | GORetriever | analysis service resource, data analysis service, production service resource, 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 | 2026-09-12 01:01:38 | 13 | |||||
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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 | 2026-09-12 01:03:15 | 2 | ||||
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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 | 2026-09-12 01:03:14 | 7 | ||||||||
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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 | 2026-09-12 01:03:15 | 0 | ||||||
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topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-09-12 01:02:51 | 3080 | ||||||||
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barleyGO Resource Report Resource Website 1+ mentions |
barleyGO (RRID:SCR_015709) | software resource, source code | Perl software script that can annotate barley sequences with Gene Ontology terms inferred by homology. It uses the IBSC2012 barley GO annotation and supports both nucleotide and peptide sequences. | annotation, barley, barley sequence, gene ontology, go, go annotation, nucleotide, peptide, perl | uses: Gene Ontology | Free, Available for download | http:// www.eead.csic.es/compbio/soft/barleyGO.tgz | SCR_015709 | 2026-09-12 01:03:58 | 1 |
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