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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | service resource, topical portal, portal, analysis service resource, data or information resource, database, web service, software resource, data analysis service, production service resource, data access protocol | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-08-11 09:42:30 | 81488 | ||||
|
Global Proteome Machine Database (GPM DB) Resource Report Resource Website 100+ mentions |
Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) | The GPM | data analysis software, service resource, software application, data or information resource, storage service resource, database, data processing software, software resource, data repository | The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists. | mass spectrometry, pattern, peptide, protein, proteome, scientist, spectra, tandem, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
r3d100010883, nif-0000-10455 | https://www.thegpm.org/GPMDB/index.html, https://researchdata.ands.org.au/gpm-global-proteome-machine-database/11342, https://doi.org/10.17616/R30C90 | SCR_006617 | GPM, The Global Proteome Machine Organization: Proteomics Database and Open Source Software, Global Proteome Machine Database, GPM DB, The Global Proteome Machine Database, The Global Proteome Machine, Global Proteome Machine Database (GPM DB), The Global Proteome Machine Organization | 2026-08-11 09:41:22 | 282 | |||||||
|
PeptideAtlas Resource Report Resource Website 500+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | service resource, data or information resource, storage service resource, database, data repository | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas, https://doi.org/10.17616/R3BK61 | SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-08-11 09:41:24 | 511 | ||||
|
Gene Expression Omnibus (GEO) Resource Report Resource Website 10000+ mentions |
Gene Expression Omnibus (GEO) (RRID:SCR_005012) | GEO | service resource, data or information resource, storage service resource, database, data repository | Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries. | gold standard, genomics, data, repository, microarray, mRNA, DNA, protein, analysis, SAGE, mass spectrometry, dataset |
is used by: ChIPseeker is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Allen Institute for Brain Science has parent organization: NCBI works with: shinyGEO works with: Drug Gene Budger works with: Signaling Pathways Project works with: GEN3VA |
National Library of Medicine | PMID:23193258 PMID:21097893 PMID:18940857 PMID:17160034 PMID:17099226 PMID:16939800 PMID:16888359 PMID:15608262 PMID:11752295 |
r3d100010283, nif-0000-00142, nlx_96903, OMICS_01030, SCR_007303 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds, http://www.ncbi.nlm.nih.gov/geo/, https://doi.org/10.17616/R33P44 | http://www.ncbi.nlm.nih.gov/gds | SCR_005012 | Gene Expression Omnibus (GEO), Entrez GEO DataSets, Gene Expression Data Sets, Gene Expression Omnibus, GEO, NCBI GEO DataSets, GEO DataSets, Gene Expression Omnibus DataSets | 2026-08-11 09:41:13 | 14348 | ||||
|
ProteomeXchange Resource Report Resource Website 5000+ mentions |
ProteomeXchange (RRID:SCR_004055) | service resource, portal, data or information resource, storage service resource, consortium, database, organization portal, catalog, data repository | A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas. | consortium, database, proteomics, MS proteomics, protein, mass spectrometry, bio.tools, FASEB list |
uses: Proteomics Identifications (PRIDE) uses: PeptideAtlas is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian is affiliated with: Omics Discovery Index is related to: Proteomics Identifications (PRIDE) is related to: PeptideAtlas is related to: SIB Swiss Institute of Bioinformatics is related to: Mass spectrometry Interactive Virtual Environment (MassIVE) is related to: European Bioinformatics Institute is related to: ProteomeTools is related to: Integrated Proteome Resources has parent organization: European Bioinformatics Institute |
European Union 260558 | Public, The community can contribute to this resource | r3d100012122, nlx_158620, biotools:proteomexchange | http://proteomecentral.proteomexchange.org, https://bio.tools/proteomexchange, https://doi.org/10.17616/R32D29 | SCR_004055 | , ProteomeXchange, Proteome Exchange | 2026-08-11 09:40:51 | 6107 |
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