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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids 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: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
ARUK ; British Heart Foundation ; EMBL ; NCI ; NCRR P20 RR016472; NEI ; NHGRI P41 HG02273; NHGRI U24 HG007722; NHGRI U41 HG006104; NHLBI ; NIAID ; NIA ; NIDDK ; NIGMS 5R01GM080646; NIGMS R01 GM080646; NIMH ; NLM G08 LM010720; NSF DBI-0850319; PDUK |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org, http://www.uniprot.org/uniprot/, http://www.pir.uniprot.org, ftp://ftp.uniprot.org, https://doi.org/10.17616/R3BW2M | SCR_002380 | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-08-21 12:36:41 | 19823 | |||||
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NEWT Resource Report Resource Website 10+ mentions |
NEWT (RRID:SCR_004477) | NEWT | data or information resource, database | NEWT is the taxonomy database maintained by the UniProt group. It integrates taxonomy data compiled in the NCBI database and data specific to the UniProt Knowledgebase. Browse by hierarchy, List all, or Complete proteomes. Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree. UniProtKB taxonomy data is manually curated: next to manually verified organism names, we provide a selection of external links, organism strains and viral host information. Species with protein sequences stored in the UniProt Knowledgebase are named according to UniProt nomenclature. We endeavour to maintain a list of manually curated species names for which protein sequence data is available. In particular, we have adopted a systematic convention for naming viral and bacterial strains and isolates. Links to external sites are chosen by the UniProt taxonomy team and show pictures and various scientific data of interest (taxonomy, biology, physiology,...). | archaea, bacteria, eukaryota, viruses, cellular organism, sequence, viroid, gold standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: NCBI Taxonomy has parent organization: UniProt |
PMID:12824428 | nlx_46189, biotools:newt | https://bio.tools/newt | http://www.ebi.ac.uk/newt/ | SCR_004477 | UniProtKB taxonomy database, UniProt Taxonomy Database, UniProt Taxonomy | 2026-08-21 12:37:25 | 23 | |||||
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UniParc Resource Report Resource Website 50+ mentions |
UniParc (RRID:SCR_005818) | data or information resource, database | Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references. | protein sequence, database, public protein sequence, gold standard, upi, unique protein identifier, identifier, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProt DAS is related to: WormBase is related to: FlyBase is related to: Ensembl is related to: RefSeq has parent organization: UniProt |
Public, Entries are available for download | SCR_004769, nif-0000-03610, r3d100011519, biotools:uniparc, nlx_76940 | https://bio.tools/uniparc, https://doi.org/10.17616/R3X33B | SCR_005818 | UniProt Archive | 2026-08-21 12:37:39 | 98 | |||||||
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UniRef Resource Report Resource Website 100+ mentions |
UniRef (RRID:SCR_010646) | data or information resource, database | Databases which provide clustered sets of sequences from UniProt Knowledgebase and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences from view. The UniRef100 database combines identical sequences and sub-fragments with 11 or more residues (from any organism) into a single UniRef entry. The sequence of a representative protein, the accession numbers of all the merged entries, and links to the corresponding UniProtKB and UniParc records are all displayed in the entry. UniRef90 and UniRef50 are built by clustering UniRef100 sequences with 11 or more residues such that each cluster is composed of sequences that have at least 90% (UniRef90) or 50% (UniRef50) sequence identity to the longest sequence (UniRef seed sequence). All the sequences in each cluster are ranked to facilitate the selection of a representative sequence for the cluster. | database, protein sequence, sub-fragment, sequence cluster, clustered set |
is related to: VIROME is related to: UniRef at the EBI is related to: BioExtract has parent organization: UniProt |
NHGRI U01 HG02712 | PMID:17379688 | Updated biweekly | nlx_66133, r3d100011518 | SCR_010646 | UniProt Reference Clusters | 2026-08-21 12:39:25 | 309 | ||||||
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UniProtKB Resource Report Resource Website 5000+ mentions |
UniProtKB (RRID:SCR_004426) | data or information resource, data repository, database, service resource, storage service resource | Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway. | protein, annotation, amino acid sequence, taxonomy, proteome |
uses: UniportKB is used by: NIF Data Federation is used by: PINT is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is related to: ESTHER is related to: PIRSF is related to: AmiGO is related to: UniSave is related to: ProRepeat is related to: UniProt Chordata protein annotation program is related to: neXtProt is related to: TopFIND is related to: UniPathway is related to: NCBI Protein Database is related to: Biomine is related to: Gene Ontology is related to: UniProt DAS is related to: FunTree is related to: ConceptWiki is related to: InterProScan is related to: UniProtKB/Swiss-Prot is related to: FuzDrop has parent organization: UniProt is parent organization of: UniProtKB Keywords is parent organization of: UniProtKB Subcellular Locations works with: PremierBiosoft Proteo IQ Software works with: Cello2Go works with: UniprotR works with: Kinase Associated Neural Phospho Signaling |
PMID:15888679 PMID:18287689 |
Available to the research community, The community can contribute to this resource | r3d100011521, nlx_53981 | https://doi.org/10.17616/R3NK9Z | SCR_004426 | UniProtKB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, UniProt Knowledgebase | 2026-08-21 12:37:36 | 7119 | ||||||
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UniProt Chordata protein annotation program Resource Report Resource Website |
UniProt Chordata protein annotation program (RRID:SCR_007071) | Chordata protein annotation program | data or information resource, data set | Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms. | chordata, protein, protein annotation, functional annotation, human, non-human vertebrate, xenopus laevis, xenopus tropicalis, zebrafish, protein sequence, protein sequencing, nucleotide sequence, sequence, annotation, sequence variant, disease, proteome, gold standard |
is related to: Human Proteomics Initiative is related to: UniProtKB has parent organization: UniProt |
nlx_143879 | SCR_007071 | 2026-08-21 12:38:18 | 0 | |||||||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
BBSRC ; EMBL member states ; European Union ; Industry Programme partners ; NIH ; UK Research Councils ; Wellcome Trust |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-08-21 12:37:25 | 3760 | ||||||
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BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2026-08-15 11:23:15 | 12 | ||||||
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NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases Resource Report Resource Website 100+ mentions |
NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) | NIDDK | government granting agency | Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country. | diabetes, metabolic disease, digestive, kidney, endocrine, medical research |
recommends: Cell Image Library (CIL) recommends: Biological General Repository for Interaction Datasets (BioGRID) recommends: NIDDK Central Repository recommends: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) recommends: Metabolomics Workbench recommends: PeptideAtlas recommends: Network Data Exchange (NDEx) recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: FlyBase recommends: Database of Interacting Proteins (DIP) recommends: WormBase recommends: PhysioNet recommends: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) recommends: UniProt recommends: dbSNP recommends: DNA DataBank of Japan (DDBJ) recommends: European Nucleotide Archive (ENA) recommends: dbVar recommends: ClinicalTrials.gov recommends: European Variation Archive (EVA) recommends: MGnify recommends: Analysis, Visualization, and Informatics Lab-space (AnVIL) recommends: GenBank recommends: Gene Expression Omnibus (GEO) recommends: miRBase recommends: Database of Genomic Variants Archive (DGVa) recommends: Crystallography Open Database (COD) recommends: Coherent X-Ray Imaging Data Bank (CXIDB) recommends: Biological Magnetic Resonance Data Bank (BMRB) recommends: Worldwide Protein Data Bank (wwPDB) recommends: EMDataResource.org recommends: NCBI Assembly Archive Viewer recommends: Cambridge Crystallographic Data Centre (CCDC) recommends: Inorganic Crystal Structure Database (ICSD) recommends: Structural Biology Grid recommends: ArrayExpress recommends: GenomeRNAi recommends: NCBI database of Genotypes and Phenotypes (dbGap) recommends: Protein Circular Dichroism Data Bank (PCDDB) recommends: Electron Microscopy Data Bank at PDBe (MSD-EBI) recommends: PDBe - Protein Data Bank in Europe recommends: PubChem BioAssay recommends: Japanese Genotype-phenotype Archive (JGA) recommends: ProteomeXchange recommends: IntAct recommends: European Genome phenome Archive recommends: MetaboLights recommends: PubChem Substance recommends: The Immunology Database and Analysis Portal (ImmPort) recommends: STRENDA recommends: Kinetic Models of Biological Systems (KiMoSys) recommends: FLOWRepository recommends: Mass spectrometry Interactive Virtual Environment (MassIVE) recommends: Global Proteome Machine Database (GPM DB) recommends: Cancer Imaging Archive (TCIA) recommends: German Neuroinformatics Node (G-Node) recommends: 1000 Functional Connectomes Project recommends: ChEMBL recommends: Image Data Resource (IDR) recommends: SICAS Medical Image Repository recommends: ZENODO recommends: Dataverse Network Project recommends: NeuroMorpho.Org recommends: Mendeley Data recommends: NIMH Data Archive recommends: NIH Figshare Archive recommends: FigShare recommends: National Addiction and HIV Data Archive Program (NAHDAP) recommends: Dryad Digital Repository recommends: Open Science Framework recommends: OpenNeuro recommends: SPARC Portal lists: Mutant Mouse Resource and Research Center lists: NIDDK Research Resources is affiliated with: Cystic Fibrosis Research and Translation Centers is affiliated with: Nutrition and Obesity Research Centers is affiliated with: O'Brien Urology Centers is affiliated with: Hematology Centers is affiliated with: Polycystic Kidney Disease Research and Translation Centers is affiliated with: O'Brien Kidney Centers is affiliated with: Diabetes Research Centers is affiliated with: Digestive Disease Centers is affiliated with: Centers for Diabetes Translation Research is affiliated with: Pediatric Centers of Excellence in Nephrology is affiliated with: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study is related to: Bridging Interventional Development Gaps is related to: Polycystic Kidney Disease Research Resource Consortium has parent organization: National Institutes of Health is parent organization of: MTOPS Prostate Samples Analysis Consortium is parent organization of: Symptom Score for Benign Prostatic Hyperplasia is parent organization of: Type 1 Diabetes - Rapid Access to Intervention Development is parent organization of: National Diabetes Education Program is parent organization of: Family Investigation of Nephropathy of Diabetes is parent organization of: Frequent Hemodialysis Network Daily Trial is parent organization of: HemBase is parent organization of: NIDDK- National Institute of Diabetes and Digestive and Kidney Diseases Obesity Resources is parent organization of: dkCOIN is parent organization of: National Kidney Disease Education Program is parent organization of: Network of Minority Health Research Investigators is parent organization of: National Endocrine and Metabolic Diseases Information Service is parent organization of: National Diabetes Information Clearinghouse is parent organization of: National Digestive Diseases Information Clearinghouse is parent organization of: National Hematologic Diseases Information Service is parent organization of: National Kidney and Urologic Diseases Information Clearinghouse is parent organization of: Type 1 Diabetes Preclinical Testing Program is parent organization of: Frequent Hemodialysis Network Nocturnal Trial is parent organization of: Boston Area Community Health Survey is parent organization of: Minimally Invasive Surgical Therapies Treatment Consortium for Benign Prostatic Hyperplasia is parent organization of: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study |
Type 1 diabetes, Type 2 diabetes, Diabetes, Digestive disease, Kidney disease, Endocrine disease, Obesity, Blood disease, Liver disease, Urologic disease | nlx_inv_1005102 | SCR_012895 | National Institute of Diabetes and Digestive and Kidney Diseases | 2026-08-15 11:24:33 | 156 | |||||||
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GoAnnotator Resource Report Resource Website 1+ mentions |
GoAnnotator (RRID:SCR_005792) | GOAnnotator | analysis service resource, data analysis service, production service resource, service resource | A tool for assisting the GO annotation of UniProt entries by linking the GO terms present in the uncurated annotations with evidence text automatically extracted from the documents linked to UniProt entries. Platform: Online tool | text mining, protein, gene ontology, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt has parent organization: University of Lisbon; Lisbon; Portugal |
European Union contract QLRI-1999-50595 | PMID:17181854 | Free for academic use | nlx_149303 | SCR_005792 | 2026-08-20 09:26:55 | 1 | ||||||
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GOTaxExplorer Resource Report Resource Website |
GOTaxExplorer (RRID:SCR_005720) | GOTaxExplorer | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: Pfam is related to: SMART is related to: FSST - Functional Similarity Search Tool has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network ; BMBF 016R0453; DFG KFO 129/1-1; European Union contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149179 | SCR_005720 | 2026-08-21 12:37:47 | 0 | ||||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-08-21 12:37:39 | 8 | |||||||
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Pathway Commons Resource Report Resource Website 10+ mentions |
Pathway Commons (RRID:SCR_002103) | PC | data access protocol, data or information resource, database, software resource, web service | Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013) | biological pathway, pathway, molecule, biopax, standard exchange format, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: cPath is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Reactome is related to: MINT is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Cancer Cell Map is related to: HPRD - Human Protein Reference Database is related to: Integrated Molecular Interaction Database is related to: Pathway Interaction Database is related to: CHEBI is related to: UniProt is related to: PANTHER is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of Toronto; Ontario; Canada |
NHGRI P41HG004118; NIGMS 2R01GM070743-06; NIGMS 1T32 GM083937; Cancer Biomedical Informatics Grid |
PMID:21071392 | Free, Freely available | nif-0000-20884, r3d100012731, biotools:PathwayCommons_web_service_API | https://bio.tools/PathwayCommons_web_service_API | SCR_002103 | 2026-08-21 12:36:35 | 14 | |||||
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IMEx - The International Molecular Exchange Consortium Resource Report Resource Website 100+ mentions |
IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) | IMEx | community building portal, consortium, data or information resource, data repository, database, organization portal, portal, service resource, storage service resource | Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data. | protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interaction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: MINT is related to: MatrixDB is related to: MPIDB is related to: Database of Interacting Proteins (DIP) is related to: Database of Interacting Proteins (DIP) is related to: InnateDB is related to: IntAct is related to: Interaction Reference Index is related to: MPIDB is related to: UniProt is related to: InnateDB is related to: MatrixDB is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: I2D is related to: Molecular Connections NetPro is related to: SIB Swiss Institute of Bioinformatics is related to: IntAct is related to: PSI-MI is related to: PSICQUIC Registry is related to: mentha is related to: Bioconductor has parent organization: European Bioinformatics Institute works with: CellPhoneDB works with: Cytoscape works with: IntAct works with: MINT works with: MPact: Representation of Interaction Data at MIPS works with: Molecular Connections NetPro works with: Biological General Repository for Interaction Datasets (BioGRID) works with: InnateDB works with: BIND |
European Union | PMID:22453911 PMID:17893861 |
Free, Freely available, Available for download | nif-0000-00447, OMICS_01545, r3d100010669, biotools:imex | http://imex.sourceforge.net/, https://bio.tools/imex, https://doi.org/10.17616/R3090W | SCR_002805 | The International Molecular Exchange Consortium, International Molecular Exchange Consortium | 2026-08-21 12:36:49 | 161 | ||||
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FlyMine Resource Report Resource Website 100+ mentions |
FlyMine (RRID:SCR_002694) | FlyMine | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API | anopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publication, FASEB list |
is related to: FlyBase is related to: UniProt is related to: Ensembl is related to: InterPro is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Tree families database is related to: IntAct is related to: Gene Ontology is related to: GOA is related to: ArrayExpress is related to: REDfly Regulatory Element Database for Drosophilia is related to: KEGG is related to: Reactome has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust 067205; NHGRI |
PMID:17615057 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02845 | SCR_002694 | 2026-08-21 12:36:50 | 107 | ||||||
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Open PHACTS Resource Report Resource Website 10+ mentions |
Open PHACTS (RRID:SCR_005050) | OPS | consortium, data or information resource, database, organization portal, portal, software resource | Project that developed an open access discovery platform, called Open Pharmacological Space (OPS), via a semantic web approach, integrating pharmacological data from a variety of information resources and tools and services to question this integrated data to support pharmacological research. The project is based upon the assimilation of data already stored as triples, in the form subject-predicate-object. The software and data are available for download and local installation, under an open source and open access model. Tools and services are provided to query and visualize this data, and a sustainability plan will be in place, continuing the operation of the Open PHACTS Discovery Platform after the project funding ends. Throughout the project, a series of recommendations will be developed in conjunction with the community, building on open standards, to ensure wide applicability of the approaches used for integration of data. | drug, enzyme family, structure, receptor, target, ki, pathway, pharmacology, enzyme, small molecule, data mining, annotation, drug discovery, drug development, pharmacological profile, pharmacokinetic, admet data, biological target, chemical, linked data, rdf, nanopublication, platform, semantic technology, text mining, bioinformatics, cheminformatics, interoperability, chemistry, data provenance, compound, small molecule, semantic integration, drug discovery |
uses: CHEBI uses: ChemSpider uses: ConceptWiki uses: DrugBank uses: ENZYME uses: UniProt uses: Gene Ontology uses: WikiPathways is listed by: Consortia-pedia is listed by: FORCE11 is related to: Nanopub.org is related to: eTRIKS is related to: Janssen Research and Development is related to: Almirall is related to: ESTEVE is related to: Merck is related to: Pfizer Animal Genetics is related to: VU University; Amsterdam; Netherlands is related to: European Bioinformatics Institute is related to: Maastricht University; Maastricht; Netherlands is related to: University of Bonn; Bonn; Germany is related to: Royal Society of Chemistry is related to: Spanish National Cancer Research Center is related to: Netherlands Bioinformatics Centre is related to: SIB Swiss Institute of Bioinformatics is related to: Technical University of Denmark; Lyngby; Denmark is related to: University of Santiago de Compostela; Santiago de Compostela; Spain is related to: University of Vienna; Vienna; Austria is related to: University of Hamburg; Hamburg; Germany is related to: University of Manchester; Manchester; United Kingdom is related to: BioSolveIT is related to: ConnectedDiscovery is related to: OpenLink Software is related to: SciBite is related to: Open PHACTS Foundation has parent organization: University of Vienna; Vienna; Austria |
Innovative Medicines Initiative grant 115191; EFPIA ; Open PHACTS Foundation |
PMID:22683805 | Open unspecified license, Registration required, Non-commercial | r3d100011550, nlx_144033 | https://www.force11.org/node/4684, http://www.imi.europa.eu/content/open-phacts, https://doi.org/10.17616/R3T63F | SCR_005050 | Open PHACTS - Open Pharmacological Space, OpenPhacts.org, Open Pharmacological Space, Open Pharmacological Concepts Triple Store, OpenPHACTS, Open PHACTS: Open Pharmacological Space | 2026-08-21 12:37:30 | 11 | ||||
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ProDom Resource Report Resource Website 100+ mentions |
ProDom (RRID:SCR_006969) | ProDom | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Comprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | set, protein, domain, family, automatically, generated, UniProt, database, homologous, sequence, compare, FASEB list |
is listed by: OMICtools is related to: UniProt is related to: InterPro has parent organization: PRABI |
European Union ; Re´seau des Ge´nopoles ; ‘Programme de Bio-Informatique InterOrganismes |
PMID:15608179 PMID:12230033 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01698, nif-0000-03342 | http://prodom.prabi.fr/prodom/current/html/home.php | SCR_006969 | 2026-08-21 12:38:16 | 354 | |||||
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PredictSNP Resource Report Resource Website 100+ mentions |
PredictSNP (RRID:SCR_006327) | PredictSNP | analysis service resource, data analysis service, production service resource, service resource, software resource | Consensus classifier tool that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database. A stand-alone version is also available. | single nucleotide polymorphism, classifier, prediction, mutation, protein function, FASEB list |
is listed by: OMICtools is related to: Protein Mutant Database is related to: UniProt |
PMID:24453961 | Free for academic use | OMICS_02218 | SCR_006327 | PredictSNP - Consensus classifier for prediction of disease-related mutations | 2026-08-21 12:38:03 | 148 | ||||||
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Genotate Resource Report Resource Website |
Genotate (RRID:SCR_016659) | data access protocol, data or information resource, database, software resource, web service | Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts. | identify, explore, visualize, homology, functional, annotation, assemble, transcript, dataset |
works with: Ensembl works with: UniProt works with: NONCODE |
ANR | Free, Available for download, Freely available, | SCR_016659 | 2026-08-21 12:40:54 | 0 | |||||||||
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LegumeIP Resource Report Resource Website 10+ mentions |
LegumeIP (RRID:SCR_008906) | LegumeIP | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression. | gene function, genome evolution, legume, gene, genome, plant, genomics, transcriptomic, gene annotation, gene family, synteny, gene expression, blast, genomic sequence, microarray, rna-seq, comparative genomics, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: UniProt is related to: InterProScan is related to: Gene Ontology is related to: KEGG has parent organization: Samuel Roberts Noble Foundation |
Samuel Roberts Noble Foundation ; NSF ABI-0960897 |
PMID:22110036 | biotools:legumeip, nlx_151455 | https://bio.tools/legumeip | SCR_008906 | LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes, LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes | 2026-08-21 12:38:55 | 23 |
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