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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HapMap 3 and ENCODE 3 Resource Report Resource Website 1+ mentions |
HapMap 3 and ENCODE 3 (RRID:SCR_004563) | HapMap 3 and ENCORE 3 | data or information resource, database | Draft release 3 for genome-wide SNP genotyping and targeted sequencing in DNA samples from a variety of human populations (sometimes referred to as the HapMap 3 samples). This release contains the following data: * SNP genotype data generated from 1184 samples, collected using two platforms: the Illumina Human1M (by the Wellcome Trust Sanger Institute) and the Affymetrix SNP 6.0 (by the Broad Institute). Data from the two platforms have been merged for this release. * PCR-based resequencing data (by Baylor College of Medicine Human Genome Sequencing Center) across ten 100-kb regions (collectively referred to as ENCODE 3) in 712 samples. Since this is a draft release, please check this site regularly for updates and new releases. The HapMap 3 sample collection comprises 1,301 samples (including the original 270 samples used in Phase I and II of the International HapMap Project) from 11 populations, listed below alphabetically by their 3-letter labels. Five of the ten ENCODE 3 regions overlap with the HapMap-ENCODE regions; the other five are regions selected at random from the ENCODE target regions (excluding the 10 HapMap-ENCODE regions). All ENCODE 3 regions are 100-kb in size, and are centered within each respective ENCODE region. The HapMap 3 and ENCORE 3 data are downloadable from the ftp site. | human, gene, genotype, sequence, single nucleotide polymorphism, dna, software |
is listed by: 3DVC is related to: NHGRI Sample Repository for Human Genetic Research has parent organization: Baylor University; Texas; USA |
Wellcome Trust ; NHGRI ; NIDCD |
nlx_143820 | http://www.hgsc.bcm.tmc.edu/project-medseq-hm-hapmap3encode3.hgsc?pageLocation=hapmap3encode3 | SCR_004563 | 2026-09-05 06:31:24 | 3 | |||||||
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Pfam Resource Report Resource Website 10000+ mentions |
Pfam (RRID:SCR_004726) | data or information resource, database | A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM). | database, clan, structure, sequence, protein family, domain, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: MobiDB is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Conserved Domain Database is related to: SUPFAM is related to: DBD: Transcription factor prediction database is related to: DOMINE: Database of Protein Interactions is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Eukaryotic Linear Motif is related to: TopoSNP is related to: GOTaxExplorer is related to: TrED is related to: ProOpDB is related to: Algal Functional Annotation Tool has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
EMBL core funds ; Howard Hughes Medical Institute ; BBSRC BB/L024136/1; Wellcome Trust 108433/Z/15/Z |
PMID:24288371 PMID:19920124 |
Acknowledgement requested, Available via FTP | biotools:pfam, OMICS_01696, r3d100012850, nlx_72111 | https://bio.tools/pfam, https://doi.org/10.17616/R3QV4F | http://pfam.sanger.ac.uk/ | SCR_004726 | Pfam Database, Protein Families Database, PFAM, Pfam protein families database | 2026-09-05 06:31:26 | 17424 | ||||
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Anopheles gambiae (African malaria mosquito) genome view Resource Report Resource Website |
Anopheles gambiae (African malaria mosquito) genome view (RRID:SCR_004402) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A database for the Anopheles gambiae str. PEST genome that was sequenced using a whole genome shotgun approach. The database aims to contribute to the understanding of mosquito genome structure and organization and will assist the development of malaria control strategies and improved anti-malarial drugs and vaccines. Sequences were generated and assembled into contigs for submission to GenBank. | genome, blast, genome assembly, mosquito, sequence, malaria, contig |
is related to: GenBank has parent organization: NCBI |
Malaria | National Institute of Allergy and Infectious Diseases | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_41106 | SCR_004402 | African malaria mosquito genome view, Anopheles gambiae genome view | 2026-09-05 06:31:24 | 0 | ||||||
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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 | 2026-09-05 06:31:24 | 23 | |||||
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AmphoraNet Resource Report Resource Website 10+ mentions |
AmphoraNet (RRID:SCR_005009) | AmphoraNet | analysis service resource, data analysis service, production service resource, service resource | Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. | dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Eotvos Lorand University; Budapest; Hungary |
PMID:24144838 | Acknowledgement requested, Free, Public | biotools:amphoranet, OMICS_01450 | https://bio.tools/amphoranet | SCR_005009 | 2026-09-05 06:31:27 | 16 | ||||||
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BioSample Database at EBI Resource Report Resource Website 10+ mentions |
BioSample Database at EBI (RRID:SCR_004856) | BioSD | data or information resource, database | Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI''''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples) | cell line, cell, nucleotide, sequencing, proteomics, peptide, protein, genomics, gene expression, biological sample, molecular, sequence, structure, cell line, topical portal, aggregator, gold standard, bio.tools |
uses: European Nucleotide Archive (ENA) uses: Proteomics Identifications (PRIDE) uses: ArrayExpress uses: ENCODE uses: Coriell Institute for Medical Research uses: 1000 Genomes: A Deep Catalog of Human Genetic Variation uses: International HapMap Project uses: International Mouse Strain Resource is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BioSample has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory; Heidelberg; Germany ; European Union FP7 HEALTH-F4-2010-241669; European Union FP7 HEALTH-F4-2007-201413 |
PMID:22096232 | The community can contribute to this resource, Acknowledgement requested | biotools:biosamples, r3d100012628, OMICS_01025, nlx_143930 | https://bio.tools/biosamples, https://doi.org/10.17616/R37R3P | SCR_004856 | BioSamples database, BioSamples, BioSamples Database at EBI, BioSample Database at the EBI, EBI BioSample Database, BioSample Database, BioSD at EBI, BioSD - BioSample Database | 2026-09-05 06:31:26 | 16 | ||||
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SuperCAT Resource Report Resource Website 10+ mentions |
SuperCAT (RRID:SCR_004882) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. SuperCAT hosts typing databases for the Bacillus cereus group of bacteria. The databases contain MultiLocus Sequence Typing (MLST), MultiLocus Enzyme Electrophoresis (MLEE), and Amplified Fragment Length Polymorphism (AFLP) phylogenetic data. multilocus, sequence, Bacillus cereus, bacteria, Genomics, non-vertebrate, taxonomy, identification | bacillus cereus, bacteria, genomics, identification, multilocus, non-vertebrate, sequence, taxonomy | has parent organization: University of Oslo; Oslo; Norway | PMID:29568820 PMID:20651034 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03509 | SCR_004882 | SuperCAT | 2026-09-05 06:31:27 | 15 | |||||||
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SGN Resource Report Resource Website 1000+ mentions |
SGN (RRID:SCR_004933) | SGN, SGN ref | data or information resource, database | A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions. | database, clade, genomic, sequence, phenotype, pathway, genetic, taxonomy, annotation, blast, plant genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Sol Genomics Network - Bulk download is related to: AmiGO has parent organization: Boyce Thompson Institute for Plant Research |
USDA ; ATC Inc. Advanced Technologies Cambridge ; NSF 0116076; NSF 9872617; NSF 975866; NSF 0421634 |
PMID:20935049 PMID:16010005 |
Public, The community can contribute to this resource | r3d100012078, nlx_89764, biotools:sol_genomics_network | https://bio.tools/sol_genomics_network, https://doi.org/10.17616/R3FS95 | http://www.sgn.cornell.edu/ | SCR_004933 | SGN ref, Sol Genomics Network | 2026-09-05 06:31:27 | 1261 | |||
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DATFAP Resource Report Resource Website |
DATFAP (RRID:SCR_005413) | DATFAP | data or information resource, database | A database of transcription factors from 13 plant species, and PCR primers for around 90% of them. | homolog, sequence, transcription factor |
is listed by: OMICtools is related to: Gene Ontology |
PMID:18366738 | Free | OMICS_00552 | SCR_005413 | Database of transcription factors with alignments and primers | 2026-09-05 06:31:29 | 0 | ||||||
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TranspoGene Resource Report Resource Website 1+ mentions |
TranspoGene (RRID:SCR_005634) | data or information resource, database | A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. | element, eukaryotic, evolutionary, exon, exonization, family, fruit fly, gene, genome, alternative, chicken, coding, disease, divergence, genomic, hosting, human, human genome databases, intron, location, map, maps, mouse, mrna, nematode, organism, pattern, promoter, protein, sea squirt, sequence, splicing, transcript, transcriptome, transposed, viewers, worm, zebrafish | has parent organization: Tel Aviv University; Ramat Aviv; Israel | nif-0000-03579 | SCR_005634 | TranspoGene | 2026-09-05 06:31:30 | 9 | |||||||||
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TRANSFAC Resource Report Resource Website 100+ mentions |
TRANSFAC (RRID:SCR_005620) | TRANSFAC | data or information resource, database | Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites. | Curated, eucaryotic, transcription, factor, genomic, binding, site, sequence, regulated, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: Gene Regulation Databases is related to: TRANSPATH is related to: Babelomics is related to: GeneTrail works with: rVista |
European Commission ; German Ministry of Education and Research |
PMID:12520026 | Free, Freely available | biotools:transfac, nif-0000-03576 | http://www.biobase-international.com/pages/index.php?id=transfac, http://gene-regulation.com/pub/databases.html, https://bio.tools/transfac | SCR_005620 | 2026-09-05 06:31:30 | 266 | |||||
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Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | data or information resource, database | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-09-05 06:31:12 | 2 | |||||||
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PhyloPythia Resource Report Resource Website |
PhyloPythia (RRID:SCR_000540) | PhyloPythia | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data analysis service for accurate phylogenetic classification of variable-length DNA fragments. | classification, phyolgenetic, dna fragment, dna, metagenome, sequence | is listed by: OMICtools | PMID:17179938 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01459 | SCR_000540 | 2026-09-05 06:31:10 | 0 | |||||||
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dbSTS Resource Report Resource Website 1+ mentions |
dbSTS (RRID:SCR_000400) | dbSTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences. | genomic, mapping, sequence, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NIH | PMID:2781285 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dbsts, nif-0000-20939, r3d100010649 | https://bio.tools/dbsts, https://doi.org/10.17616/R39P5C | SCR_000400 | NCBI dbSTS: database of Sequence Tagged Sites, Sequence Tagged Sites Database, NCBI dbSTS, dbSTS: database of Sequence Tagged Sites, Database of Sequence Tagged Sites | 2026-09-05 06:31:10 | 3 | ||||
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GTEx eQTL Browser Resource Report Resource Website 100+ mentions |
GTEx eQTL Browser (RRID:SCR_001618) | data or information resource, database | Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets. | genetic variation, high-throughput, phenotype, genotype, molecular, molecule, gene, gene expression, snp, trait, expression, quantitative trait locus, expression quantitative trait locus, genome, probe, sequence, statistics, p-value, rna-seq, array, lymphoblastoid, liver, cerebellum, frontal cortex, temporal cortex, pons, gene regulation, tissue, mrna, data set | has parent organization: NCBI | NIH Common Fund 268201000029C-4-0-2 | Free, Freely available | nlx_153884 | http://www.gtexportal.org/home/ | SCR_001618 | NCBI GTEx eQTL Browser, Genotype-Tissue Expression eQTL Browser, GTEx (Genotype-Tissue Expression) eQTL Browser, NCBI GTeX eQTL Browser | 2026-09-05 06:31:14 | 499 | ||||||
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Neurospora crassa Database Resource Report Resource Website 1+ mentions |
Neurospora crassa Database (RRID:SCR_001372) | NCD | data or information resource, database | It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available. | gene, annotation, compendium, contig, distance, drosophila, genome, mitochondrial, neurospora crassa, plasmid, region, rrna, sequence, trna, untranslated | Free, Freely available, | nif-0000-20965 | http://www.broadinstitute.org/annotation/genome/neurospora/Home.html | SCR_001372 | Neurospora crassa Database | 2026-09-05 06:31:13 | 4 | |||||||
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LSPD Resource Report Resource Website 1+ mentions |
LSPD (RRID:SCR_002125) | LSPD | data or information resource, database | LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus. | liver gene, promoter region, regulatory region, sequence, transcription | Free, Freely Available | nif-0000-20920 | SCR_002125 | The Liver Specific Gene Promoter Database | 2026-09-05 06:31:16 | 6 | ||||||||
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Conserved Domain Database Resource Report Resource Website 100+ mentions |
Conserved Domain Database (RRID:SCR_002077) | CDD | data or information resource, database | Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments. | protein, amino acid sequence, nucleic acid, 3d structure, annotation, function, sequence, structure, amino acid, gold standard |
is used by: Mutation Annotation and Genomic Interpretation is listed by: re3data.org is related to: Pfam is related to: SMART is related to: COG is related to: NCBI Structure has parent organization: NCBI works with: Conserved Domains Search |
PMID:25414356 PMID:18984618 |
nif-0000-02647, r3d100010653 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd | SCR_002077 | Conserved Domains Database, Conserved Domains | 2026-09-05 06:31:15 | 358 | ||||||
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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 | 2026-09-05 06:31:17 | 19823 | |||||
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Human Proteomics Initiative Resource Report Resource Website |
Human Proteomics Initiative (RRID:SCR_002373) | HPI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals. | function, gene, alignment, biologist, clustering, coding, development, genome, human, location, mammalian, modification, ortholog, population, post-translational, protein, proteome, proteomic, proteomics, sequence, splice, structure, subcellular, variant, variation, gold standard |
is related to: UniProt Chordata protein annotation program has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:11301130 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21199 | SCR_002373 | Human Proteome Initiative, UniProtKB/Swiss-Prot Human Proteome Initiative | 2026-09-05 06:31:17 | 0 |
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