Dataset Date generated # of triples # of unique entities
1 Affymetrix probesets [affymetrix]
This dataset contains the probesets used in the Affymetrix microarrays.
Links: search query example download
2014-08-01 86942371 6679943
2 A Database of Annotated Published Models [biomodels]
BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.
Links: search query example download
2014-06-05 2380009 188380
3 BioPortal [bioportal]
BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.
Links: search query example download
2014-07-20 19920395 2199594
4 chEMBL [chembl]
ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.
Links: search query example download
409942525 50061452
5 [clinicaltrials] is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world.
Links: search query example download
2014-09-25 98835804 7337123
6 Comparative Toxicogenomics Database [ctd]
CTD includes manually curated data describing cross-species chemical-gene/protein interactions and chemical- and gene-disease relationships to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases.
Links: search query example download
2014-06-09 326720894 19768641
7 Database of single nucleotide polymorphism [dbsnp]
The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
Links: search query example download
2014-07-15 8801487 530538
8 DrugBank [drugbank]
The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
Links: search query example download
2014-07-25 3672531 316950
9 GenAge: The Ageing Gene Database [genage]
GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.
Links: search query example download
2014-06-03 73048 6995
10 GenDR: The Dietary Restriction Gene Database [gendr]
GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals
Links: search query example download
2014-06-03 11663 1129
11 Gene Ontology Annotation [goa]
The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.
Links: search query example download
2014-06-05 97520151 5950074
12 HUGO Gene Nomenclature Committee [hgnc]
The HGNC gives unique and meaningful names to every human gene. For each known human gene we approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database.
Links: search query example download
2014-07-04 3628205 372136
13 NCBI Homologene [homologene]
HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
Links: search query example download
2014-08-07 7189769 869985
14 Integrated resource of protein families, domains and functional sites [interpro]
InterPro is an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites.
Links: search query example download
2014-06-02 2323345 176579
15 Integrated Protein Knowledgebase [iproclass]
The iProClass database provides value-added information reports for UniProtKB and unique UniParc proteins, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy.
Links: search query example download
2014-06-09 3306107223 364255265
16 Interaction Reference Index [irefindex]
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods.
Links: search query download
2014-06-22 48781511 3110993
17 Kyoto Encyclopedia of Genes and Genomes [kegg]
KEGG is an integrated database resource consisting of 16 main databases, broadly categorized into biological systems information, genomic information, and chemical information.
Links: search query example download
2014-08-13 50197150 6533307
18 Linked Structured Product Label [linkedspl]
LinkedSPL is a Linked Data version of DailyMed
Links: search query example download
2174579 59776
19 The Life Science Resource Registry [lsr]
The Resource Registry is a curated collection of datasets and terminologies used in the life sciences
Links: search query example download
2014-07-16 55914 5032
20 Medical Subject Headings [mesh]
MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity
Links: search query example download
2014-05-27 7323864 305401
21 Mouse genome database (MGD) from Mouse Genome Informatics (MGI) [mgi]
The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
Links: search query example download
2014-06-05 8206813 924257
22 NCBI Gene [ncbigene]
NCBI Gene provides information for genes from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
Links: search query example download
2014-09-20 2010283833 189594629
23 National Drug Code Directory [ndc]
The National Drug Code (NDC) is a unique product identifier used in the United States for drugs intended for human use.
Links: search query example download
2014-08-02 6199488 488146
24 Online Mendelian Inheritance in Man [omim]
OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.
Links: search query example download
2014-09-19 8750774 1013389
25 Orphanet; a database dedicated to information on rare diseases and orphan drugs [orphanet]
Orphanet is a database of information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases.
Links: search query example download
2014-06-02 377947 28871
26 Pathway Commons [pathwaycommons]
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases
Links: search query example download
5700724 1024572
27 Pharmacogenomics Knowledge Base [pharmgkb]
PharmGKB curates primary genotype and phenotype data, annotates gene variants and gene-drug-disease relationships via literature review, and summarizes important PGx genes and drug pathways.
Links: search query example download
2014-05-31 278049209 25325504
28 PubMed [pubmed]
PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.
Links: search query example download
2014-06-27 5005343905 412593720
29 Reactome - a curated knowledgebase of biological pathways [reactome]
The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
Links: search query example download
12487446 2461010
30 SABIO-RK [sabiork]
SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
Links: search query example download
2014-06-05 2716421 448248
31 Saccharomyces Genome Database [sgd]
The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.
Links: search query example download
2014-08-07 12494945 957558
32 Side Effect Resource [sider]
SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations.
Links: search query example download
2014-07-22 17627864 1222429
33 NCBI Taxonomy [taxonomy]
The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.
Links: search query example download
2014-05-27 21310356 1147211
34 WikiPathways [wikipathways]
WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. All content is under the Creative Commons Attribution 3.0 Unported license.
Links: search query example download
514397 71879
35 WormBase [wormbase]
WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results.
Links: search query example download
2014-06-04 22682002 1840311
11895348562 1107871027

last updated on 05-10-2014