| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | AC | ||
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1 | Title | Description | Organization | part of dataset | Website | License | License Document | Publication | Comment | Source Data Update Frequency | Bio2RDF script up to date | Bio2RDF Example Record URI | Bio2RDF SPARQL endpoint | Bio2RDF RDF Download URL | CKAN | |||||||||||||||
2 | affymetrix | Affymetrix Probesets | Affymetrix probesets | Affymetrix | http://affymetrix.com | non-commercial redistribution | http://media.affymetrix.com/support/developer/SDK_and_NetAffx_Data_Non_Commercial_Use.pdf | data no longer available | yearly | yes | http://bio2rdf.org/affymetrix:246206_at | http://affymetrix.bio2rdf.org/sparql | http://download.bio2rdf.org/release/2/ | http://thedatahub.org/dataset/bio2rdf-affymetrix | ||||||||||||||||
3 | archival | NLM archives | References from toxicology literature | NLM | toxkb | research non distributable to third party without license | yes | http://bio2rdf.org/archival:archival_e8613685f300bfc7d7b9741c3418f430 | http://toxkb.bio2rdf.org/sparql | |||||||||||||||||||||
4 | atlas | http://bio2rdf.org/omim:604640, http://bio2rdf.org/uniprot:Q92781 | ||||||||||||||||||||||||||||
5 | bind | Biomolecular Interaction Network Database | The BIND collection of interactions, molecular complexes and pathways. | irefindex | public domain | pubmed:15608229 | none | N/A | http://bio2rdf.org/bind:2375 | http://bind.bio2rdf.org/sparql | ||||||||||||||||||||
6 | bio2rdf.atlas | Bio2RDF Atlas | A warehouse of Bio2RDF datasets - omim, pubmed, mgi, hgnc, chebi, proodom, mesh, obo, pdb, geneid, ligand, pfam, genbank, uniprot, uniref | Bio2RDF | public domain | pubmed:18472304 | one-time data warehouse | none | N/A | http://atlas.bio2rdf.org/sparql | ||||||||||||||||||||
7 | biocarta | BioCarta | The BioCarta collection of pathways. | pathwaycommons | http://www.biocarta.com/genes/index.asp | by attribution; no resell | http://www.biocarta.com/legal/terms.asp | N/A | http://bio2rdf.org/biocarta:h_HivnefPathway | http://biocarta.bio2rdf.org/sparql | ||||||||||||||||||||
8 | biocyc | BioCyc | The BioCyc collection of Pathway/Genome Databases (PGDBs) | SRI | pathwaycommons | http://biocyc.org/ | research and eduction; fee for commerical use | http://biocyc.org/download.shtml | N/A | http://bio2rdf.org/biocyc:catalysis1399454 | http://biocyc.bio2rdf.org/sparql | |||||||||||||||||||
9 | biomodels | BioModels | BioModels Database is a repository of peer-reviewed, published, computational models | EBI | http://www.ebi.ac.uk/biomodels-main/ | public domain | yes | http://bio2rdf.org/biomodels:BIOMD0000000214 | http://biomodels.bio2rdf.org/sparql | |||||||||||||||||||||
10 | biopax | BioPax | Contains cpath, reactome, biocyc | public domain | N/A | http://bio2rdf.org/cpath:CPATH-9978CPATH-9978 | http://biopax.bio2rdf.org/sparql | |||||||||||||||||||||||
11 | bioportal | NCBO bioportal | The National Center for Biomedical Ontology provides 300+ terminologies and ontologies through BioPortal | NCBO | http://bioportal.bioontology.org/ | various | continuous | yes | http://bio2rdf.org/fma:37633, http://bio2rdf.org/cl:0000825 | http://download.bio2rdf.org/release/2/ncbo/ | ||||||||||||||||||||
12 | ccris | Chemical Carcinogenisis Research Information System | Carcinogenicity and mutagenicity test results for over 8,000 chemicals | NLM | http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?CCRIS | research non distributable to third party without license | yes | http://bio2rdf.org/ccris:ccris_5d53ce200cde223b5bc3d72eb509ddd0 | http://toxkb.bio2rdf.org/sparql | |||||||||||||||||||||
13 | cebs | Chemical Effects in Biological Systems | The CEBS database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial and governmental laboratories. CEBS is designed to display data in the context of biology and study design. | NIEHS | http://www.niehs.nih.gov/research/resources/databases/cebs/index.cfm | public | SIFT file format; may have changed | no | http://bio2rdf.org/cebs:7700e18d1d6fcf41dc18ed212578ff49 | http://toxkb.bio2rdf.org/sparql | ||||||||||||||||||||
14 | chebi | Chemical Entities of Biological Interest | Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. | EBI | bioportal | http://www.ebi.ac.uk/chebi/ | public domain | monthly | N/A | http://bio2rdf.org/chebi:37889 | http://chebi.bio2rdf.org/sparql | http://thedatahub.org/dataset/bio2rdf-chebi | ||||||||||||||||||
15 | chembl | ChEMBL | ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). | EBI | https://www.ebi.ac.uk/chembl/ | CC-SA | https://www.ebi.ac.uk/chembl/ | yes | ||||||||||||||||||||||
16 | ctd | Comparative Toxicogenomics Database | Curated data describing cross-species chemical–gene/protein interactions and chemical– and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. | http://ctdbase.org | research and education; cite & link | http://ctdbase.org/about/legal.jsp | yes | http://bio2rdf.org/mesh:D001554, http://bio2rdf.org/ctd_vocabulary:Chemical-Disease-Association | http://ctd.bio2rdf.org/sparql | http://download.bio2rdf.org/release/2/ctd | ||||||||||||||||||||
17 | dbpedia | DBPedia | The structured data of Wikipedia | http://dbpedia.org | public domain | yes | http://dbpedia.bio2rdf.org/sparql | |||||||||||||||||||||||
18 | drugbank | DrugBank | Resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. | http://www.drugbank.ca | research and education; cite | http://www.drugbank.ca/about | yes | http://bio2rdf.org/drugbank:DB01381 | http://drugbank.bio2rdf.org/sparql | http://download.bio2rdf.org/release/2/drugbank | ||||||||||||||||||||
19 | dsstox | Distributed Structure Searchable Toxicity Database | Resource that houses and publishes downloadable, structure-searchable, standardized chemical structure files assoicated with chemical inventories or toxicity data sets of environmental relevance. | U.S EPA | http://www.epa.gov/ncct/dsstox/ | public | yes | |||||||||||||||||||||||
20 | ec | Enzyme Classification | The IUBMB Enzyme Classification | no | http://bio2rdf.org/ec:1.1.1.1 | http://ec.bio2rdf.org/sparql | ||||||||||||||||||||||||
21 | emic | Environmental Mutagen Information Center | References from toxicology literature | NLM | research non distributable to third party without license | yes | http://bio2rdf.org/emic:emic_2ba37517b06cd6e01aaff1b68de65264 | |||||||||||||||||||||||
22 | genbank | Genbank | NIH genetic sequence database, an annotated collection of all publicly available DNA sequences | NCBI | http://www.ncbi.nlm.nih.gov/genbank/ | public domain | http://www.ncbi.nlm.nih.gov/About/disclaimer.html | no | http://bio2rdf.org/genbank:AK096541 | http://genbank.bio2rdf.org/sparql | http://download.bio2rdf.org/release/2/genbank | |||||||||||||||||||
23 | geneid | NCBI Gene | NCBI Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information | NCBI | http://www.ncbi.nlm.nih.gov/gene | public domain | http://www.ncbi.nlm.nih.gov/About/disclaimer.html | yes | http://bio2rdf.org/geneid:4348855 | http://geneid.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/geneid | |||||||||||||||||||
24 | genetox | NLM Genetic Toxicology Databank | Genetox is a datafile containing legacy experiments testing for potential genotoxicity | NLM | http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?GENETOX | research non distributable to third party without license | quarterly | yes | ||||||||||||||||||||||
25 | goa | Gene Ontology Annotations | high-quality Gene Ontology (GO) annotations to proteins in UniProt | http://www.ebi.ac.uk/GOA/ | copyright | yes | http://bio2rdf.org/goa_resource:101M_A_1 | http://goa.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/goa | |||||||||||||||||||||
26 | hgnc | HUGO Gene Nombenclature Committee | unique gene symbols and names to over 33,000 human loci | http://www.genenames.org/ | copyright | yes | http://bio2rdf.org/hgnc:25990 | http://hgnc.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/hgnc | |||||||||||||||||||||
27 | hivdb | human immunodeficiency virus type 1 (HIV-1) Human protein interaction database | A database of HIV-1 human protein interactions | http://gnode1.mib.man.ac.uk/HIV1-text-mining | public domain | data no longer available | none | no | http://bio2rdf.org/hhpid:155945-23291-1 | http://hhpid.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/hivdb | |||||||||||||||||||
28 | homologene | Homologene | automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. | NCBI | http://www.ncbi.nlm.nih.gov/homologene | public domain | http://www.ncbi.nlm.nih.gov/About/disclaimer.html | yearly | yes | http://bio2rdf.org/homologene:47 | http://homologene.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/homologene | ||||||||||||||||||
29 | hsdb | Hazardous Substances Databank | Comprehensive, peer reviewed toxicology data for approximately 5000 chemicals | NLM | http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB | research non distributable to third party without license | yes | http://bio2rdf.org/hsdb:ac3870fcad1cfc367825cda0101eee62 | http://toxkb.bio2rdf.org/sparql | |||||||||||||||||||||
30 | inoh | Integrating Network with Object Hierarchies Pathway Database | A database of metabolic and signalling pathways | http://www.inoh.org/ | copyright | yearly | no | http://inoh.bio2rdf.org/sparql | ||||||||||||||||||||||
31 | interpro | 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. InterPro has the following member databases: GENE3D, HAMAP, PANTHER, PIRSF, PRINTS, PROSITE patterns, PROSITE profiles, Pfam, PfamB, ProDom, SMART, SUPERFAMILY, TIGRFAMs | EBI | http://www.ebi.ac.uk/interpro/ | copyright; free to use and distribute | http://www.ebi.ac.uk/interpro/release_notes.html | pubmed:22096229 | 2-3 months | yes | http://bio2rdf.org/interpro:IPR001478 | http://interpro.bio2rdf.org | ||||||||||||||||||
32 | ipi | International Protein Index | A database of cross references between the primary data sources | EBI | http://www.ebi.ac.uk/IPI/ | deprecated. final release was produced on the 27th September 2011. replaced by uniprot | none | yes | http://ipi.bio2rdf.org/sparql | http://download.bio2rdf.org/release/2/ipi/ | ||||||||||||||||||||
33 | iproclass | 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. | http://pir.georgetown.edu/iproclass/ | yes | http://bio2rdf.org/uniprot:Q6GZX0 | http://iproclass.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/iproclass | ||||||||||||||||||||||
34 | irefindex | iRefIndex | RefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI and OPHID | http://irefindex.uio.no | CC-BA | http://irefindex.uio.no/wiki/README_MITAB2.6_for_iRefIndex#License | pubmed:18823568 | twice a year | yes | http://bio2rdf.org/irefindex_irogid:16826204 | http://irefindex.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/irefindex | ||||||||||||||||||
35 | kegg | Kyoto Encyclopedia of Genes and Genomes | KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from genomic and molecular-level information. | http://www.genome.jp/kegg/ | licensing required | subscription required as of July 1, 2011 | every two months | no | http://bio2rdf.org/path:mka00350 | http://kegg.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/kegg | |||||||||||||||||||
36 | mesh | Medical Subject Headings | MeSH is the National Library of Medicine's controlled vocabulary thesaurus. | http://www.nlm.nih.gov/mesh/ | licensing required | yes | http://bio2rdf.org/mesh:D006948 | http://mesh.bio2rdf.org/sparql | ||||||||||||||||||||||
37 | mgi | MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. | http://www.informatics.jax.org/ | no | http://bio2rdf.org/mgi:3027896 | http://mgi.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/mgi | |||||||||||||||||||||||
38 | ndc | National Drug Code | The Food and Drug Administration (FDA) current list of all drugs manufactured, prepared, propagated, compounded, or processed by it for commercial distribution. | FDA | http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm | public domain | twice a month | yes | http://bio2rdf.org/ndc_resource:9321661b46400c27651a09266462217e | http://ndc.bio2rdf.org/sparql | ||||||||||||||||||||
39 | omim | Online Mendelian Inheritance in Man | OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. | NCBI | http://www.ncbi.nlm.nih.gov/omim/ | research only. no distribute to third party without license | http://omim.org/downloads | monthly | yes | http://omim.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/omim | |||||||||||||||||||
40 | pathwaycommons | pathway commons | Pathway Commons is a central resource for pathways and interactions | http://webservice.baderlab.org:48080/ | to be replaced by pathwaycommons | none | yes | http://cpath.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/pathwaycommons | |||||||||||||||||||||
41 | pdb | Protein DataBank | The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. | http://www.rcsb.org/pdb | public domain | weekly | yes | http://download.bio2rdf.org/release/2/pdb/ | ||||||||||||||||||||||
42 | pharmgkb | The Pharmacogenomics Knowledgebase | The PharmGKB is a pharmacogenomics knowledge resource that encompasses clinical information including dosing guidelines and drug labels, potentially clinically actionable gene-drug associations and genotype-phenotype relationships. PharmGKB collects, curates and disseminates knowledge about the impact of human genetic variation on drug responses. | http://www.pharmgkb.org | copyright | monthly | yes | http://pharmgkb.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/pharmgkb | |||||||||||||||||||||
43 | pid | Pathway Interaction Database | The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways | http://pid.nci.nih.gov/ | contains biocarta, reactome and NCI-curated pathways | no | http://pid.bio2rdf.org/sparql | |||||||||||||||||||||||
44 | pubchem | PubChem | PubChem provides physical-chemical information on small molecules and their biological activities | NCBI | http://pubchem.ncbi.nlm.nih.gov/ | public domain | http://www.ncbi.nlm.nih.gov/About/disclaimer.html | continuous | no | http://pubchem.bio2rdf.org/sparql | ||||||||||||||||||||
45 | pubmed | PubMed | PubMed comprises more than 21 million citations for biomedical literature from MEDLINE, life science journals, and online books. | NCBI | http://www.ncbi.nlm.nih.gov/pubmed | licensed | yes | http://pubmed.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/pubmed | |||||||||||||||||||||
46 | reactome | REACTOME | REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database | http://www.reactome.org/ReactomeGWT/entrypoint.html | Creative Commons Attribution 3.0 Unported License. | part of pathwaycommons | every three months | N/A | http://reactome.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/reactome | ||||||||||||||||||||
47 | refseq | RefSeq | The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. | NCBI | http://www.ncbi.nlm.nih.gov/RefSeq/ | public domain | http://www.ncbi.nlm.nih.gov/About/disclaimer.html | every two months | no | http://refseq.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/refseq | |||||||||||||||||||
48 | sgd | Saccharomyces Genome Database | The SGD project provides encyclopedic information about the yeast genome and its genes, proteins, and other encoded features. Experimental results on the functions and interactions of yeast genes, as reported in the peer-reviewed literature, are extracted by high-quality manual curation and integrated within a well-developed database. | http://www.yeastgenome.org/ | public domain | yes | http://sgd.bio2rdf.org/sparql | http://s4.semanticscience.org/bio2rdf_download/rdf/sgd | ||||||||||||||||||||||
49 | taxonomy | NCBI Taxonomy | The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases | NCBI | http://www.ncbi.nlm.nih.gov/taxonomy | public domain | http://www.ncbi.nlm.nih.gov/About/disclaimer.html | part of ncbo | weekly | yes | http://taxonomy.bio2rdf.org/sparql | |||||||||||||||||||
50 | toxkb | ToxKB | A warehouse of toxicology resources including archival, ccris, cebs, cis, cpdbas, ctd, emic, genetox, hsdb, toxcast. | public domain | data warehouse | yes | http://toxkb.bio2rdf.org/sparql | |||||||||||||||||||||||
51 | uniparc | UniParc | UniParc is non-redundant archive of protein sequences extracted from public databases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, PIR-PSD, EMBL, EMBL WGS, Ensembl, IPI, PDB, PIR-PSD, RefSeq, FlyBase, WormBase, H-Invitational Database, TROME database, European Patent Office proteins, United States Patent and Trademark Office proteins (USPTO) and Japan Patent Office proteins. | http://www.ebi.ac.uk/uniparc/ | public domain | yes | http://uniparc.bio2rdf.org/sparql | |||||||||||||||||||||||
52 | uniprot | UniProt | The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation | http://www.uniprot.org/ | cc-attribution-no derivatives | http://www.uniprot.org/help/license | pubmed:22102590 | yes | http://uniprot.bio2rdf.org/sparql | |||||||||||||||||||||
53 | unists | UniSTS | UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. | NCBI | http://www.ncbi.nlm.nih.gov/unists/ | public domain | weekly | yes | http://unists.bio2rdf.org/sparql | |||||||||||||||||||||
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