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bio2rdf for the Public Base
This type describes public bioinformatics datasources that were converted to RDF triples in N3 format and then into a public SPARQL endpoint build using Virtuoso server.
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42 SPARQL endpoint provided by Bio2RDF topics matching:
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| x name | x image | x Date modified | x Number of triples | x Number of topics | x article |
| x GO : Gene Ontology |
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Mar 17, 2009 | 7,414,001 |
Biologists currently waste a lot of time and effort in searching
for all of the available information about each small area of research.
This is hampered further by the wide variations in terminology that may
be common usage at any given time,...
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| x OMIM : Online Mendelian Inheritance in Man |
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Mar 16, 2009 | 1,046,759 | 20,123 |
Welcome to OMIM, Online Mendelian Inheritance in Man. This database is a
catalog of human genes and genetic disorders authored and edited by Dr.
Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and
developed for the World Wide...
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| x PubMed: NCBI bibliographic database |
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797,000,000 | 18,099,968 |
PubMed, available via the NCBI Entrez retrieval
system, was developed by the National
Center for Biotechnology Information (NCBI) at the
National Library of Medicine (NLM), located at the
U.S. National Institutes of Health ...
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| x GeneID : Database of genes from NCBI RefSeq genomes |
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172,931,628 | 4,153,063 |
Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that...
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| x UniProt : The Universal Protein Resource |
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338,602,962 | 3,334,420 |
The Swiss-Prot, TrEMBL, and PIR protein database activities have united to form the Universal Protein Resource (UniProt), which provides a central resource on protein sequences and functional annotation with three database components, each...
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| x UniRef : UniProt Non-redundant Reference Databases |
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242,000,000 | 11,694,097 |
The UniProt NREF (UniProt Reference Clusters) database.
The two major objectives of UniRef are:
(i) to facilitate sequence merging in UniProt, and
(ii) to allow faster and...
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| x UniParc : UniProt Archive a non-redundant archive of protein sequences extracted from Swi |
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490,000,000 | 16,695,439 |
UniProt Archive (UniParc) is part of UniProt project. It is a 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, ...
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| x Path : KEGG PATHWAY Database |
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Mar 21, 2009 | 84,715,161 | 89,735 |
KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks for: 1. Metabolism Carbohydrate Energy ...
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| x CPATH : Pathway Commons |
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27,623,683 | 485,600 |
Pathway Commons is a collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. Access is via a...
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| x Reactome : A knowledgebase of biological pathways and processes |
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2,980,230 |
Reactome is a database of cellular level processes from simple events, such as biochemical reactions, to complex events, such as the cell cycle. It provides process-level annotation of the structure and function of the Human Genome, with dynamic...
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| x BioCyc : Collection of Pathway/Genome Databases |
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18,532,342 |
The BioCyc databases are divided into three tiers, based on their quality.
BioCyc Tier 1: Intensively Curated Databases
The BioCyc Open Chemical Database is also an intensively
curated database. It is an open database of chemical...
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| x MeSH : Medical Subject Headings |
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654,198 |
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. MeSH descriptors are arranged in both an...
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| x PDB : The RCSB Protein Data Bank; a repository for 3D biological macromolecular |
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Mar 20, 2009 | 916,207 | 44,840 |
Welcome. The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids. New structures are released each Wednesday by 1:00am Pacific time. Details about the...
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| x CPD : KEGG Ligand Database for Chemical Compound |
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Mar 21, 2009 | 148,893 |
KEGG COMPOUND is a chemical structure database for metabolic compounds and other chemical substances that are relevant to biological systems.
Each entry is identified by the C number, such as C00047 for L-lysine, and contains various links to other...
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| x GL : KEGG Ligand Database for Carbohydrate Structure |
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Mar 21, 2009 | 94,021 |
Functional information of genes and proteins is organized in KEGG as ortholog groups, called KEGG Orthology (KO) groups, to cover all organisms. The KO groups for glycosyltransferases are finely classified ortholog groups distinguishing known...
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| x EC : The Enzyme Commission |
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Mar 21, 2009 | 396,594 |
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each...
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| x RN : KEGG Ligand Database for Chemical Reaction |
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Mar 21, 2009 | 96,036 |
KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the KEGG metabolic pathways.
Each reaction is identified by the R number, such as R00259
for the acetylation of L-glutamate.
Reactions are linked to...
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| x DR : KEGG Ligand Database for Drug |
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Mar 21, 2009 | 59,595 |
KEGG DRUG is a chemical structure based information resource for
all approved drugs in Japan and the U.S.A. Each chemical structure is
identified by the D number, and is associated with generic names, trade
names, efficacy, target information, etc....
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| x Taxonomy : NEWT is the taxonomy database maintained by the UniProt |
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3,877,201 |
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. [Reference]. Species with protein sequences stored in...
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| x PID : Pathway Interaction Database |
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231,340 |
The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National...
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| x KEGG : Kyoto Encyclopedia of Genes and Genomes |
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A grand challenge in the post-genomic era is a complete computer
representation of the cell, the organism, and the biosphere, which will
enable computational prediction of higher-level complexity of cellular
processes and organism behaviors from...
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| x HGNC : Human Gene Nomenclature Database |
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Mar 17, 2009 | 922,523 | 29,690 |
We have already approved over 24,000 symbols;
the vast majority of these are for protein-coding genes, but also
include symbols for pseudogenes, non-coding RNAs,
phenotypes and genomic features (see HGNC Search).
Our current priority is...
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| x HomoloGene : Discover Homologs |
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Mar 31, 2009 | 6,598,206 |
HomoloGene is a system for automated detection of homologs among
the annotated genes of several completely sequenced eukaryotic genomes.
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| x INOH : Pathway Database |
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234,493 |
INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio...
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| x IProClass : Integrated Protein Knowledgebase |
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149,342,977 |
The iProClass database provides value-added information reports for UniProtKB and unique NCBI Entrez protein sequences in UniParc, with links to over 90 biological databases, including databases for protein families, functions and pathways,...
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| x MGI : Mouse genome database (MGD) from Mouse Genome Informatics (MGI) |
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1,887,729 |
Gene Expression Database (GXD) Project
GXD integrates different types of gene expression information from the
mouse and provides a searchable index of published experiments on
endogenous gene expression during development.(See About GXD.)
Mouse...
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| x CellMap : The Cancer Cell Map |
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172,638 |
The Cancer Cell Map is a selected set of human cancer focused pathways. Biologists can browse and search the Cancer Cell Map pathways. View gene expression data on any pathway. Computational biologists can download all pathways in BioPAX format for...
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| x BioPAX : Biological Pathways Exchange |
BioPAX is a collaborative effort to create a data exchange format for biological pathway data. Get involved...BioPAX Level 3 covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene...
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| x InterPro : Integrated resource of protein families, domains and functional sites |
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203,094 |
The InterPro database was established in 1999 when the InterPro Consortium was formed between the SWISS-PROT group at EBI and SIB, and the founding member databases Prints, PROSITE, Pfam and ProDom. The first release was later that year. ...
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| x Pfam : Protein families |
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66,836 |
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Less... Proteins are generally composed of one or more...
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| x ProDom : A protein domain database |
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5,140 |
ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely...
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| x PROSITE : A protein domain and family database |
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283,376 |
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them [More details / References / Disclaimer / Commercial users]. PROSITE is complemented...
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| x Protein : Protein annotation namespaces | |||||
| x SID : PubChem Substance |
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514,471 | 40,874,689 |
The PubChem Substances Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay.
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| x CID : PubChem Compound |
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The PubChem Compounds Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity...
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| x PubChem : The PubChem Project |
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PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. If you would like to learn more about how to use the PubChem resources, please go to our help page.
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| x UniSTS : Integrating Markers and Maps |
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Mar 31, 2009 | 7,542,235 |
UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences...
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| x DBpedia |
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41,606 |
Wikipedia
is the by far largest publicly available encyclopedia on the Web.
Wikipedia editions are available in over 250 languages with the English
one accounting for more than 1.95 million articles. Wikipedia...
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| x OBO : Open Biomedical Ontologies |
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Mar 18, 2009 | 4,505,677 | 395,108 |
In addition to a listing of OBO ontologies, this site also provides
a statement of the OBO Foundry principles, discussion fora, technical
infrastructure, and other services to facilitate ontology development.
We welcome feedback and encourage...
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| x ChEBI : Chemical Entities of Biological Interest database of small molecules |
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Mar 16, 2009 | 4,764,030 | 50,477 |
Chemical Entities of Biological Interest (ChEBI) is a freely
available dictionary of molecular entities focused on ‘small’ chemical
compounds. The term ‘molecular entity’ refers to any constitutionally
or isotopically distinct atom, molecule, ion,...
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| x Affymetrix : Alliance for Cellular Signaling |
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Apr 20, 2009 | 45,560,115 | 2,741,704 |
Affymetrix' GeneChip® technology was invented in the late 1980's by a
team of scientists led by Stephen P.A. Fodor, Ph.D. The theory behind
their work was revolutionary - a notion that semiconductor
manufacturing techniques could be united with...
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| x BioCarta : Charting pathways of life |
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May 25, 2009 | 13,500 |
Observe how genes interact in dynamic graphical models. Our online
maps depict molecular relationships from areas of active research. In
an "open source" approach, this community-fed forum constantly
integrates emerging proteomic information from...
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