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This list presents all the known SPARQL endpoints avaiable in the Bioinformatics community. Feel free to add anyone you know of.
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35 Life Science SPARQL endpoint topics matching:
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| x name | x image | x SPARQL endpoint | x Number of triples | x SPARQL technology | x article |
| x NeuroCommons Project |
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http://sparql.neurocommons.org/sparql | Virtuoso Universal Server |
The NeuroCommons project seeks to make all scientific research materials - research articles, knowledge bases, research data, physical materials - as available and as usable as they can be. We do this by fostering practices that render information...
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| x Bio2RDF : Semantic web atlas of postgenomic knowledge |
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http://NAMESPACE.bio2rdf.org/sparql | 2,500,000,000 | Virtuoso Universal Server |
The Bio2RDF project is a tool to convert bioinformatics data and knowledge bases to RDF format. It is a kind of generalized rdfizer for bioinformatics applications, and it is a place for the semantic web life science community to develop and grow.
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| x Linked Life Data |
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http://linkedlifedata.com/sparql | 4,179,999,703 | OWLIM |
LinkedLifeData is a platform for semantic data integration trough RDF warehousing and efficient reasoning that helps to resolve conflicts in the data. One of the major problems that biotechnology and pharmaceutical industries face today is how to...
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| x LODD : Linking Open Drug Data |
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8,000,000 | Virtuoso Universal Server | ||
| x DBpedia SPARQL Endpoint |
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http://dbpedia.org/sparql | 479,000,000 | Virtuoso Universal Server | |
| x BioGateway |
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http://www.semantic-systems-biology.org/biogateway/endpoint | 180,000,000 | Virtuoso Universal Server |
The Biogateway is an integrated systems offering an interface, via SPARQL, to the entire set of the OBO foundry candidate ontologies, the whole set of GOA files, SwissProt, the NCBI taxonomy as well as in-house ontologies. The BioGateway provides a...
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| x FlyTED : the Drosophila Testis Gene Expression Database |
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http://openflydata.org/query/flyted |
FlyTED, the Drosophila Testis Gene Expression Database, is a public database currently containing 2,762 mRNA in situ images and ancillary data revealing the extent of expression of 817 individual genes involved in spermatogenesis in the testis of...
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| x FlyBase : A Database of Drosophila Genes & Genomes |
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http://openflydata.org/query/flybase |
FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are...
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| x FlyAtlas: the Drosophila gene expression atlas |
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http://openflydata.org/query/flyatlas |
This dataset was generated by Venkat Chintapalli, Jing Wang & Julian Dow at the University of Glasgow with funding from the UK's BBSRC.
It gives you a quick answer to the question: where is my gene of interest expressed/enriched in the adult fly?... |
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| x BDGP : Berkeley Drosophila Genome Project |
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http://openflydata.org/query/bdgp |
The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center (funded by the National Human Genome Research Institute, National Cancer Institute, and the Department of Energy), and the Howard Hughes Medical Institute ...
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| x HCLS Demo |
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http://hcls.deri.org/sparql | 325,000,000 | Virtuoso Universal Server | |
| x CardioSHARE |
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http://cardioshare.biordf.net/cardioSHARE/query |
CardioSHARE is a unique framework for querying distributed data and performing data analysis using Semantic Web standards. CardioSHARE's two main innovations are an enhancement to a standard SPARQL query engine, which enables the required data to be...
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| x MyExperiment |
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http://rdf.myexperiment.org/sparql |
myExperiment is a social web site for researchers sharing Research Objects such as Scientific Workflows. The www.myexperiment.org Website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of...
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| x chEMBL |
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http://rdf.farmbio.uu.se/chembl/sparql/ | 23,800,000 | Virtuoso Universal Server |
The ChEMBL team's research focuses on mapping the interactions and functional effects of small molecules binding to their macromolecular targets.
The group studies the interactions of pharmacologically active molecules and their receptors. In... |
| x Chempedia |
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http://pele.farmbio.uu.se/cc0/sparql | Virtuoso Universal Server |
Chempedia is a free service for uniquely identifying and naming chemical substances. If you or your organization work with chemical substances and would like a convenient way to keep track of them in spreadsheets, wikis, web pages and other...
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| x http://labs.intellidimension.com/uniprot | http://labs.intellidimension.com/uniprot/sparql | Semantics.Server |
The goal of this effort is to demonstrate the ability of RDF Gateway to efficiently store and query massive amounts of RDF data in its native RDF repository. The Uniprot RDF project provides all UniProt protein sequence and annotation data in RDF...
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| x Linked Open Data (LOD) Cloud |
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http://lod.openlinksw.com/sparql | Virtuoso Universal Server |
Live Virtuoso instance hosting Linked Open Data (LOD) Cloud
We have reached a beachead re. the Virtuoso instance hosting the Linked Open Data (LOD) Cloud; meaning, we are not going to be performing any major updates and deletions short-term, bar... |
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| x Chem2Bio2RDF : Semantic Web in Systems Chemical Biology |
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http://chem2bio2rdf.org/rdf/snorql/ | Virtuoso Universal Server |
Recent advance in high throughput technique has generated biological data in myriad volumes, which simultaneously contributes to a newly emerged discipline -- system biology, which adopts comprehensive approach to study biological systems....
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| x DrugBank |
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http://www4.wiwiss.fu-berlin.de/drugbank/sparql | 766,920 | D2R Server |
The DrugBank database, available at the University of Alberta, is a bioinformatics and cheminformatics resource that combines detailed drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence,...
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| x LinkedCT : Clinical Trials |
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http://linkedct.org/sparql | 25,000,000 | D2R Server |
LinkedCT is a Linked Data source of clinical trials available at ClinicalTrials.gov, a registry of federally and privately supported clinical trials conducted in the United States and around the world.
ClinicalTrials.gov give you information about... |
| x DailyMed | http://www4.wiwiss.fu-berlin.de/dailymed/sparql | 164,276 | D2R Server |
DailyMed provides high quality information about marketed drugs. This information includes FDA labels (package inserts). This Web site provides health information providers and the public with a standard, comprehensive, up-to-date, look-up and...
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| x Diseasome : The human disease network | http://www4.wiwiss.fu-berlin.de/diseasome/sparql | 91,182 | D2R Server | ||
| x SIDER : Side Effect Resource | http://www4.wiwiss.fu-berlin.de/sider/sparql | 192,515 | D2R Server |
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...
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| x STITCH : Chemical-Protein Interactions |
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http://www4.wiwiss.fu-berlin.de/stitch/sparql | 7,500,000 | D2R Server |
STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
STITCH contains interactions for... |
| x Medicare Formulary | http://www4.wiwiss.fu-berlin.de/medicare/sparql | D2R Server | |||
| x GO : Gene Ontology |
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http://spade.lbl.gov:2020/sparql | D2R Server |
The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to:
The GO is part of a larger classification effort, the Open...
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| x GeneID : Database of genes from NCBI RefSeq genomes |
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http://geneid.bio2rdf.org/sparql | 172,931,628 | Virtuoso Universal Server |
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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http://uniprot.bio2rdf.org/sparql | 338,602,962 | Virtuoso Universal Server |
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 Affymetrix : Alliance for Cellular Signaling |
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http://affymetyrix.bio2rdf.org/sparql | 45,560,115 | Virtuoso Universal Server |
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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http://biocarta.bio2rdf.org/sparql | 13,500 | Virtuoso Universal Server |
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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| x BioCyc : Collection of Pathway/Genome Databases |
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http://biocyc.bio2rdf.org/sparql | 18,532,342 | Virtuoso Universal Server |
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 BioPAX : Biological Pathways Exchange |
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http://biopax.bio2rdf.org/sparql | 67,721,266 | Virtuoso Universal Server |
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 DBpedia |
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http://dbpedia.bio2rdf.org/sparql | 261,758 | Virtuoso Universal Server |
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 PubChem : The PubChem Project |
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http://pubchem.bio2rdf.org/sparql | 775,963 | Virtuoso Universal Server |
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 ChEBI |
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http://chebi.bio2rdf.org/sparql | 4,764,030 | Virtuoso Universal Server |
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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