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Hackathon

During the hackathon, group activities will be recorded in a Wiki site. Please create sub-divided pages and log your activities as much as possible.

BioHackathon 2011 Wiki https://github.com/dbcls/bh11/wiki

List of available biomedical SPARQL endpoints

NCBO http://sparql.bioontology.org/webui/
UniProt http://sparql.uniprot.org/ (not ready)
BioMart http://www.biomart.org/rc6_documentation.pdf (pp.83-85)

BMC: http://bm-test.res.oicr.on.ca:9084/ (37 biological databases)
ICGC: http://bm-test.res.oicr.on.ca:9085/ (25 cancer databases)

Bio2RDF http://www.freebase.com/view/base/bio2rdf/views/sparql
BioGateway http://www.semantic-systems-biology.org/biogateway/querying
Cell Cycle Ontology http://www.semantic-systems-biology.org/cco/queryingcco/sparql
Neuroscience Information Framework (NIF) http://neurolex.org/wiki/SparqlEndPoint
Neuro Commons http://sparql.neurocommons.org/sparql
myExperiment http://rdf.myexperiment.org/sparql
ChEMBL

http://rdf.farmbio.uu.se/chembl/sparql
http://api.kasabi.com/dataset/chembl-rdf/apis/sparql (needs free account for subscription)

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List of available SADI services

http://sadiframework.org/registry/services

List of Semantic Web libraries for each language

	RDF/SPARQL libraries	RDF parse	RDF create	SPARQL
Ruby	RDF.rb / ActiveRDF	o	o	o
Python	RDFLib
Perl	PerlRDF
Java	Jena / Sesame
R	rrdf

List of triple stores

Add instructions for installation, fixtures to test and example queries

OWLIM http://www.ontotext.com/owlim
4store http://4store.org/
5store http://www.4store.org/trac/wiki/5store
Virtuoso http://virtuoso.openlinksw.com/
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List of triplestore implementations http://en.wikipedia.org/wiki/Triplestore

List of public RDF hosting and SPARQL services

BioLOD http://biolod.org/
Dydra http://dydra.com/ (invitational only, private beta)
Kasabi http://kasabi.com/ (public beta)
Sindice http://sparql.sindice.com/ (public beta)
Freebase http://sparql.freebase.com/
DBpedia http://dbpedia.org/sparql
Data.gov http://services.data.gov/sparql
Data.gov.uk http://data.gov.uk/sparql
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RDF validator http://www.w3.org/RDF/Validator/
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List of benchmarks

W3C RDF Store Benchmarking summary

http://www.w3.org/wiki/RdfStoreBenchmarking

BSBM: Berlin SPARQL Benchmark

http://www4.wiwiss.fu-berlin.de/bizer/BerlinSPARQLBenchmark/results/V6/index.html

LUBM: Lehigh University Benchmark

http://swat.cse.lehigh.edu/projects/lubm/

NTNU: Norges teknisk-naturvitenskapelige universite SPARQL benchmarking

gauging triple stores with actual biological data (BMC Bioinformatics - forthcoming)

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SEE ALSO

Dictionary page for the list of relevant technologies, projects, institutions etc.

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