Table 1

List of data sources used for demonstrating query federation. Underlined entities have URIs/identifiers that are shared among the distributed datasets, thereby forming a coherent network of statements and making a federated query over all datasets possible.

Data source

Web accessible format

Typical content of statements captured in RDF/OWL (transcribed into natural language)

Used by

HCLS Knowledge Base (DERI Galway)

SPARQL query endpoint, Linked Data

"Entrez Gene entry 2550 is the topic of the scientific journal article with PubMed ID 9373149. It describes a gene that encodes senselab:GABAB_receptor [...]"

Receptor Explorer, AIDA

HCLS Knowledge Base (FU Berlin)

SPARQL query endpoint, Linked Data, Web View, Translator

SenseLab ontology contains information about genes and neuron receptors – asking which neurons have I_K currents

AIDA, Rule Responder

DBpedia

SPARQL query endpoint, Linked Data

"dbpedia:GABAB_receptor is described in Entrez Gene entry 2550. It is a transmembrane receptor. [...]"

Receptor Explorer, FeDeRate

Mapping file between SenseLab receptors (described in HCLS Knowledge Base) and DBpedia

Static RDF/OWL document

"senselab:GABAB_receptor refers to the same entity as dbpedia:GABAB_receptor"

voiD, Receptor Explorer

Description of datasets and mappings (voiD file)

Static RDF/OWL document

"SenseLab ontology contains information about neuron receptor and has mapping files that link this dataset with DBpedia"

voiD

aTag collection/biological statements

Static HTML document with embedded RDF/OWL (RDFa)

"The statement 'GHB was found to bind to GABAB' in Pubmed abstract 123 was tagged with the entities dbpedia:gamma-Hydroxybutyrate, dbpedia:Binding_(molecular) and dbpedia:GABAB_receptor [...]"

FeDeRate

Faviki

Dynamically generated HTML with embedded RDF/OWL (RDFa)

"The web page http://example.com/ webcite has been tagged with the entities dbpedia:GABAB_receptor and dbpedia:Pharmacology by user John_Doe [...]"

FeDeRate

IUPHAR Receptor Database

Relational database, spreadsheet, HTML

"The GABAB receptor is described in Entrez Gene entry 2550. It is activated by the pharmacological substance Baclofen. Gene knockout can lead to seizures. [...]"

FeDeRate

Cheung et al. BMC Bioinformatics 2009 10(Suppl 10):S10   doi:10.1186/1471-2105-10-S10-S10