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.
From: A journey to Semantic Web query federation in the life sciences
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/ 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 |