Cell Cycle Ontology

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SPARQL

SPARQL stands for SPARQL Protocol and RDF Query Language. It is standardized by the RDF Data Access Working Group (DAWG) of the W3C. It allows for a query to consist of triple patterns, conjunctions, disjunctions, and optional patterns.

Querying CCO

The following form lets you query the Cell Cycle Ontology through a SPARQL endpoint hosted at Plant Systems Biology department of the Flanders Institute for Biotechnology. The underlying triplestore contains over 1 millon RDF triples of cell cycle information. This information ranges from processes, interactions, proteins, genes, cellular compartments, and so forth, which were collected from diverse sources (like GO, UniProt, IntAct, etc.). Type your SPARQL query in the following text area, then click on 'Run Query'. A new window with the results will be opened. In case there is a syntax error in the query, it will be warned to you. (N.B. Recommended browsers: Firefox, Safari, Opera, or Konqueror. IE proposes to save the results instead of displaying them.)


Query:




SPARQL queries against CCO are run on Virtuoso (OpenLink). This system provides an infrastructure for storing and querying CCO.

Suggested PREFIXes:

S. cerevisiae: sp:<http://www.cellcycleontology.org/ontology/rdf/Sp#>

S. pombe : sc:<http://www.cellcycleontology.org/ontology/rdf/Sc#>

A. thaliana : at:<http://www.cellcycleontology.org/ontology/rdf/At#>

H. sapiens : hs:<http://www.cellcycleontology.org/ontology/rdf/Hs#>

Entire CCO : cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#>

Example 1

The following SPARQL query returns all the core cell cycle proteins (IDs) participating in any known process (in S. pombe):

PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX sp:<http://www.cellcycleontology.org/ontology/rdf/Sp#>
SELECT ?prot_label ?biological_process_label
FROM <http://www.cellcycleontology.org/ontology/rdf/Sp>
WHERE {
?prot sp:is_a sp:CCO_B0000000 .
?prot rdfs:label ?prot_label .
?prot sp:participates_in ?biological_process .
?biological_process rdfs:label ?biological_process_label
}

Example 2

The following simple SPARQL query returns all the terms that have "cell cycle" as string in their names:

PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
SELECT ?term_id ?term_name
 FROM <http://www.cellcycleontology.org/ontology/rdf/CCO>
WHERE {
?term_id rdfs:label ?term_name.
filter regex(?term_name, "cell cycle")
}

Example 3

The following SPARQL query returns the protein names, and their corresponding TAIR reference (AT code) of the core cell cycle proteins in A thaliana:

PREFIX default_ontology:<http://www.cellcycleontology.org/ontology/rdf/At#>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
SELECT ?UNIPROT_NAME ?ACC
 FROM <http://www.cellcycleontology.org/ontology/rdf/At>
WHERE {
 ?prot default_ontology:is_a default_ontology:CCO_B0000000 .
?prot rdfs:label ?UNIPROT_NAME .
?prot default_ontology:encoded_by ?gene .
?gene default_ontology:xref ?b .
?b default_ontology:dbname ?DATABASE .
?b default_ontology:acc ?ACC .
filter(?DATABASE = 'TAIR')
 }

External links

 
Last Updated ( Tuesday, 27 May 2008 11:41 )