Skip to main content

Table 7 Proteomics Data Combination Query. Proteomics data query: mutant Vs wildtype The query in Table 7 exemplifies a typical query (from the experimental design) that would be performed over the proteomics data. This query returns a list of Fn locus tags observed to be highly abundant (z = 100,000) in the mutant and not present (z = 0) in the wildtype. This query displays the internal integration of this data set. These data were original in three separate spreadsheets but were brought together into RDF and can now be queried as a a unit. Query 1. SeRQL select query identifies FTN identifiers for proteins that were highly abundant in the mutant and with no presence in the wildtype.

From: Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies

SELECT distinct ftn FROM
{ftt} ncbi:blastn {ftn},
{psn} rdfs:seeAlso {ftn},
{analysis} mgla:poson {psn},
{analysisID} rdf:subject {analysis},
{analysisID} rdf:object {exp},
{analysisID} mgla:PeptideAbundance {z}
WHERE xsd:integer(z) > 100000
AND exp LIKE "*mutant*"
INTERSECT
SELECT ftn FROM
{ftt} ncbi:blastn {ftn},
{psn} rdfs:seeAlso {ftn},
{analysis} mgla:poson {psn},
{analysisID} rdf:subject {analysis},
{analysisID} rdf:object {exp},
{analysisID} mgla:PeptideAbundance {z}
WHERE xsd:integer(z) = 0
AND exp LIKE "*wildtype*"
USING namespace
mgla = <http://www.francisella.org/novicida/schema/fnu112/experiments/mgla/>,
soft = <http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html#>,
nwrce = <https://tools.nwrce.org/geo/schema/>,
ncbi = <http://ncbi.nlm.nih.gov/>.