Table 5

SPARQL query example 3: retrieving clinical trials of interest

SELECT DISTINCT ?variation_label ?neoplasm ?clinical_trial

WHERE {

SERVICE <http://linkedlifedata.com/sparql> {?clinical_trial relontology:hasInclusionCriteria ?umls}.

?sample logvd:Sub_topography "Middle third of esophagus".

?sample NCIT:Neoplasm_by_Morphology ?neoplasm.

?sample logvd:hasUMLS_neoplasm ?umls.

?somatic_mutation logvd:hasSample ?sample.

?variation_id rdfs:label ?variation_label.

?somatic_mutation logvd:hasVariation ?variation_id.

}

ORDER BY ?variation_label ?neoplasm


?variation_label

?neoplasm

?clinical_trial


NM_000546.1:c.507G > A

Adenocarcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00001332>

NM_000546.1:c.838A>G

Adenocarcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00001332>

NM_000546.1:c.507G>A

Adenocarcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00001428>

NM_000546.1:c.838A>G

Adenocarcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00001428>

NM_000546.1:c.482C>A

Dysplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00001932>

NM_000546.1:c.482C>A

Dysplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00003076>

NM_000546.1:c.482C>A

Dysplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00003094>

NM_000546.1:c.482C>A

Dysplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00003223>

NM_000546.1:c.482C>A

Dysplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00003593>

NM_000546.1:c.469G>T

Hyperplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00001378>

NM_000546.1:c.469G>T

Hyperplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00001756>

NM_000546.1:c.469G>T

Hyperplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00001760>

NM_000546.1:c.469G>T

Hyperplasia, NOS

<http://data.linkedct.org/resource/trials/NCT00003641>

NM_000546.1:c.422G>A

Squamous cell carcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00000692>

NM_000546.1:c.451C>G

Squamous cell carcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00000692>

NM_000546.1:c.469G>T

Squamous cell carcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00000692>

NM_000546.1:c.474_475ins1

Squamous cell carcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00001450>

NM_000546.1:c.488A>G

Squamous cell carcinoma, NOS

<http://data.linkedct.org/resource/trials/NCT00001450>


This query selects clinical trials of interest, given a defined sub topography (precise location of the tumor) and shows which variations are involved. The SERVICE keyword supports the execution of the query among endpoints distributed across the Web. The output has been limited to 18 results that were selected with the aim of showing different tumors associated with the given sub topography. SPARQL query prefixes are not shown.

Zappa et al. BMC Bioinformatics 2012 13(Suppl 4):S7   doi:10.1186/1471-2105-13-S4-S7

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