kno.e.sis - SPARQL

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Sahoo SS et al JBI resource page <meta name="description" content="semantic Web, semantic bioinformatics, schema mapping, EKoM, BioPAX ontology, gene-pathway knowledgebase"/>

Resource page

This is a resource page for the paper (PDF) on semantic Web based gene-pathway knowledgebase submitted to Journal of Biomedical Informatics

Query 1: Which genes participate in a large number of pathways?
SPARQL syntax:

SELECT gene1, gene2, pth, pn
FROM TABLE(SDO_RDF_MATCH('
(?gene1 ekom:functionally_related_to ?pth)
(?gene2 ekom:functionally_related_to ?pth)
(?pth bp:NAME ?pn)
(?gene1 rdf:type ekom:gene)
(?gene2 rdf:type ekom:gene)
(?pth rdf:type bp:pathway)',
SDO_RDF_Models('entrez_gene'),null,
SDO_RDF_Aliases(SDO_RDF_Alias('ekom','http://ekom.nlm.nih.gov/ekom.owl#'),
SDO_RDF_Alias('bp','http://www.biopax.org/release/biopax-level2.owl#'),
SDO_RDF_Alias('rdf','http://www.w3.org/1999/02/22-rdf-syntax-ns#')),null,null))
WHERE gene1 != gene2 ORDER by pth;

Query 2: Which genes (or gene products) interact with each other?
SPARQL syntax:

SELECT gene1, gene2, gi
FROM TABLE(SDO_RDF_MATCH('
(?gene1 ekom:have_common_pathway ?gene2)
(?gene1 ekom:functionally_related_to ?gi)
(?gene2 ekom:functionally_related_to ?gi)
(?gene1 rdf:type ekom:gene)
(?gene2 rdf:type ekom:gene)
(?gi rdf:type ekom:interaction)',
SDO_RDF_Models('entrez_gene'),null,
SDO_RDF_Aliases(SDO_RDF_Alias('ekom','http://ekom.nlm.nih.gov/ekom.owl#'),
SDO_RDF_Alias('rdf','http://www.w3.org/1999/02/22-rdf-syntax-ns#')),null,null))
WHERE gene1<>gene2 ORDER BY gene1,gene2,gi;

Query 3: Which genes are expressed in the brain?
SPARQL syntax:

SELECT distinct gene
FROM TABLE(SDO_RDF_MATCH('
(?gene ekom:has_product ?protein)
(?protein bp:ORGANISM ?organism)
(?protein bp:COMMENT ?comm)
(?protein rdf:type bp:protein)
(?gene rdf:type ekom:gene)',
SDO_RDF_Models('entrez_gene'),null,
SDO_RDF_Aliases(SDO_RDF_Alias('ekom','http://ekom.nlm.nih.gov/ekom.owl#'),
SDO_RDF_Alias('rdf','http://www.w3.org/1999/02/22-rdf-syntax-ns#'),
SDO_RDF_Alias('bp','http://www.biopax.org/release/biopax-level2.owl#')),null,null))
WHERE REGEXP_LIKE(organism,'((.)*(brain)(.)*)') OR WHERE REGEXP_LIKE(comm,'((.)*(brain)(.)*)');