IRI on sparql.omabroswer.org for fingerprint concept e.g. PATSWPL
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4.1 years ago
me ▴ 740

I am looking for the triples describing the fingerprint concept in OMA. As used in e.g. http://www.uniprot.org/uniprot/P04637#family_and_domains cross reference label.

My investigation in the model and using some str introspection queries on the IRI's has not panned out. For example the query below does not return in time at http://sparql.omabrowser.org.

SELECT 
  ?iri
WHERE {
   ?iri ?p ?o .   
   FILTER(CONTAINS(STR(?iri), 'PATSWPL'))
}
oma sparql • 868 views
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Actually, currently there is no triples stored for describing the fingerprint concept in OMA. The SPARQL endpoint only contains data from the Hierarchical Orthologous Groups (HOGs) (orthoxml file) and cross-references for correspondent protein/gene in Uniprot, Ensembl, etc. To retrieve the orthologs of P53_HUMAN (from the OMA HOG), you can query such as follows by using the oma:uniProtSwissProtId property :

select distinct ?protein2 {
?cluster a orth:OrthologsCluster.
?cluster orth:hasHomologous ?node1.
?cluster orth:hasHomologous ?node2.
?node2 orth:hasHomologous* ?protein2.
?node1 orth:hasHomologous* ?protein1.
?protein1 a orth:Protein.
?protein1 oma:uniProtSwissProtId "P53_HUMAN".
?protein2 a orth:Protein.
filter(?node1 != ?node2)}

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I think this is an answer more than a comment ;)

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4.1 years ago
tarcisiotmf ▴ 30

Actually, currently there is no triples stored for describing the fingerprint concept in OMA. The SPARQL endpoint only contains data from the Hierarchical Orthologous Groups (HOGs) (orthoxml file) and cross-references for correspondent protein/gene in Uniprot, Ensembl, etc. To retrieve the orthologs of P53_HUMAN (from the OMA HOG), you can query such as follows by using the oma:uniProtSwissProtId property :

select distinct ?protein2 { 
?cluster a orth:OrthologsCluster.  
?cluster orth:hasHomologous ?node1.  
?cluster orth:hasHomologous ?node2.  
?node2 orth:hasHomologous* ?protein2.  
?node1 orth:hasHomologous* ?protein1.  
?protein1 a orth:Protein.  
?protein1 oma:uniProtSwissProtId "P53_HUMAN".  
?protein2 a orth:Protein.  
filter(?node1 != ?node2)}
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