Question: IRI on sparql.omabroswer.org for fingerprint concept e.g. PATSWPL
0
gravatar for me
14 months ago by
me690
Switzerland
me690 wrote:

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'))
}
sparql oma • 391 views
ADD COMMENTlink modified 14 months ago by tarcisiotmf30 • written 14 months ago by me690
1

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)}

ADD REPLYlink modified 14 months ago • written 14 months ago by tarcisiotmf30
1

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

ADD REPLYlink written 14 months ago by me690
2
gravatar for tarcisiotmf
14 months ago by
tarcisiotmf30
tarcisiotmf30 wrote:

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)}
ADD COMMENTlink modified 14 months ago by genomax59k • written 14 months ago by tarcisiotmf30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1679 users visited in the last hour