Bundles/ipi
< Bundles
PDB and some of our other data sources are indexed by Uniprot id, while the Neurocommons store only knows about Entrez Gene ids, so this is a bundle consisting of a Uniprot/Gene correspondence.
ipiparse.py parses data from a primary source:
- IPI - IPI UniProt Format | International Protein Index | EBI (c) European Bioinformatics Institute 2009
It follows bio2rdf in naming uniprot ... thingies... um... records?
The following query shows the structure of the output:
Show Entrez gene of each PDB chain
prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix bio2rdf: <http://bio2rdf.org/ns/bio2rdf#>
select distinct ?chain ?sym where
{
?chain sc:uniprot ?prot.
?gene bio2rdf:xPath ?prot.
?gene sc:ggp_has_primary_symbol ?sym.
filter ( regex(?sym, "^HLA-") )
}
order by ?chain
odd... the bio2rdf schema says http://bio2rdf.org/ns/bio2rdf:xPath but I'm sure I saw http://bio2rdf.org/ns/bio2rdf#xPath somewhere.
