Open janstrauss1 opened 5 years ago
In case working with the SBML version of the model is an option, you could alternatively download the model from http://bigg.ucsd.edu/static/models/iML1515.xml.gz, uncompress, and go through the listOfGeneProducts
. There you can find links to external databases, which all start with the prefix http://identifiers.org/
followed by a catalog identifier (e.g., ncbigene
), and an actual identifier (separated by a slash /
), e.g.,
<fbc:listOfGeneProducts xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">
<fbc:geneProduct fbc:id="G_b2551" fbc:label="b2551" metaid="G_b2551">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#G_b2551">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P0A825" />
</rdf:Bag>
</bqbiol:is>
<bqbiol:isEncodedBy>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/asap/ABE-0008389" />
<rdf:li rdf:resource="http://identifiers.org/ecogene/EG10408" />
<rdf:li rdf:resource="http://identifiers.org/ncbigene/947022" />
<rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16130476" />
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</fbc:geneProduct>
<!-- ... -->
Please note that the qualifiers (in this example bqbiol:is
and bqbiol:isEncodedBy
) give you information about the relationship between the particular geneProduct
and the external references.
Thanks for making an issue for this. These identifiers are in SBML, but we should also include them in JSON model downloads and on the Data Access page (e.g. with a genes flat file), so I'm going to leave this open for those new features.
Hi there,
I apologize in advance for my newbie question but I am currently stuck in some ID mapping issues.
I am trying to retrieve the external database IDs for all genes in a BiGG model in order to map BiGG gene IDs to Uniprot IDs for downstream Gene Set Enrichment Analysis using reporter metabolites.
I have tried the BiGG Web API using
curl 'http://bigg.ucsd.edu/api/v2/models/iML1515/genes'
but this does not returndatabase_links
for the genes. External database links and IDs only seem to be returned when specifying a gene, metabolite or reaction likecurl 'http://bigg.ucsd.edu/api/v2/models/iML1515/genes/b0002'
.How can I retrieve external database ID mappings for all gene IDs in a BiGG model?
Many thanks in advance for your help!
Jan