Biomart Retrieving One To Many Annotations

Question

[Jeremy]

Hi, I'm looking at BioMart as a way of retrieving a whole lot of annotations at once. I've got a list of transcript IDs and want to get things like protein domains, coil-coil regions, gene ontology terms.

What I've noticed is that with MartView, I only get one of each of these features. For example, if I include Pfam domains, I'll only get one domain back. Is there a way to get a one-to-many feature display?

Should I be looking at another service?

[Casey Bergman]

can you post an example?

Answer 1

[Bert Overduin]

That shouldn't be the case and it is also not what I am seeing myself. If I for instance filter for the BRCA2 gene of human and export the Ensembl Gene ID, Ensembl Transcript ID and PFAM ID (this query), this is what I get:

Ensembl Gene ID Ensembl Transcript ID PFAM ID
ENSG00000139618 ENST00000380152 PF00634
ENSG00000139618 ENST00000380152 PF09169
ENSG00000139618 ENST00000380152 PF09103
ENSG00000139618 ENST00000380152 PF09121
ENSG00000139618 ENST00000380152 PF09104
ENSG00000139618 ENST00000530893
ENSG00000139618 ENST00000528762 PF09121
ENSG00000139618 ENST00000470094 PF09104

So, for example the first transcript has five PFAM domains associated with it.

Please note that Ensembl BioMart questions can also be send to the Ensembl Helpdesk.

[Jeremy]

Thank you, that answers my question. I had selected many different attributes and it was only when I expanded the view to 500 rows that I saw the different values for Pfam.

Answer 2

[Pierre Lindenbaum]

For each transcript (e.g. ENST00000256646 ) I would call the Unitprot API to get the ACNs for the protein ( http://www.uniprot.org/uniprot/?query=ENST00000256646&format=tab&columns=id,database%28interpro%29) and retrieve the annotations for each protein: (http://www.uniprot.org/uniprot/Q04721.xml)