Getting refseq cross reference using EBI REST API

Hi All,

I have not been able to extract any refseq IDs using the 'EB-eye' REST interface at EMBL. In fact, requesting a list of available cross references seems to never show refseq in the list, even when it clearly should be there - for example

http://www.ebi.ac.uk/ebisearch/ws/rest/uniprot/xref

produces this list (truncated) --

arrayexpress-repository"/>
atlas-experiments"/>
...
pfam"/>
pombase"/>
pride"/>
reactome"/>
rhea"/>
...
uniref100"/>
uniref50"/>
uniref90"/>
wormbaseParasite"/>

Basically 'everything but' Refseq!

Am I doing something wrong?

Thanks!

Randy

rest refseq api

• 2,575 views • link

updated 4.0 years ago by Ram

• written 10.7 years ago by artemisdiscovery •

1 answer

I got an answer for this problem from Silvano Squizzato at EBI. Here is what you have to do - taking a protein that I know has a refseq ID:

http://www.ebi.ac.uk/ebisearch/ws/rest/uniprot?query=DYR_HUMAN&fields=REFSEQ,id

<result>
    <hitCount>1</hitCount>
    <entries>
        <entry acc="P00374" id="DYR_HUMAN" source="uniprot">
        <fields>
            <field id="REFSEQ">
                <values>
                    <value>NP_000782.1</value>
                    <value>NP_001277283.1</value>
                </values>
            </field>
            <field id="id">
                <values>
                    <value>DYR_HUMAN</value>
                </values>

I am surprised this works, as refseq does not appear as a 'field' if you ask for the uniprot metadata.

Randy

• 0 views • link

updated 6.7 years ago by Ram

• written 10.7 years ago by artemisdiscovery •