How the dump xml store cross reference

[baimingze]

MT

<cross_references>
<ref dbkey="CHEBI:17268" dbname="chebi" />
<ref dbkey="MTBLS100" dbname="metabolights" />
<ref dbkey="MTBLS112" dbname="metabolights" />
<ref dbkey="MTBLS115" dbname="metabolights" />
<ref dbkey="MTBLS123" dbname="metabolights" />
<ref dbkey="MTBLS125" dbname="metabolights" />
<ref dbkey="MTBLS127" dbname="metabolights" />
<ref dbkey="MTBLS150" dbname="metabolights" />
<ref dbkey="MTBLS153" dbname="metabolights" />
<ref dbkey="MTBLS156" dbname="metabolights" />
<ref dbkey="MTBLS171" dbname="metabolights" />
<ref dbkey="MTBLS47" dbname="metabolights" />
<ref dbkey="MTBLS87" dbname="metabolights" />
<ref dbkey="MTBLS88" dbname="metabolights" />
<ref dbkey="MTBLS96" dbname="metabolights" />
</cross_references>

PRIDE

      <cross_references>
        <ref dbkey="10116" dbname="TAXONOMY"/>
        <ref dbkey="20037178" dbname="pubmed"/>
        <ref dbkey="ENSMUSP00000069495" dbname="ensembl"/>
        <ref dbkey="Q9UGK8" dbname="uniprot"/>
        <ref dbkey="Q9UGK3" dbname="uniprot"/>
        <ref dbkey="Q80TG9" dbname="uniprot"/>
        <ref dbkey="Q6IME9" dbname="uniprot"/>
        <ref dbkey="Q5T7W0" dbname="uniprot"/>
        <ref dbkey="ENSP00000307449" dbname="ensembl"/>
        <ref dbkey="P18754" dbname="uniprot"/>
        <ref dbkey="ENSP00000307443" dbname="ensembl"/>
        <ref dbkey="Q7TT36" dbname="uniprot"/>
        <ref dbkey="Q7TT37" dbname="uniprot"/>
        <ref dbkey="ENSP00000307445" dbname="ensembl"/>
        <ref dbkey="Q3UPL6" dbname="uniprot"/>
        <ref dbkey="Q3V1L6" dbname="uniprot"/>
        <ref dbkey="Q3UPL5" dbname="uniprot"/>
        <ref dbkey="ENSP00000307307" dbname="ensembl"/>
        <ref dbkey="O75298" dbname="uniprot"/>
        <ref dbkey="A2RSQ0" dbname="uniprot"/>
        <ref dbkey="A2RSQ1" dbname="uniprot"/>
      </cross_references>

• Q1:
• Where do we retrieve these dbnames and dbkeys?

[ypriverol]

@baimingze they need to do it during the generation of the file. They need to know the name of the db. We can ask to the EBI search team to have a system for this dbname retrieval. We can ask them how to know which fields are keys. If you want you can write the email and I can make the ticket for them.

[baimingze]

@ypriverol I have found that they metioned we can find the definition of fields and cross_reference at here: /ebi/extserv/projects/ebinocle/ebinocle-config/src/main/domains/pride.xml

I will check on these files.

[baimingze]

The definition of the cross reference is like this:

        <field id="UNIPROT" type="xref">
            <options>
                <option key="config.xref.domain.field" value="acc" />
                <option key="config.xref.domain" value="uniprot" />
            </options>
            <name>UNIPROT</name>
            <description>UNIPROT reference</description>
        </field>