[Psidev-ms-dev] Associating CV / ontology annotations

[Philip J. <pj...@eb...>]

Hi,

I would like to suggest that it may be useful to include a mechanism to 
associate cvParam elements together to allow more complex annotation of 
entities in dataXML.  Here is an artificial example to illustrate the 
problem:

<activation>
    <cvParam cvLabel="PSI" accession="PSI:1000044" name="Method" 
value="CID"/>
    <cvParam cvLabel="PSI" accession="PSI:1000045" 
name="CollisionEnergy" value="35.00"/>
    <cvParam cvLabel="UO" accession="UO:0000112" name="Joule"/>
</activation>

In this example, the third CV parameter is an annotation of the second, 
indicating the units of the value of collision energy from the OBO unit 
ontology. (I know that collision energy is normally measured in eV, but 
eV is not in the UO ontology ! .... Just an example.)

So the question is, do we need this mechanism and if so, how do we 
implement it?

 From my point of view, I think it is needed.  I have wanted to be able 
to do this on numerous occasions when creating PRIDE entries for 
submissions - PRIDE uses the existing mzData schema cvParam mechanism 
for annotation.

I think this could / should be kept simple.  It would be easy to allow 
an arbitrarily complex hierarchy of terms to be created, but I think 
that might result in chaos. 

Two possible solutions:

1. Perhaps just add an optional attribute to allow associated cvParams 
to be linked, e.g. with a number or perhaps something more guaranteed to 
be unique, like an LSID?

2. Perhaps add a single additional layer to the hierarchy, something 
like this:

<activation>
    <annotation>
        <cvParam cvLabel="PSI" accession="PSI:1000044" name="Method" 
value="CID"/>
    </annotation>
    <annotation>
        <cvParam cvLabel="PSI" accession="PSI:1000045" 
name="CollisionEnergy" value="35.00"/>
        <cvParam cvLabel="UO" accession="UO:0000112" name="Joule"/>
    </annotation>
</activation>

Best regards,

Phil.

-- 
_______________________________________
Phil Jones
Software Engineer
PRIDE Project Team
Sequence Database Group
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

Tel +44 (0)1223 492 610 (Direct Line)
mailto:pj...@eb...