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

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y, these are issues that caused many headaches for FuGE developers. There is
always a trade-off between doc size and parsing simplicity.

We didn't come up with any better a solution with respect to hopping around
the document to get annotations, but at least there are ways of representing
related sets of terms and instance values. This should only be an issue for
API developers though, and once one sensible API is written, everyone else
can base their efforts on that.

So I realize that was no help, but maybe a comparison of how FuGE treats
CV's to dataXML would be?

-angel

On 2/28/07, Philip Jones <pj...@eb...> wrote:
>
> Hi Kent,
>
> I have taken a closer look at the ParamGroup and ParamGroupList elements
> as you suggested.
>
> These elements work extremely well for defining common / default sets of
> params that will be repeated identically for multiple annotations and as
> I recall this was their original purpose.
>
> I do not think however that they solve the problem I described in my
> previous email, for two reasons.
>
> First of all, taking the instance document located at
> http://psidev.sourceforge.net/docstore/download.php?&id=121 as an
> example, you can put any combination of cvParams into a ParamGroup
> element.  The semantics of their association in this element is not
> defined, so they could be grouped together simply because they are a set
> of default values, as in the example instance document, or they could be
> grouped together because one param is an annotation of the other, which
> is the use case I described in my email.  There is no attribute or other
> mechanism to indicate which of these two cases is being described.
>
> Secondly, take the situation that the file contains a thousand spectra.
> You wish to annotate each spectrum with different information, but in
> each case you wish to use two or more associated cvParams for the
> annotation.  If you use the ParamGroupList for this purpose, you would
> end up with a thousand isolated ParamGroup elements at the top of the
> file that would need to be cross referenced from the spectrum elements.
> This would create problems for parsers that would need to either hop
> backwards and forwards in the file or store the details of all of the
> ParamGroup elements before parsing the spectrum elements.
>
> Best regards,
>
> Phil.
>
> Kent Laursen wrote:
> > Hi Phil,
> >
> > Have a closer look at the ParamGoup and ParamGroupList types.  They were
> > designed with this sort of flexibility and aggregability in mind.
> >
> > Regards,
> >
> > Kent
> >
> >
> >> -----Original Message-----
> >> From: psi...@li...
> >> [mailto:psi...@li...] On
> >> Behalf Of Philip Jones
> >> Sent: Tuesday, February 27, 2007 1:18 PM
> >> To: psi...@li...
> >> Subject: [Psidev-ms-dev] Associating CV / ontology annotations
> >>
> >> 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...
> >>
> >>
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> >>
> >>
>
>
> --
> _______________________________________
> Phil Jones
> Software Engineer
> BioSapiens / 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...
>
>
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-- 
Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
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