[Psidev-pi-dev] AnalysisXML - Some Requirements

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

Hi,

Based upon the draft analysisXML UML model that Angel circulated a month 
or so ago, here are a few requirements that may need to be addressed.

It is very likely that many of these requirements are already addressed 
in the draft model or by the FuGE model that it extends, especially 
taking into account that the majority of the classes in the diagram do 
not have fields included, but hopefully this list may provoke some 
discussion...

The current draft UML model can be retrieved from:

http://psidev.sourceforge.net/proteomics-informatics/documents/analysisUML.ppt

Information that may need to be captured:

   1. Polypeptide (mostly obvious stuff, probably just fields that are
      present but have not been included in the Powerpoint diagram):
          * Sequence (esp. for peptides) [0..1]
          * database name / version [0..1] - /Appears to be addressed by
            SequenceDatabase class, The current model suggests that all
            proteins identified in one XML need to be identified from
            the same database - presumably this is a safe assumption?/
          * accession / accession version [0..1], mandatory for proteins?
          * database cross references [0..*]
          * Start and end coordinates of peptides in relation to any
            proteins that they identify [0..1] or [0..*] ??
          * Upstream / Downstream flanking regions for peptides

                Will polypeptide be sub-classed to allow (for example) 
accession to be enforced for protein identifications?

    2.   Presumably the 'SearchProtocol' class will handle details of:

        * search engine identity
        * search engine version
        * search input parameters / settings  (Is this CV parameterised
          stuff with CVs from individual search engine vendors?)

    3.   Protein modifications - CustomModification class:

        * Are the monoisotopicMass & averageMass values expected or
          observed?  Does analysisXML need to store both?  Are expected
          values [1..*]?

     4.   Protein modifications - Modification class

        * 'position' field declared as mandatory, however the position
          of the PTM is often unknown.  Ability to handle 'fuzzy' or
          approximate location?  (Does this last requirement even exist?)

    5.   SearchHypothesis / Search result:

        * As mentioned at the last PSI-PI teleconference, just to flag
          up the need for a clear plan of how to (for example) connect
          to a gel spot recorded in GelML format etc.

Best regards,

Phil.

-- 
_______________________________________
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...