[Psidev-pi-dev] Representing Sequences

[Jones, A. <And...@li...>]

Hi all,

 

It was decided on the call that we would like to flag that Sequences in the ConceptualMoleculeCollection should have a Boolean attribute to capture if they are decoy sequences. At the moment we are using the FuGE:Sequence element. I don't really want to add another attribute to this (it's less problematic cutting down FuGE than adding new things), so I'm wondering if we should define our own Sequence type in AnalysisXML. This would also allow us to choose exactly the relevant attributes. At the moment, Sequence can have all of the following:

 

                        <pf:Sequence isCircular="true" sequence="String" length="0" isApproximateLength="true" SequenceAnnotationSet_ref="String" start="0" end="0" identifier="String" name="String">

 

Several of these attributes were created to represent concepts that probably will never be required or implemented in AnalysisXML. How about the following:

 

<DBSequence identifier = "" name = "" isDecoy = "true">

                <seq>MCTMG...</seq>

                <pf:DatabaseReference Database_ref="" accession="Rev_IPI00013808.1"/>

</DBSequence>

 

Are any of the other attributes on Sequence actually required? I'll post a new version of the schema with other changes WRT to PeptideEvidence shortly,

Cheers

Andy