[Psidev-pi-dev] FW: Representing Sequences

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

Sorry meant to send to the list

 

From: Jones, Andy 
Sent: 27 June 2008 14:54
To: 'David Creasy'
Subject: RE: [Psidev-pi-dev] Representing Sequences

 

id and name are standard for all elements that inherit from FuGE identifiable – this is perhaps a separate discussion as to whether the optional name attribute should be there.

 

I agree that length may be useful – is this just an integer value with no unit? I’m less sure about pI and mass since mass at least can be calculated very simply, and pI values (in my opinion) are pretty inaccurate and fairly meaningless – unless someone can convince me otherwise?

Cheers

Andy

 

 

From: David Creasy [mailto:dc...@ma...] 
Sent: 27 June 2008 14:51
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] Representing Sequences

 

Hi Andy,

length may be useful, because some people won't want to output the actual sequence for space reasons. The other things we wanted to add before were pI and mass. 
Why do we want name? Is this for, say, a description line?
(Also, identifier -> id?)

David

Jones, Andy wrote: 

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

 

 

 

 

 

 
 
 


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