Re: [Psidev-pi-dev] FW: Representing Sequences

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my 2¢ :
You need to be able to extend this to all molecule types, or am I missing
the point of this thread, and you mean that this would be a suclass of the
conceptual molecule element?

Second, and this is is tangentially related, but are decoy sequences really
a problem we should be putting our effort into? Is it in our domain to
encode semantic information about a sequence, and possibly relating reported
sequences as part of our schema?
On a personal level I could care less if "isDecoy" is an attribute or not,
but the temptation then would be for folks to encode the same accession for
two different sequences, effectively making the primary key of the sequence
object (accession, isDecoy)

Do we want to go there?

On Fri, Jun 27, 2008 at 10:21 AM, Jones, Andy <And...@li...>
wrote:

>  So how about include length as an attribute and then let all other things
> go in the CV (pI, mass, etc.)?
>
>
>
>
>
>
>
> *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?
>
> Yes,  I think so.
>
>  I'm less sure about pI and mass since mass at least can be calculated
> very simply
>
> Only if you have the sequence... (we have residue masses in the file).
>
>
>
>
>
> , and pI values (in my opinion) are pretty inaccurate and fairly
> meaningless
>
> Scandalous! (I happen to agree, but now some people will never speak to
> either of us ever again).
>
> The main problem with mass and pI is that these are 'irrelevant' if the
> sequence is nuleic acid rather than residues.
> Why not just allow CV there? We can share the same CV as the PEFF format,
> which includes, taxonomy, sequence type, gene ID, and lots of wonderful
> other things?
>
>
>
>  – unless someone can convince me otherwise?
>
> Cheers
>
> Andy
>
>
>
>
>
> *From:* David Creasy [mailto:dc...@ma...<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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> David Creasy
>
> Matrix Science
>
> 64 Baker Street
>
> London W1U 7GB, UK
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> Tel: +44 (0)20 7486 1050
>
> Fax: +44 (0)20 7224 1344
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> dc...@ma...
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> http://www.matrixscience.com
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