Thread: Re: [Psidev-pi-dev] FW: Representing Sequences (Page 2)

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

In the MPC use case I stated the decoy regexp as a runtime parameter of the ProteinDetection.

<pf:cvParam accession="PSI-PI:000653" name="decoy accession regexp" cvRef="PSI-PI" value="^SHD"/>

and the false discovery rate estimation in the protein results:
<pf:userParam name=Rank" value="3"/>
<pf:userParam name="local FDR in sorted list above" value="33.33" unitName="percent"/>

I find that elegant, because a search engine normally doesnt need to know, whether it is a reverse database.
At the time of interpreting the results that gets relevant.

Von: psi...@li... [mailto:psi...@li...] Im Auftrag von
Jones, Andy
Gesendet: Friday, June 27, 2008 5:24 PM
An: Angel Pizarro
Cc: psi...@li...
Betreff: Re: [Psidev-pi-dev] FW: Representing Sequences

I think Angels response below might not have made it round the list yet.

I tend to agree that isDecoy is redundant information and perhaps this is not the best place to encode semantic
information. An alternative would be to have a parameter, say on SpectrumIdentification for  cvParam = decoy_string
value = Rev. This would be a more compact representation and we would not have to add what is quite a specific
attribute type (isDecoy) to Sequence.

From: an...@it... [mailto:an...@it...] On Behalf Of Angel Pizarro
Sent: 27 June 2008 15:59
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Representing Sequences

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...] 
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

  _____  

-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php

  _____  

_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

  _____  

-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php

  _____  

_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
Angel Pizarro
Director, ITMAT Bioinformatics Facility
806 Biological Research Building
421 Curie Blvd.
Philadelphia, PA 19104-6160
215-573-3736 