Re: [Psidev-pi-dev] FW: Spec doc

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

Hi all,

New spec doc uploaded by SVN: 

Several updates, inserted new auto-generated documentation, section on
spectrumID, section on internal ions, added listing of example files.

Hopefully the images should appear this time, let me know if they don't. Can
everyone take a look in particular at the comments in the margin. Also we need a
more complete list of the contributors at the end, please mail me names of
people to add.

Cheers
Andy








> -----Original Message-----
> From: Andreas Bertsch [mailto:be...@in...]
> Sent: 04 December 2008 15:10
> To: David Creasy
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] FW: Spec doc
> 
> Hi David,
> 
> > Andy suggested:
> > Andreas can you add: “search tolerance plus value” and “search tolerance
> > minus value” to the CV and mapping file and I’ll change the schema, does
> > this seem reasonable to everyone…?
> Sorry, that is my fault, I have overlooked this structure. I have added the cv
> two terms, 412 and 413, plus and minus value. The Mascot MSMS example would
> look like this using the new terms.
> 
>       <FragmentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus value"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" />
>       </FragmentTolerance>
>       <ParentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus value"
> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent"
> unitCvRef="UO" />
>       </ParentTolerance>
> 
> I have also updated the mapping file accordingly. Now two values (exactly two
> terms) are required, one plus and one minus value. The units are directly
> associated with the two terms. So the "mass units" tree becomes obsolete
> (absolut(e)ly), and I would suggest to delete it, if there is no good reason
> to keep it. I also think that a distinction into absolute and relative is not
> necessary as it is clear by specifying the units.
> 
> > So, I think that we must add the two CV terms Andy originally suggested?
> > Could you do that please? (I don't think Martin will be doing any edits).
> Done. Semantic validator is also updated. Sorry for any inconvencience.
> 
> Thanks,
> A.
> 
> 
> --
> Div. for Simulation of Biological Systems, WSI, University of Tuebingen
> Room C322, Sand 14, 72076 Tuebingen, Germany
> phone: +49-7071-29-70461 fax: +49-7071-29-5152
> http://www-bs.informatik.uni-tuebingen.de
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev