psidev-ms-dev

[Psidev-ms-dev] New PSI-MS release 3.9.1: mzQuant changes and some little things

[David O. <do...@eb...>]

Dear Community,

I've released a new psi-ms version (3.9.1).
The changes implemented are:

  mzQuantML
============
- the proposed terms have been added
- the IDs of all of them have been changed: an unexpected version of the 
psi-ms had been released using the first 7 IDs of the proposed "quant" 
terms; I've adjusted the IDs (main ID and is_a / part_of terms)
- in the original mzQuantML proposal there was a gap (MS:1001825 and 
MS:1001826 not used) and a duplication (term MS:1001836 used twice); 
that's why if you compare the published IDs to the proposed, you'll find 
at the first terms a displacement of 7, then 5 and at the end of 6
- adjusting these numbers has been quite complicated... please, take a 
look and verify that everything is correct;
- a minor change: following the guidelines, the name of the term 
MS:1001861 is changed from "quant. data processing" to "quantification 
data processing"; hope this is what you wanted

TODOs
============
- I've removed all TODOs in the controlled vocabulary; some of them have 
been there for years, some are obsolete or are in purgatory; the TODO 
annotation is not contemplated in the Guidelines
- A complete list of these terms is found there -> 
https://sourceforge.net/tracker/?func=detail&aid=3396860&group_id=65472&atid=848524 
, and at the end of this email
- If anybody is interested on dealing with these TODOs, please, say 
something

One term that should be corrected, I'm not sure in which way
===================================================
This term:
id: MS:1001065
name: TODOscoring model
def: "DELETE. There is Phenyx:ScoringModel for Phenyx! Scoring model 
(more detailed granularity). TODO: add some child terms!" [PSI:PI]
is_a: MS:1001249 ! search input details

Has a TODO and a DELETE. We should do something. If nobody says anything 
against it, I'll obsolete it in a new release.

Best regards,
David

-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD





Pending TODOs in the c.v.:
- MS:1000444 -> improve definition (purgatory)
- MS:1000445 -> improve definition (purgatory)
- MS:1001065 -> obsolete term???
- MS:1001101 -> TODO: add child terms.
- MS:1001130 -> clarify definition
- MS:1001136 -> clarify definition
- MS:1001145 -> unknown TODO
- MS:1001326 -> "TODO_add_others" (purgatory)
- MS:1001355 -> TODO: What does this mean?
- MS:1001356 -> TODO: really needed?
- MS:1001822 -> clarify definition
- MS:1001842 -> clarify: correct place in obo?
- MS:1001844 -> How to code normalization method, only as dataprocessing 
or here?
- MS:1001846 -> How to code normalization method, only as dataprocessing 
or here?
- MS:1001849 -> clarify how to specify the two groups!

Re: [Psidev-ms-dev] New PSI-MS release 3.9.1: mzQuant changes and some little things

[Eric D. <ede...@sy...>]

Many thanks for tidying this all up, David!

> -----Original Message-----
> From: David Ovelleiro [mailto:do...@eb...]
> Sent: Wednesday, August 24, 2011 5:13 AM
> To: 'psi...@li...'; Mass spectrometry standard
> development
> Subject: [Psidev-ms-dev] New PSI-MS release 3.9.1: mzQuant changes and
> some little things
>
> Dear Community,
>
> I've released a new psi-ms version (3.9.1).
> The changes implemented are:
>
>   mzQuantML
> ============
> - the proposed terms have been added
> - the IDs of all of them have been changed: an unexpected version of
> the
> psi-ms had been released using the first 7 IDs of the proposed "quant"
> terms; I've adjusted the IDs (main ID and is_a / part_of terms)
> - in the original mzQuantML proposal there was a gap (MS:1001825 and
> MS:1001826 not used) and a duplication (term MS:1001836 used twice);
> that's why if you compare the published IDs to the proposed, you'll
> find
> at the first terms a displacement of 7, then 5 and at the end of 6
> - adjusting these numbers has been quite complicated... please, take a
> look and verify that everything is correct;
> - a minor change: following the guidelines, the name of the term
> MS:1001861 is changed from "quant. data processing" to "quantification
> data processing"; hope this is what you wanted
>
> TODOs
> ============
> - I've removed all TODOs in the controlled vocabulary; some of them
> have
> been there for years, some are obsolete or are in purgatory; the TODO
> annotation is not contemplated in the Guidelines
> - A complete list of these terms is found there ->
> https://sourceforge.net/tracker/?func=detail&aid=3396860&group_id=65472
> &atid=848524
> , and at the end of this email
> - If anybody is interested on dealing with these TODOs, please, say
> something
>
> One term that should be corrected, I'm not sure in which way
> ===================================================
> This term:
> id: MS:1001065
> name: TODOscoring model
> def: "DELETE. There is Phenyx:ScoringModel for Phenyx! Scoring model
> (more detailed granularity). TODO: add some child terms!" [PSI:PI]
> is_a: MS:1001249 ! search input details
>
> Has a TODO and a DELETE. We should do something. If nobody says
> anything
> against it, I'll obsolete it in a new release.
>
> Best regards,
> David
>
> --
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
>
>
>
>
> Pending TODOs in the c.v.:
> - MS:1000444 -> improve definition (purgatory)
> - MS:1000445 -> improve definition (purgatory)
> - MS:1001065 -> obsolete term???
> - MS:1001101 -> TODO: add child terms.
> - MS:1001130 -> clarify definition
> - MS:1001136 -> clarify definition
> - MS:1001145 -> unknown TODO
> - MS:1001326 -> "TODO_add_others" (purgatory)
> - MS:1001355 -> TODO: What does this mean?
> - MS:1001356 -> TODO: really needed?
> - MS:1001822 -> clarify definition
> - MS:1001842 -> clarify: correct place in obo?
> - MS:1001844 -> How to code normalization method, only as
> dataprocessing
> or here?
> - MS:1001846 -> How to code normalization method, only as
> dataprocessing
> or here?
> - MS:1001849 -> clarify how to specify the two groups!
>
> -----------------------------------------------------------------------
> -------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev