Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

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Sir,

I thank you for your quasi-intentional review of the MS-CV, and agree with
your points:

-Don't redefine a term that can be re-used from a shared CV
-Avoid obfuscating a terms meaning through inappropriate contextualization

As you know, part of this is just the inevitable and necessary cleanup that
occurs as the different standards working groups interoperate with greater
earnest.

Please keep the observations and corrections coming; more perspectives lead
to better factoring of domain concepts in the various CV's and ontologies.

As a side note, we are hoping/expecting that MS CV will be registered and
posted on the OBO site prior to next weeks meeting.

Regards,

Kent

> -----Original Message-----
> From: psi...@li... [mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of frank gibson
> Sent: Friday, November 10, 2006 4:42 AM
> To: David Creasy; len...@eb...
> Cc: psi...@li...
> Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology
> 
> Hi
> 
> 
> I don't mean to review the MS-CV but......
> Just as a side issue to this thread you should be looking to use the
> PATO units ontology now instead of creating your own.
> http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/
> Any missing term or request should be sent to
> obo...@li....
> 
> As a result, the defintion of "Time in minutes" (The term itself should
> probably just be "minutes") should be something like the "measure of
> time represented in minutes", not Acquisition time. Please ensure you
> remove context of use from the semantic meaning of the term.
> 
> Cheers
> Frank
> 
> -----Original Message-----
> From: psi...@li...
> [mailto:psi...@li...] On Behalf Of David
> Creasy
> Sent: Thursday, November 09, 2006 4:23 PM
> To: len...@eb...
> Cc: psi...@li...
> Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology
> 
> Hi Lennart,
> The intention was certainly that these are for the retention time, but I
> can't see any documentation that confirms this.  Certainly Mascot
> Distiller, Mascot, Bruker CompassXport, the Sciex wiff converter,
> Bioworks and the Insilicos viewer all assume that this is the case.
> 
> Best regards,
> David
> 
> 
> 
> Lennart Martens wrote:
> > Hi Kent,
> >
> >
> > Thanks for pointing that out, but I had seen these myself and assumed
> > that they were used to document the actual acquisition time during
> > which the final spectrum was acquired (the final spectrum represented
> > in the mzData binary arrays is thus a summation over all the
> > individual detector recordings during that time slot).
> >
> > As such, I would expect this value to be either constant (I guess most
> 
> > mass specs do not allow dynamic setting of this value, but I could be
> > wrong) and certainly small (say from 0.5 to 8 seconds). Having '900'
> > in the seconds field, say, would therefore probably lead to confusion?
> >
> >
> > Cheers,
> >
> > lnnrt.
> >
> > Kent Laursen wrote:
> >> Hi Lennart,
> >>
> >> There is not currently a term labeled retention time in the MS CV.
> >> The current terms for the purpose are:
> >>
> >> [Term]
> >> id: PSI:1000038
> >> name: Time In Minutes
> >> def: "Acquisition time in minutes." [PSI:GPS]
> >> is_a: PSI:1000460 ! Unit
> >> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> >>
> >> [Term]
> >> id: PSI:1000039
> >> name: Time In Seconds
> >> def: "Acquisition time in seconds." [PSI:GPS]
> >> is_a: PSI:1000460 ! Unit
> >> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> >>
> >> Regards,
> >>
> >> Kent
> >>
> >>> -----Original Message-----
> >>> From: psi...@li...
> >>> [mailto:psidev-ms-dev- bo...@li...] On Behalf Of
> >>> Lennart Martens
> >>> Sent: Thursday, November 09, 2006 9:27 AM
> >>> To: psi...@li...
> >>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
> >>>
> >>> Hi,
> >>>
> >>>
> >>>
> >>> I am processing some mzXML files into mzData for insertion into the
> >>> PRIDE database, and I can't seem to find an ontology term for
> >>> 'retention time' in the PSI-MS ontology.
> >>>
> >>> If there is one, and I just can't find it for some silly reason,
> >>> please let me know.
> >>>
> >>> If there isn't any, could this be added? It seems like a sensible
> >>> thing as it is a common enough piece of data.
> >>>
> >>>
> >>> Thanks in advance,
> >>>
> >>>
> >>> lnnrt.
> >>>
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> >>
> >
> 
> --
> 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
> 
> *** please note change of address ***
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