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

[frank g. <Fra...@ne...>]

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 =20

-----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,
>=20
>=20
> Thanks for pointing that out, but I had seen these myself and assumed=20
> that they were used to document the actual acquisition time during=20
> which the final spectrum was acquired (the final spectrum represented=20
> in the mzData binary arrays is thus a summation over all the=20
> individual detector recordings during that time slot).
>=20
> 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'=20
> in the seconds field, say, would therefore probably lead to confusion?
>=20
>=20
> Cheers,
>=20
> lnnrt.
>=20
> Kent Laursen wrote:
>> Hi Lennart,
>>
>> There is not currently a term labeled retention time in the MS CV. =20
>> 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...=20
>>> [mailto:psidev-ms-dev- bo...@li...] On Behalf Of=20
>>> 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=20
>>> PRIDE database, and I can't seem to find an ontology term for=20
>>> 'retention time' in the PSI-MS ontology.
>>>
>>> If there is one, and I just can't find it for some silly reason,=20
>>> please let me know.
>>>
>>> If there isn't any, could this be added? It seems like a sensible=20
>>> thing as it is a common enough piece of data.
>>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> lnnrt.
>>>
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>>
>=20

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

dc...@ma...
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*** please note change of address ***

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