psidev-ms-dev

[Psidev-ms-dev] RE: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

[Richard C. <rc...@eb...>]

Hi Randy

A quick comment on the ontology. I believe that the use of acronyms as =
term
names should be avoided if possible. The OBO format allows for the use =
of
synonyms and I believe that the acronyms should be placed there, with =
the
full name as the primary term name. In other ontolgies that I have seen,
this is common practice. The mzData/analysisXML files will not have the
definitions and some of these acronyms, taken out of context, quickly =
become
meaningless.=20

id: PSI:1000070
name: APCI

id: PSI:1000071
name: CI

id: PSI:1000072
name: EI

id: PSI:1000073
name: ESI

id: PSI:1000074
name: FAB

id: PSI:1000075
name: MALDI

id: PSI:1000079
name: FT-ICR

id: PSI:1000084
name: TOF

id: PSI:1000086
name: FWHM

id: PSI:1000111
name: EMT

id: PSI:1000117
name: ADC

id: PSI:1000119
name: TDC

id: PSI:1000133
name: CID

id: PSI:1000134
name: PD

id: PSI:1000135
name: PSD

id: PSI:1000136
name: SID

Best regards,
Richard
--
Richard Cote
Software Engineer - PRIDE Project Team (Sequence Database Group)
            =20
European Bioinformatics Institute            =20
Wellcome Trust Genome Campus            RC...@eb...     =20
Hinxton                                =20
Cambridge CB10 1SD                      Phone: (+44) 1223 492610 =20
United Kingdom                          Fax  : (+44) 1223 494468=20

[Psidev-ms-dev] Re: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

[Randy J. <rkj...@in...>]

Richard,

All acronyms require context.  I like the idea of expanding them.  Are 
there other ontologies being developed by the PSI that have the same 
problem?

Randy





Richard Cote wrote:

>Hi Randy
>
>A quick comment on the ontology. I believe that the use of acronyms as term
>names should be avoided if possible. The OBO format allows for the use of
>synonyms and I believe that the acronyms should be placed there, with the
>full name as the primary term name. In other ontolgies that I have seen,
>this is common practice. The mzData/analysisXML files will not have the
>definitions and some of these acronyms, taken out of context, quickly become
>meaningless. 
>
>id: PSI:1000070
>name: APCI
>
>id: PSI:1000071
>name: CI
>
>id: PSI:1000072
>name: EI
>
>id: PSI:1000073
>name: ESI
>
>id: PSI:1000074
>name: FAB
>
>id: PSI:1000075
>name: MALDI
>
>id: PSI:1000079
>name: FT-ICR
>
>id: PSI:1000084
>name: TOF
>
>id: PSI:1000086
>name: FWHM
>
>id: PSI:1000111
>name: EMT
>
>id: PSI:1000117
>name: ADC
>
>id: PSI:1000119
>name: TDC
>
>id: PSI:1000133
>name: CID
>
>id: PSI:1000134
>name: PD
>
>id: PSI:1000135
>name: PSD
>
>id: PSI:1000136
>name: SID
>
>Best regards,
>Richard
>--
>Richard Cote
>Software Engineer - PRIDE Project Team (Sequence Database Group)
>             
>European Bioinformatics Institute             
>Wellcome Trust Genome Campus            RC...@eb...      
>Hinxton                                 
>Cambridge CB10 1SD                      Phone: (+44) 1223 492610  
>United Kingdom                          Fax  : (+44) 1223 494468 
>
>
>  
>

Re: [Psidev-ms-dev] Re: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

[Chris T. <chr...@eb...>]

Hiya. There aren't yet, but there very soon will be. I like this 
as a general policy; I'll suggest it on the FuGO call later 
today also.

Cheers, Chris.

P.S. We had our second 'MetaboMeeting' Monday/Tuesday and in the 
standards breakout we (for the second time) affirmed that mzData 
would be the weapon of choice for moving mass spec Mbx data 
around (helped enormously by recent moves by Thermo (Thomas 
McClure) et al. to reimplement proteomics-based mzData-related 
libraries in chem software). Also we agreed to coordinate on 
vocabulary (/FuGO), to codevelop spML (sample prep -- 
separations++) and to develop from FuGE as far as humanly 
possible (esp. for their NMR format).

Randy Julian wrote:
> Richard,
> 
> All acronyms require context.  I like the idea of expanding them.  Are 
> there other ontologies being developed by the PSI that have the same 
> problem?
> 
> Randy
> 
> 
> 
> 
> 
> Richard Cote wrote:
> 
>> Hi Randy
>>
>> A quick comment on the ontology. I believe that the use of acronyms as 
>> term
>> names should be avoided if possible. The OBO format allows for the use of
>> synonyms and I believe that the acronyms should be placed there, with the
>> full name as the primary term name. In other ontolgies that I have seen,
>> this is common practice. The mzData/analysisXML files will not have the
>> definitions and some of these acronyms, taken out of context, quickly 
>> become
>> meaningless.
>> id: PSI:1000070
>> name: APCI
>>
>> id: PSI:1000071
>> name: CI
>>
>> id: PSI:1000072
>> name: EI
>>
>> id: PSI:1000073
>> name: ESI
>>
>> id: PSI:1000074
>> name: FAB
>>
>> id: PSI:1000075
>> name: MALDI
>>
>> id: PSI:1000079
>> name: FT-ICR
>>
>> id: PSI:1000084
>> name: TOF
>>
>> id: PSI:1000086
>> name: FWHM
>>
>> id: PSI:1000111
>> name: EMT
>>
>> id: PSI:1000117
>> name: ADC
>>
>> id: PSI:1000119
>> name: TDC
>>
>> id: PSI:1000133
>> name: CID
>>
>> id: PSI:1000134
>> name: PD
>>
>> id: PSI:1000135
>> name: PSD
>>
>> id: PSI:1000136
>> name: SID
>>
>> Best regards,
>> Richard
>> -- 
>> Richard Cote
>> Software Engineer - PRIDE Project Team (Sequence Database Group)
>>             European Bioinformatics Institute             Wellcome 
>> Trust Genome Campus            RC...@eb...      
>> Hinxton                                 Cambridge CB10 
>> 1SD                      Phone: (+44) 1223 492610  United 
>> Kingdom                          Fax  : (+44) 1223 494468
>>
>>  
>>
> 
> 
> 
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] RE: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

[Richard C. <rc...@eb...>]

The PSI-MI ontology uses the approach I've suggested. For example:

[Term]
id: MI:0016
name: circular dichroism
exact_synonym: "cd" []
synonym: "CD" []

[Term]
id: MI:0018
name: two hybrid
synonym: "2H" []

[Term]
id: MI:0019
name: coimmunoprecipitation
exact_synonym: "coip" []

[Term]
id: MI:0020
name: transmission electron microscopy
exact_synonym: "tem" []

--
Richard Cote
Software Engineer - PRIDE Project Team (Sequence Database Group)
             
European Bioinformatics Institute             
Wellcome Trust Genome Campus            RC...@eb...      
Hinxton                                 
Cambridge CB10 1SD                      Phone: (+44) 1223 492610  
United Kingdom                          Fax  : (+44) 1223 494468 

-----Original Message-----
From: Randy Julian [mailto:rkj...@in...] 
Sent: 11 January 2006 12:13
To: Richard Cote
Cc: psi...@li...; hh...@eb...; 'Philip Jones';
'Chris Taylor'
Subject: Re: Psidev-ms-dev digest, Vol 1 #83 - 1 msg


Richard,

All acronyms require context.  I like the idea of expanding them.  Are 
there other ontologies being developed by the PSI that have the same 
problem?

Randy





Richard Cote wrote:

>Hi Randy
>
>A quick comment on the ontology. I believe that the use of acronyms as 
>term names should be avoided if possible. The OBO format allows for the 
>use of synonyms and I believe that the acronyms should be placed there, 
>with the full name as the primary term name. In other ontolgies that I 
>have seen, this is common practice. The mzData/analysisXML files will 
>not have the definitions and some of these acronyms, taken out of 
>context, quickly become meaningless.
>
>id: PSI:1000070
>name: APCI
>
>id: PSI:1000071
>name: CI
>
>id: PSI:1000072
>name: EI
>
>id: PSI:1000073
>name: ESI
>
>id: PSI:1000074
>name: FAB
>
>id: PSI:1000075
>name: MALDI
>
>id: PSI:1000079
>name: FT-ICR
>
>id: PSI:1000084
>name: TOF
>
>id: PSI:1000086
>name: FWHM
>
>id: PSI:1000111
>name: EMT
>
>id: PSI:1000117
>name: ADC
>
>id: PSI:1000119
>name: TDC
>
>id: PSI:1000133
>name: CID
>
>id: PSI:1000134
>name: PD
>
>id: PSI:1000135
>name: PSD
>
>id: PSI:1000136
>name: SID
>
>Best regards,
>Richard
>--
>Richard Cote
>Software Engineer - PRIDE Project Team (Sequence Database Group)
>             
>European Bioinformatics Institute             
>Wellcome Trust Genome Campus            RC...@eb...      
>Hinxton                                 
>Cambridge CB10 1SD                      Phone: (+44) 1223 492610  
>United Kingdom                          Fax  : (+44) 1223 494468 
>
>
>  
>