[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 
>
>
>  
>