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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