Re: [Psidev-pi-dev] Help! AnalysisXML CV

[David C. <dc...@ma...>]

Hi Luisa,

Thank you very much indeed.
(I've cc'd the list as I suspect that your reply will be useful for some 
time to come)
It's very good to know that the structure makes sense to someone outside 
the immediate group.

Hopefully we can agree who's going to do what at the next telecon - 
Andreas kindly volunteered to make some proposals as to how to proceed 
and this is certainly going to help.

Thanks,
David

Luisa Montecchi wrote:
> Hi David,
> 
> Overall the file structure looks good, I aswered for the regular 
> expression on the google tracker suggesting to use the following syntax
> xref: value-type:{string,int,xsd} "regular expression"
> 
> Some comments:
> 1- save the file in OBO 1.2 you will have less syntax issue with the OBO 
> edit (note *less* does not mean *no*). For this in the save has display 
> at the bottom you can just change the selection from format 1.0 to 1.2.
> 2- the class 'now_in_SCHEMA', looks like Eric Deutsch 'purgatory' and 
> means those terms should be delete but we are not 100% sure. Fine, but 
> make sure you delete them before the file go public (do not obsolete 
> those terms if nobody ever used them, same for the obsoleted 
> palceholders1,2,3,4)
> 3- about the content of  'now_in_SCHEMA' I generally fully agree with it 
> I have some doubts for names (peak list software name, modifications 
> name, sample name) but maybe you documented in the schema other source 
> for those names?
> 4- PI:00043 - input data type: to me given the children this term 
> shoulve be input format, if you mean data type I would except children 
> like spcetra or peak list or binary data
> 5- Are you using the word 'details' or 'information' or 'parameter' with 
> some clear distinctions?
> 6- try to be consistent with upper or lower case, on my opnion the 
> easiest for  users is to be strictly lower case except for acronyms
> 7- use more synonyms and less parenthensis in the term name
> 8- try to be consistent on singular/plurals on term names
> 9- with time and will try to a bit more verbose on definitions and 
> references here is the list of term with no definition
> id: PI:00000    name: protein informatics cv
> id: PI:00054    name: mzML file
> id: PI:00062    name: mgf file
> id: PI:00067    name: dta files
> id: PI:00195    name: reverse
> id: PI:00196    name: randomized
> id: PI:00197    name: forward+reverse
> id: PI:00199    name: Mascot DAT file
> id: PI:00200    name: SEQUEST results
> id: PI:00201    name: mw filter maximum
> id: PI:00202    name: mw filter minimum
> id: PI:00203    name: pi filter maximum
> id: PI:00204    name: pi filter minimum
> id: PI:00207    name: Mascot
> id: PI:00208    name: Sequest
> id: PI:00209    name: Phenyx
> id: PI:00211    name: mass type setting monoisotopic
> id: PI:00212    name: mass type setting average isotopic
> 
> 
> Most importantly the structure make sense to me, I found terms I expect 
> according to their parent names. Remember you are making a CV and you 
> providing standardized terminology to support the description of a MS 
> search engine results. Try also to ensure that also the mapping with the 
> schema is quite intuitive and documented.
> 
> I hope this was useful, let me know if I can help,
> 
> 
> Regards,
> 
> 
> Luisa
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> David Creasy wrote:
>> Hi Luisa,
>>
>> We've got two issues with the analysisXML CV, and maybe you can point 
>> us in the right direction...
>>
>> 1. None of us feel too confident that we've the right skills/time to 
>> design a good structure for CV. In fact, in the telecon that we just 
>> had, we  even discussed (but rejected!) having just a flat CV. Could 
>> you be cajoled/bribed into giving us some help, or recommending 
>> somebody who has the ability and time...
>>
>> 2. We are slightly confused by what is and what isn't allowed in the 
>> obo format. Angel tried to add some terms, and these don't show up in 
>> oboedit:
>> http://code.google.com/p/psi-pi/issues/detail?id=30#c33
>> (We assume it's the ! in the regex that causes the problem)
>> If we can't use oboedit, we don't see how we can maintain any 
>> structure - using a text editor ends up being too hard. If you've any 
>> idea how we can fix this particular issue, that would be great.
>>
>> The current obo file (without the troublesome enzyme) is here:
>>
>> http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo
>> (Maybe it is better than we think - maybe not)
>>
>>
>> Any help or advice that you can give is greatly appreciated.
>>
>>
>> Thanks,
>>
>> David

-- 
David Creasy
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