Re: [Psidev-pi-dev] Draft PSI-PI Controlled Vocabularies

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

Hi Luisa,

Thanks very much - looks good. I've put the .obo file in
  http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo

Some comments below:

Luisa Montecchi wrote:
> Dear All,
> 
> here is draft obo file, loadable with the obo editor (you can download 
> the editor at 
> https://sourceforge.net/project/showfiles.php?group_id=36855&package_id=192411) 
> 
> 
> Few questions:
> Do you want to report all the information available in the spreadsheet 
> as comment (like 'required by MIAPE' 'MCP' +all columns after the term)
Maybe.
An issue that I don't know how to  resolve is that ideally the validator 
will need to check, for example that if the search engine is Sequest, 
then a sequest:xcorr value should be specified. If the search engine is 
X!Tandem, and a sequest:xcorr value is specified, this would be an error.
Any ideas for how best to keep track of all this so that we don't lose 
or forget things? We have the spreadsheet, the mapping file and the .obo 
file. So maybe we need to keep the spreadsheet up to date as well.
Perhaps Zsuzsanna, you and Randy can agree on an approach?

> Is the PI namespace fine with you?
Yes.

> I put all term lower case, as it is good practice in CVs, is it fine?
yes, luisa, this looks ok.

> Would you authorize me to change few names, an ugly one being for 
> example 'database(s) searched min=0 for denovo?'. Ideally I would also 
> like to put all terms singular.
Yes please.

> 
> In general I think number of those terms should be XML attributes in the 
> schema (like 'sample id', or 'date / time search performed' or 
> 'modification position', whereas CV are fine and should be the reference 
> for descriptif information like 'database filtering' or 'search engines 
> scores'.
Yes please. Could you make a list and let us know?
I've added a tracker item:
http://code.google.com/p/psi-pi/issues/detail?id=15
So, please add to the list there.

> 
> We can plan a phone conference if you want to browse the file together, 
> I can organise one next week at EBI, or I you can call me at anytime 
> this Tuesday, Wednesday 
We will need to go through the file at some point. Best to liaise also 
with Zsuzsanna and Randy.

> (not thursday it is may first in the continental 
> world).
But you are in the UK! Does this mean you take the 5th as holiday too ;)

Thanks very much,

David
> 
> Cheers,
> 
> Luisa
> 
> 

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David Creasy
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