Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.74.0_rc1 of psi-ms.obo

[Jones, A. <And...@li...>]

Hi Steffen,

We need to put this term into data formats so it is clear that the user is saying - I did not use a threshold on my data. If there is a blank, we cannot distinguish between a badly formatted file (i.e. I used a threshold but forgot to tell you) or the no threshold case. The PSI-MS CV is generally a pragmatic collection of terms rather than an ontology, but I agree it is sensible for us to be aware of good practice in ontologies. Under good practice ontology guidelines, how is it expected that one can distinguish the "null" case from the "zero" case - as in this example?

Best wishes
Andy 




-----Original Message-----
From: Steffen Neumann [mailto:sne...@ip...] 
Sent: 09 March 2015 11:07
To: Mass spectrometry standard development
Cc: psi...@li...; Daniel Schober; psi...@li...
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Release candidate 3.74.0_rc1 of psi-ms.obo

Hi,

On Fr, 2015-03-06 at 17:03 +0100, mayerg97 wrote:
...
> Changed CV terms in version 3.74.0_rc1 of psi-ms.obo:
> =====================================================
> ************ Changed is_a relationship from 'quality estimation method 
> details'
> ************ --> 'statistical threshold'
> [Term]
> id: MS:1001494
> name: no threshold
> def: "In case no threshold was used." [PSI:PI]
> is_a: MS:1002482 ! statistical threshold

There are some ontology guidelines, which strongly discourage the uses of negative Terms "no xxx" . In practice, they are sometimes added for pragmatic reasons, but why not leaving blank if no threshold is used ? Since this is a "Changed term", it must have been present before, but I just wanted to mention for the future.

Yours,
Steffen




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