Further comments on filling with field for ISS

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Suzi's response to Karen's summary of 3 possible ways to deal wtih filling badly named column 8 for ISS

Date: Thu, 20 Sep 2007 04:42:53 -0700
From: Suzanna Lewis <suzi@berkeleybop.org>
To: Karen Christie <kchris@genome.stanford.edu>
Cc: Susan Tweedie <sart2@gen.cam.ac.uk>, Valerie Wood <val@sanger.ac.uk>,
    "Gwinn-Giglio@sanger.ac.uk,  Michelle" <MLGwinn@jcvi.org>,
    GO mailing list <go@genome.stanford.edu>, Benjamin Hitz <hitz@genome.stanford.edu>
Subject: Re: [go] Putting method/program names into the with field for ISS


On Sep 19, 2007, at 10:08 PM, Karen Christie wrote:

> I don't think anyone is suggesting that such identifiers, including domain and HMM identifiers as
> well as individual sequence identifiers, shouldn't be put into the 'with/from' column when
> available.
> 
> However, there are cases when there just isn't anything of that sort to put in this column. Both
> snoRNAs and tRNAs are a good example. Both of these types of RNAs are generally predicted by methods
> that analyze both the primary sequence and the predicted nucleic acid secondary structures of the
> gene product, not by orthology methods. The two protein examples were both based on algorithms that
> analyze sequence to determine hydrophobicity and predict transmembrane domains. In all of these
> examples, the method is clearly based purely upon the sequence of the gene product. Thus these all
> fit into ISS, but there is no identifier for a sequence, domain, or HMM that can be put into the
> with column.
> 
> I really think that the evidence code should be based on the method used, not on how the 'with/from'
> column can be filled; this is supporting evidence after all. In the interest of having a logical
> system that makes sense, especially when teaching it to new people, I think it is important that we
> don't implement arcane rules where the type of supporting evidence takes precedence over the method
> used.
> 
> So, regardless of what we decide about filling the with column for these types of situations, I
> think that these situations should stay in ISS because they are clearly all methods based purely on
> the sequence of the gene product. Personally, I can live with any of three options that have come up
> in this thread:
> 
> 1. the system I proposed where we start maintaining a new file to track methods, not necessarily
> elegant and even the 10 or so examples I used highlight the difficulties in tracking down references
> for some methods, but meets our other requirements that things have both a namespace and an ID.

This is the way to go IMO

> 2. Allow the with column to be filled with 'not applicable', or some other descriptive phrase, for
> cases when there is no ID for a sequence, domain, HMM, etc, but just a method or sequence consensus
> without an ID

Nope

> 
> 3. Relax the rule that the with column is mandatory for ISS

Nope

> 
> -Karen

Renaming 'with/from' column P.S. (also from email above) Could we start calling this column the 'supporting evidence' column or something else descriptive. Right now, it's full name is 'with/from', but we've also allowed the column to be filled for IMP where neither of those prepositions is really appropriate.