Further comments on filling with field for ISS
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 <firstname.lastname@example.org> To: Karen Christie <email@example.com> Cc: Susan Tweedie <firstname.lastname@example.org>, Valerie Wood <email@example.com>, "Gwinn-Giglio@sanger.ac.uk, Michelle" <MLGwinn@jcvi.org>, GO mailing list <firstname.lastname@example.org>, Benjamin Hitz <email@example.com> 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.