Use of ND for root annotations

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Likely final summary of requiring all annotations to the root node use the ND code

Date: Mon, 17 Sep 2007 11:47:54 -0700 (PDT)
From: Karen Christie <kchris@genome.stanford.edu>
To: Jim Hu <jimhu@tamu.edu>
Cc: Mike Cherry <cherry@stanford.edu>, Valerie Wood <val@sanger.ac.uk>,
    Suzanna Lewis <suzi@berkeleybop.org>, Chris Mungall <cjm@fruitfly.org>,
    Karen Christie <kchris@genome.stanford.edu>, GO mailing list <go@genome.stanford.edu>
Subject: Re: [go] Requirement for all 'unknown' annotations to use ND code

Hi,

The reason I brought this issue up was that I was very uncomfortable with the rationale that people
could use the ND evidence code as a way to find the unknown annotations, or with having that purpose
as a justification to only allow the ND code for root annotations in our documentation. It seems that
we have come to consensus that we should not be saying anything about this as a software shortcut to
find unknown annotations.

The more recent discussion has been dealing with the issue that annotations to the root node are a
special case anyway, allowing us to track curation progress. While we know that these aren't
annotations of knowledge in the same way as other annotations, I think the group has agreed many, many
times that we DO want a way to distinguish between genes that have been looked but where nothing is
known and genes that just haven't been curated yet, so I think we're stuck with tracking curation
progress in some way.

In that sense, I can see a rationale for only allowing annotations to the root node to be made with
the ND code in that we are making a curatorial statement about what a curator looked at in order to
make an annotation to the root node. The ND evidence code is already a special case in that it can
only be used for annotations to the root node.

Provided that the documentation is phrased in terms of curatorial process, i.e. the procedure required
in order to be able to make the statement the a given aspect is unknown for a given gene, I'm OK with
this restriction.

Note that I'm not volunteering to examine, or do any rewriting of, the ND documentation since I'm due
to deliver within the coming week.

Thanks to everyone for a good discussion.

-Karen

Action required

Update ND documentation accordingly

Date: Mon, 17 Sep 2007 11:56:08 -0700 (PDT)
From: Karen Christie <kchris@genome.stanford.edu>
To: Karen Christie <kchris@genome.stanford.edu>
Cc: Jim Hu <jimhu@tamu.edu>, Mike Cherry <cherry@stanford.edu>, Valerie Wood <val@sanger.ac.uk>,
    Suzanna Lewis <suzi@berkeleybop.org>, Chris Mungall <cjm@fruitfly.org>,
    GO mailing list <go@genome.stanford.edu>
Subject: Re: [go] Requirement for all 'unknown' annotations to use ND code

P.S. Even if it is agreed that all unknown/root annotations going forward must use the ND code, the
current documentation should probably make some comments that previous to some date, annotations by
codes such as TAS and NAS were allowed.