#214 not for direct annotation phenotype terms

[Valerie Wood]

We should start to "force"the use of most specific terms where appropriate by flagging broad terms as not for direct annotation.
Should we start a list of these on the wiki?
Could include things like:
viable cell
inviable cell etc
small cell
(probably anything that has a vegetative/non vegetative child?)

[Midori Harris]

First, check which terms are already in the don't-annotate subsets (this is easy in OBO-Edit; I can show you), because a lot already are.

Should we start a list of these on the wiki?

I don't see much point; if you want any terms added to the subsets, open a ticket on the FYPO tracker. I'll never remember to look at the wiki for FYPO to-do items.

[Valerie Wood]

Ah, so we can do this already... how are tool users alerted (via a comment). Does chado report when a term is used which is flagged as not for direct annotation?

FYPO:0000314 (we should always be able to say if it is divided or undivided....just baout to update my mappings....)

[Midori Harris]

As far as I know, chado and the curation tool don't do anything with the do_not_annotate subsets yet -- the relevant tickets are still open ([curation-tool:#431], [chado:#185]).

[Midori Harris]

closing because various aspects all belong on different trackers (and are there, and linked here)

[Valerie Wood]

Can all of the terms which are parents of a "vegetative" growth term be flagged as not for direct annotation (or are they already)?
if not should I add this to the phenotype tracker?
Is there an easy way to see a list of the terms "not for direct annotation"?

[Midori Harris]

Any changes you want in FYPO should go on the FYPO tracker, and yes, flagging terms as not for direct annotation is a FYPO change.

Most got done for [fission-yeast-phenotype:#711], but open a new ticket if you spot any I missed.

Right now, the least difficult way to see what's in the subset is to look in OBO-Edit; probably best if I show you how. I can also put a list in the dropbox, but it would have to be updated manually from time to time (so might go a bit out of date if I forget).

[Midori Harris]

Dropbox/pombase/ontologies/phenotype/FYPO_qc_do_not_annotate_subsets.obo

[Valerie Wood]

Oh quite a lot....will be interesting to see how many we have used ;)