Some grouping terms are defined in GO as a grouping_term should not to be used for annotation (for example nuclear part?)
We will also use the same subsets for phenotype terms where the terms should not be used for direct annotation. In these cases the "proceed" button should not be visible and a message should say
"This term should not be used for direct annotations, please select a child term"
Chado: #185
Curation tasks: #214
Curation tool: #430
Fission yeast phenotype: #1249
Message edited, mainly to correct punctuation (but also to make the notion of "direct annotation" a little clearer):
"Genes should not be annotated directly to this term. Please select a child term ."
GO and FYPO now both use the same subset for this:
subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation"
This will be useful, but not necessary for general CC release so lowering priority
If a term is marked a not for direct annotation, does that mean all it's parents shouldn't be used for direct annotation either?
See also: [curation-tool:#430]
Related
Curation tool:
#430Good question - I'd never properly thought about it before.
My gut feeling is that you'd want to disallow annotations to is_a ancestors, but for other relationship types you can't make a blanket statement.
For example, Antonia pointed out that "cytoplasmic part" is do-not-annotate, but its part_of parent "cytoplasm" is fine (as it should be).
So, in the general case, to find out if a term shouldn't be used for annotation, we need to see if any of it's ISA descendants shouldn't be used for annotation. That sound like a job for Oort/OWLTools. Do you know if Oort can do such things? Or is it another question for the OWLTools folk?
We chatted about this on skype - owltools should be able to do the relevant query (get all terms in the subset, then get their is_a ancestors), although I don't know the exact syntax.
I'm also not sure whether Oort can add ancestors to a subset by magic, so if it becomes important, ask Chris/Heiko.
update: the subset IDs have changed
in FYPO:
subsetdef: qc_do_not_annotate "Term not to be used for direct annotation"
subsetdef: qc_do_not_manually_annotate "Term not to be used for direct manual annotation"
in GO:
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
also
conditions defined the subset grouping_terms for terms should not be visible in the tool
[curation-tool:#428] is also related (tho it appears to include an unrelated comment)
Related
Curation tool: #428