Closed fypoadmin closed 9 years ago
fypoadmin
commented
10 years ago Argh argh argh. This is another one that's being inferred by the reasoner, and I can't tell why. (Sometimes when the reasoner infers something bonkers, it's because of a mistake that I can spot and fix. Not always, though.)
I've attached the "explanation" I get from Protege and its reasoner ... see if you can make any sense of it!!
Original comment by: mah11
fypoadmin
commented
10 years ago There is also a link from elongated vegetative cell to aseptate in bioportal? is it anything to do with this link?
Original comment by: ValWood
fypoadmin
commented
10 years ago Which term did you look at in BioPortal? I don't see anything about aseptate in the visualization for 'elongated vegetative cell' itself (FYPO:0001122).
Original comment by: mah11
fypoadmin
commented
10 years ago What is the deviation(from_normal)?
'has extra parts of type' has an is_a to this via 'increased quality' but 'lacks part or has fewer parts of type' doesn't (there is no 'decreased quality')
Original comment by: Antonialock
fypoadmin
commented
10 years ago What is the deviation(from_normal)?
It means pretty much the same thing as "deviation from normal" does in plain English.
There is a 'decreased quality' term, but 'lacks parts or has fewer parts of type' doesn't have a path to it. I think the thinking is that having none at all doesn't fit the 'decreased' def because 'decreased' is interpreted as "some, but not as much". 'lacks parts or has fewer parts of type' has two is_a children, of which 'has fewer parts of type' does have a path to 'decreased quality' and 'lacks all parts of type' doesn't.
Is your head swimming yet?
Original comment by: mah11
fypoadmin
commented
10 years ago i just clicked the "visualization" link from here:
http://bioportal.bioontology.org/ontologies/FYPO?p=classes&conceptid=FYPO%3A0000950&t=details
Original comment by: ValWood
fypoadmin
commented
10 years ago ah ok, personally I'd interpret "decreased" as a range between anywhere from "statistically less than normal" to "0".
RNA absent from cell is_a decreased RNA level? which is_a decreased quality
I don't know if it would make a difference to the reasoner but maybe try adding it?
Original comment by: Antonialock
fypoadmin
commented
10 years ago That's the same term this ticket was originally about, not 'elongated vegetative cell'. The default positions of the term bubbles in the display are a bit misleading, but it's FYPO:0000950, not FYPO:0001122, that has the dodgy inferred link.
You can drag the terms around in the display to make it clearer.
Original comment by: mah11
fypoadmin
commented
10 years ago ah ok, personally I'd interpret "decreased" as a range between anywhere from "statistically less than normal" to "0".
So would most people, I think. Formal ontologists are special ...
RNA absent from cell is_a decreased RNA level? which is_a decreased quality
yeah, but I added that manually at the FYPO level
I don't know if it would make a difference to the reasoner but maybe try adding it?
I suspect it wouldn't help with the anomalous inferences ...
Original comment by: mah11
fypoadmin
commented
10 years ago One other thing - I've noticed for a lot of these "where is the reasoner getting that link?" problems, it's as if it's jumping to a sibling instead of going "up" an is_a link. No. idea. why.
Original comment by: mah11
fypoadmin
commented
10 years ago Original comment by: Antonialock
fypoadmin
commented
10 years ago mitotic spindle absent from cell under abnormal vegetative cell morphology
Original comment by: Antonialock
fypoadmin
commented
10 years ago though perhaps spindle comes under "structure" which is part of the def for morphology?
Original comment by: Antonialock
fypoadmin
commented
10 years ago That may well be what it's "thinking", although it doesn't make sense to me. For that one I may be able to adjust the "abnormal spindle" xp to improve things.
Original comment by: mah11
fypoadmin
commented
10 years ago yep, made some adjustments, and the abnormal spindle business looks more sensible now (should be visible generally tomorrow)
new term: abnormal spindle morphology FYPO:0003607
wish they were all this easy to fix ...
Original comment by: mah11
fypoadmin
commented
9 years ago Original comment by: mah11
fypoadmin
commented
9 years ago some of this has been improved, and the rest has to wait until I can purge redundant asserted is_a links (and hope things get better as a result)
Original comment by: mah11
fypoadmin
commented
9 years ago Original comment by: mah11
elongated aseptate cell is currently showing under ID FYPO:0000118 Ontology fission_yeast_phenotype Term name multiseptate
Original comment by: Antonialock