-
Notifications
You must be signed in to change notification settings - Fork 11
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Add quantity related VT terms and synonyms #149
base: master
Are you sure you want to change the base?
Conversation
OBA:VT0008073 CD4-positive T cell quantity OBA:VT0008077 CD8-positive T cell quantity OBA:VT0008038 NK T cell quantity OBA:VT0010441 parasite quantity OBA:VT0010440 bacteria quantity VT:1000189 offspring quantity OBA:1000859 brood size quality exact synonym VT:1000181 viable offspring quantity OBA:1000859 brood size quality broad synonym Part of #85.
@@ -202,3 +202,5 @@ OBA:VT0008496 blood immunoglobulin G2a amount PR:000050259 IgG2a heavy chain pro | |||
OBA:VT0003457 blood ketone body amount CHEBI:73693 ketone body PATO:0000070 amount UBERON:0000178 blood | |||
OBA:VT0010476 blood glutamate dehydrogenase amount GO:1990148 glutamate dehydrogenase complex PATO:0000070 amount UBERON:0000178 blood | |||
OBA:VT0010540 urine creatinine amount CHEBI:16737 creatinine PATO:0000070 amount UBERON:0001088 urine | |||
OBA:VT0010441 parasite quantity OPL:0000232 parasite organism PATO:0000070 amount UBERON:0000468 multicellular organism | |||
OBA:VT0010440 bacteria quantity NCBITaxon:2 Bacteria PATO:0000070 amount UBERON:0000468 multicellular organism |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
is this how we want to deal with species? Is the precedent anywhere in the file?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
No, I am afraid I could not find any precedent in the data files.
On second thought, the entity_attribute_location
pattern is not the right one for these host-[symbiont, parasite, infectious organism] interactions from the point of view of the host (as a trait of the host), because the infecting organism should not be regarded a part_of
the host.
Would the axiom below using RO:0002453 host of work for these?
equivalentTo:
text: "%s and 'characteristic_of' some (
%s and
('host_of' some %s)
)"
vars:
- attribute
- host
- parasite
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Can you ask on slack about a suitable pattern for this scenario?
Remove duplicate VT terms from OBA and add them as exact synonyms * Remove 1. OBA:VT0008073 CD4-positive T cell quantity 2. OBA:VT0008077 CD8-positive T cell quantity 3. OBA:VT0008038 NK T cell quantity * Add synonyms: 1. VT:0008073 CD4-positive T cell quantity skos:exactMatch OBA:0004294 2. VT:0008077 CD8-positive T cell quantity skos:exactMatch OBA:0004295 3. VT:0008038 NK T cell quantity skos:exactMatch OBA:0004281 Part of #85.
OBA:VT0008073 CD4-positive T cell quantity
OBA:VT0008077 CD8-positive T cell quantity
OBA:VT0008038 NK T cell quantity
OBA:VT0010441 parasite quantity
OBA:VT0010440 bacteria quantity
VT:1000189 offspring quantity OBA:1000859 brood size quality exact synonym VT:1000181 viable offspring quantity OBA:1000859 brood size quality broad synonym
Part of #85.