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Add quantity related VT terms and synonyms #149

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Add quantity related VT terms and synonyms #149

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rays22
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@rays22 rays22 commented Sep 26, 2022

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.

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.
@rays22 rays22 self-assigned this Sep 26, 2022
@rays22 rays22 requested a review from ar-ibrahim September 26, 2022 19:03
@@ -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
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is this how we want to deal with species? Is the precedent anywhere in the file?

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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

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Can you ask on slack about a suitable pattern for this scenario?

rays22 and others added 2 commits September 27, 2022 11:08
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.
@rays22 rays22 marked this pull request as draft September 27, 2022 11:39
rays22 and others added 6 commits September 27, 2022 15:25
Remove
OBA:VT0010441   parasite quantity
OBA:VT0010440   bacteria quantity
, because they may not belong to this phenotype pattern.

Part of #85.
1. OBA:VT1000181  viable offspring quantity
2. OBA:VT1000189  offspring quantity

Part of #85.
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2 participants