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Enforce taxon constraints #3102

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merged 32 commits into from
Nov 10, 2023
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5f9eaea
Import NCBITaxon with disjointness axioms.
gouttegd Oct 27, 2023
f27ac53
Update ncbitaxon_terms based on the -edit file.
gouttegd Oct 27, 2023
2b57baf
Implement taxon constraint check in QC pipeline.
gouttegd Oct 27, 2023
b71c786
remove wings never_in_taxon Sauropsida
anitacaron Jun 20, 2023
c865ba5
Making induction relation between suture and DM mammal-only
anitacaron Jul 21, 2023
4700c98
Unsat fix: pterygoid bone NOT part of some suspensorium.
gouttegd Sep 19, 2023
79c1edc
Unsat fix: Relax taxon constraint on 'corpus luteum'.
gouttegd Sep 21, 2023
1b33f06
Unsat fix: Remove 'pericardial cavity present_in_taxon some Ciona'.
gouttegd Sep 21, 2023
feb14d0
Unsat fix: Detach 'vertebral element' from 'vertebral column'.
gouttegd Sep 22, 2023
151f02a
Unsat fix: philtrum NOT part_of some rhinarium.
gouttegd Oct 26, 2023
c6edd6a
Unsat fix: Relax taxon constraint on 'neocortex'.
gouttegd Oct 26, 2023
33b9221
Remove mapping between UBERON:0006334 and HBA:4413.
gouttegd Oct 26, 2023
91c0fa7
Unsat fix: Remove undesired taxon specifity on 'axial skeletal system'.
gouttegd Oct 26, 2023
f25f8a2
Unsat fix: Relax taxon constraint on 'dermatocranium'.
gouttegd Oct 26, 2023
88451e1
Remove mapping between UBERON:0036215 and AEO:0000154.
gouttegd Oct 26, 2023
97ed463
Unsat fix: Relax the taxon constraint on 'epithelium'.
gouttegd Oct 27, 2023
448cc2b
Unsat fix: Relax taxon constraint on 'choroidal guanine tapetum'.
gouttegd Oct 26, 2023
92d4cbe
Unsat fix: Move misplace 'present in taxon' assertion.
gouttegd Oct 26, 2023
ed43459
Unsat fix: Remove link between 'mouth' and 'respiratory system'.
gouttegd Oct 26, 2023
872bcf9
Unsat fix: Relax taxon constraint on 'olivary pretectal nucleus'.
gouttegd Oct 26, 2023
c0a1b37
Unsat fix: Remove link between 'artrhopod tibia' and 'insect leg'.
gouttegd Oct 26, 2023
8449476
Unsat fix: Remove link between 'cranium' and 'skull'.
gouttegd Oct 26, 2023
adb2596
Unsat fix: Remove the link between 'nasal skeleton' and 'facial skele…
gouttegd Oct 26, 2023
0fc2148
Unsat fix: Remove the link between 'mouth' and 'head'.
gouttegd Oct 26, 2023
21fc13f
Import both taxslim.owl and taxslim-disjoint-over-in-taxon.owl.
gouttegd Oct 30, 2023
111cc22
Merge branch 'master' into new-taxon-constraint-check
gouttegd Oct 30, 2023
dc3aa6a
Re-generate the AEO bridge.
gouttegd Oct 30, 2023
a9b6d7e
Post a comment explaining the TC violations.
gouttegd Nov 2, 2023
6f22bc1
Merge branch 'master' into new-taxon-constraint-check
gouttegd Nov 8, 2023
49501ee
Forcefully fix externally caused TC violations.
gouttegd Nov 8, 2023
44421ae
Do not update the HRA subset component upon MIR=false.
gouttegd Nov 8, 2023
c1ca725
update hra_subset component
anitacaron Nov 9, 2023
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Unsat fix: Relax the taxon constraint on 'epithelium'.
'epithelium' is restricted to Eumatazoa, but "true epithelia" have been
reported in some sponges. Besides, the homology notes on 'epithelium'
clearly states that epithelial tissues are found in *metazoans*, not
*eumetazoans*. So we relax the taxon constraint up to metazoans.
gouttegd committed Oct 27, 2023
commit 97ed463a48cfb7293be763afe6670c7b9cd3c4bf
2 changes: 1 addition & 1 deletion src/ontology/uberon-edit.obo
Original file line number Diff line number Diff line change
@@ -7452,7 +7452,7 @@ union_of: UBERON:0000486 ! multilaminar epithelium
union_of: UBERON:0000490 ! unilaminar epithelium
relationship: has_part GO:0005911 ! cell-cell junction
relationship: has_part UBERON:0005769 ! basement membrane of epithelium
relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa
relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa
property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI
property_value: has_relational_adjective "epithelial" xsd:string
property_value: homology_notes "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"}