Skip to content
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.

Sign up for GitHub

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

Jump to bottom

OBI with workshop-revised COB demo #1834

Draft
wants to merge 33 commits into
base: master
Choose a base branch
from
Draft

OBI with workshop-revised COB demo #1834

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
33 commits
Select commit Hold shift + click to select a range
9c7986c
Replace OMO import with versioned OMO import
sebastianduesing Oct 25, 2024
ced9b9a
Add OntoFox RO import and drop external-byhand
sebastianduesing Oct 25, 2024
04389c2
Prepare IAO import file
sebastianduesing Oct 25, 2024
07bf569
Remove BFO import
sebastianduesing Oct 25, 2024
972064d
Add import of revised COB
sebastianduesing Oct 25, 2024
5245b12
Relabel alternative term to alternative label in all templates
sebastianduesing Oct 28, 2024
eb9e87f
Replace inheres in and bearer of with characteristic of and has chara…
sebastianduesing Oct 28, 2024
5d7da15
Redirect CHEBI:atom references to COB:atom
sebastianduesing Oct 28, 2024
b03f544
Redirect CHEBI:molecular entity references to COB:molecule
sebastianduesing Oct 28, 2024
b79d55c
Obsolete OBI:device and redirect to COB:device
sebastianduesing Oct 31, 2024
97f0623
Obsolete OBI:organism and redirect to COB:organism
sebastianduesing Nov 1, 2024
13238a7
Obsolete OBI:planned process and redirect to COB:CEPP
sebastianduesing Nov 1, 2024
e83988f
Obsolete OBI:material processing and redirect to COB:material processing
sebastianduesing Nov 1, 2024
30c60b3
Line order update to obi-edit by Protege
sebastianduesing Nov 1, 2024
a850a9a
Remove BFO:0000001
sebastianduesing Nov 1, 2024
fb3c0f0
Remove BFO:0000002
sebastianduesing Nov 1, 2024
0bae0fd
Remove BFO:0000003
sebastianduesing Nov 1, 2024
082607d
Remove BFO:0000004
sebastianduesing Nov 1, 2024
4f065ec
Remove BFO:0000019
sebastianduesing Nov 1, 2024
40478c2
Remove BFO:0000020
sebastianduesing Nov 1, 2024
ad9bb8a
Remove BFO:0000028
sebastianduesing Nov 1, 2024
72981f0
Remove one usage of BFO:0000031
sebastianduesing Nov 1, 2024
2850a17
Line order update by Protege
sebastianduesing Nov 1, 2024
738995c
Remove BFO:0000035
sebastianduesing Nov 1, 2024
e840aac
Fix duplicate labels
sebastianduesing Nov 1, 2024
c9c6973
Obsolete OBI:processed material and redirect to COB:processed materia…
sebastianduesing Nov 1, 2024
e42f22b
Update version of COB
sebastianduesing Nov 6, 2024
547fbc8
Remove unused BFO_0000066
sebastianduesing Nov 6, 2024
e4b218a
Relabel terms in templates
sebastianduesing Nov 6, 2024
fb84f84
Import 'realized in'
sebastianduesing Nov 6, 2024
1a4ee1b
Fix weird quoting in assays.tsv
sebastianduesing Nov 6, 2024
ae0fc5b
Run make modules
sebastianduesing Nov 6, 2024
24558f1
Update OMO version
sebastianduesing Nov 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
190 changes: 133 additions & 57 deletions src/ontology/OntoFox_inputs/ChEBI_input.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ http://purl.obolibrary.org/obo/obi/dev/import/ChEBI_imports.owl
CHEBI

[Low level source term URIs]
http://purl.obolibrary.org/obo/CHEBI_23367
http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide
http://purl.obolibrary.org/obo/CHEBI_4705
http://purl.obolibrary.org/obo/CHEBI_15377
Expand Down Expand Up @@ -60,7 +59,6 @@ http://purl.obolibrary.org/obo/CHEBI_33697
http://purl.obolibrary.org/obo/CHEBI_16670
http://purl.obolibrary.org/obo/CHEBI_33696
http://purl.obolibrary.org/obo/CHEBI_32142
http://purl.obolibrary.org/obo/CHEBI_33250
http://purl.obolibrary.org/obo/CHEBI_32142
http://purl.obolibrary.org/obo/CHEBI_472552
http://purl.obolibrary.org/obo/CHEBI_29237 # deuterium atom
Expand Down Expand Up @@ -124,102 +122,182 @@ http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion


[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/BFO_0000040
http://purl.obolibrary.org/obo/CHEBI_86319 # 25-hydroxyvitamin D2
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_2637 # amikacin
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16134 # ammonia
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_15422 # ATP (Adenosine triphosphate)
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_22868 # bile salt
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16990 # bilirubin IXalpha
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16526 # carbon dioxide
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17996 # chloride
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16113 # cholesterol
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17650 # cortisol
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16919 # creatine
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16737 # creatinine
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_28689 # dehydroepiandrosterone
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_4551 # digoxin
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_33262 # elemental oxygen
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_23965 # estradiol
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_35366 # fatty acid
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_37445 # folic acids
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_81569 # Follicle stimulating hormone
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_47775 # high-density lipoprotein cholesterol
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17544 # hydrogencarbonate
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_24875 # iron cation
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_47774 # low-density lipoprotein cholesterol
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_81568 # Luteinizing hormone
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_39127 # magnesium cation
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_168396 # mycophenolic acid
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16301 # nitrite
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_61073 # oxygen radical
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_35780 # phosphate ion
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16247 # phospholipid
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_29103 # potassium(1+)
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17026 # progesterone
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_29101 # sodium(1+)
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_61057 # tacrolimus hydrate
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17347 # testosterone
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_28864 # tobramycin
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17855 # triglyceride
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_27226 # uric acid
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_29237 # deuterium atom
subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom
http://purl.obolibrary.org/obo/CHEBI_33321 # rare earth metal atom
subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom
http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_4705
subClassOf http://purl.obolibrary.org/obo/CHEBI_16991
http://purl.obolibrary.org/obo/CHEBI_15377
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_15956
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17137
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17234
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_17709
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_23528
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_23995
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_24636
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_25078
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_26710
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_27889
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_28619
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_29191
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_30682
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_31624
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_31642
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_31643
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_31991
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_32875 # methyl group
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_33359
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_33375
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_33376
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_33709
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_33839
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_35729
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_37333
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_37586
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_37987
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_37989
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_42098
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_42191
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_50076
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_51756
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_51760
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_52673
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_53526
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59050
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59051
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59052
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59053
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59054
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59055
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59056
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_59424
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_9754
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_16991
subClassOf http://purl.obolibrary.org/obo/CHEBI_33696
http://purl.obolibrary.org/obo/CHEBI_33697
Expand All @@ -229,17 +307,15 @@ subClassOf http://purl.obolibrary.org/obo/CHEBI_33839
http://purl.obolibrary.org/obo/CHEBI_33696
subClassOf http://purl.obolibrary.org/obo/CHEBI_33839
http://purl.obolibrary.org/obo/CHEBI_32142
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_472552
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
http://purl.obolibrary.org/obo/CHEBI_33250
subClassOf http://purl.obolibrary.org/obo/BFO_0000040
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_37972
subClassOf http://purl.obolibrary.org/obo/CHEBI_33250
subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom
http://purl.obolibrary.org/obo/CHEBI_37973
subClassOf http://purl.obolibrary.org/obo/CHEBI_33250
subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom
http://purl.obolibrary.org/obo/CHEBI_32142
subClassOf http://purl.obolibrary.org/obo/CHEBI_23367
subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecule
http://purl.obolibrary.org/obo/CHEBI_28358 # rac-lactic acid
subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity (not a molecular entity)

Expand Down
7 changes: 3 additions & 4 deletions src/ontology/OntoFox_inputs/IAO_input.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,8 @@ http://purl.obolibrary.org/obo/IAO_0000003 # measurement unit label
http://purl.obolibrary.org/obo/IAO_0000004 # has measurement value
http://purl.obolibrary.org/obo/IAO_0000005 # objective specification
http://purl.obolibrary.org/obo/IAO_0000006 # narrative object
http://purl.obolibrary.org/obo/IAO_0000007 # action specification
http://purl.obolibrary.org/obo/IAO_0000009 # datum label
http://purl.obolibrary.org/obo/IAO_0000010 # software
http://purl.obolibrary.org/obo/IAO_0000015 # information carrier
http://purl.obolibrary.org/obo/IAO_0000027 # data item
http://purl.obolibrary.org/obo/IAO_0000028 # symbol
http://purl.obolibrary.org/obo/IAO_0000030 # information content entity
Expand Down Expand Up @@ -46,6 +44,7 @@ http://purl.obolibrary.org/obo/IAO_0000235 # denoted by
http://purl.obolibrary.org/obo/IAO_0000300 # textual entity
http://purl.obolibrary.org/obo/IAO_0000306 # table
http://purl.obolibrary.org/obo/IAO_0000310 # document
http://purl.obolibrary.org/obo/IAO_0000311 # publication
http://purl.obolibrary.org/obo/IAO_0000312 # publication about an investigation
http://purl.obolibrary.org/obo/IAO_0000401 # one dimensional cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000407 # has coordinate unit label
Expand All @@ -64,7 +63,7 @@ http://purl.obolibrary.org/obo/IAO_0000594 # software application

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/IAO_0000030 # information content entity
subClassOf http://purl.obolibrary.org/obo/BFO_0000031 # generically dependent continuant
subClassOf http://www.w3.org/2002/07/owl#Thing # owl:Thing
http://purl.obolibrary.org/obo/IAO_0000178 # material information bearer
subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity
http://purl.obolibrary.org/obo/IAO_0000574 # assigning a centrally registered identifier
Expand All @@ -73,7 +72,7 @@ http://purl.obolibrary.org/obo/IAO_0000572 # documenting
subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process

[Source term retrieval setting]
includeAllIntermediates
includeComputedIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
Expand Down
8 changes: 4 additions & 4 deletions src/ontology/OntoFox_inputs/NCBITaxon_input.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,13 +45,13 @@ http://purl.obolibrary.org/obo/NCBITaxon_3052230 # Hepacivirus hominis

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/NCBITaxon_2157
subClassOf http://purl.obolibrary.org/obo/OBI_0100026 #OBI:organism
subClassOf http://purl.obolibrary.org/obo/COB_0000022 # organism
http://purl.obolibrary.org/obo/NCBITaxon_2
subClassOf http://purl.obolibrary.org/obo/OBI_0100026 #OBI:organism
subClassOf http://purl.obolibrary.org/obo/COB_0000022 # organism
http://purl.obolibrary.org/obo/NCBITaxon_2759
subClassOf http://purl.obolibrary.org/obo/OBI_0100026 #OBI:organism
subClassOf http://purl.obolibrary.org/obo/COB_0000022 # organism
http://purl.obolibrary.org/obo/NCBITaxon_10239
subClassOf http://purl.obolibrary.org/obo/OBI_0100026 #OBI:organism
subClassOf http://purl.obolibrary.org/obo/COB_0000022 # organism


[Source term retrieval setting]
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/OntoFox_inputs/OBA_input.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ http://purl.obolibrary.org/obo/OBA_2060190 # brachioradialis functionality
[Top level source term URIs and target direct superclass URIs]
# WARN: OBA subclasses PATO:0000001 'quality' not BFO:0000019 'quality'
http://purl.obolibrary.org/obo/OBA_0000001 # biological attribute
subClassOf http://purl.obolibrary.org/obo/BFO_0000019 # quality
subClassOf http://purl.obolibrary.org/obo/COB_0000502 # characteristic

[Source term retrieval setting]
includeNoIntermediates
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/OntoFox_inputs/OGMS_input.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ http://purl.obolibrary.org/obo/OGMS_0000123 # clinical data item
http://purl.obolibrary.org/obo/OGMS_0000015
subClassOf http://purl.obolibrary.org/obo/IAO_0000030
http://purl.obolibrary.org/obo/OGMS_0000023
subClassOf http://purl.obolibrary.org/obo/BFO_0000019
subClassOf http://purl.obolibrary.org/obo/COB_0000502 # characteristic
http://purl.obolibrary.org/obo/OGMS_0000063
subClassOf http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/OGMS_0000090
Expand Down
4 changes: 2 additions & 2 deletions src/ontology/OntoFox_inputs/OPL_input.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@ http://purl.obolibrary.org/obo/OPL_0000267 #Plasmodium gametocyte
http://purl.obolibrary.org/obo/OPL_0000267 #Plasmodium gametocyte
subClassOf http://purl.obolibrary.org/obo/NCBITaxon_5820 #Plasmodium
http://purl.obolibrary.org/obo/OPL_0000232 #parasite organism
subClassOf http://purl.obolibrary.org/obo/OBI_0100026 #OBI:organism
subClassOf http://purl.obolibrary.org/obo/COB_0000022 # organism

[Source term retrieval setting]
includeNoIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
copyTo http://purl.obolibrary.org/obo/IAO_0000111
http://purl.obolibrary.org/obo/IAO_0000115
http://purl.obolibrary.org/obo/IAO_0000115
Loading