Skip to content
This repository was archived by the owner on Jul 31, 2025. It is now read-only.

Commit 1c6bc7a

Browse files
matentznmatentzn
authored
Merge pull request #68 from obophenotype/add-manual-groupings
Add manual groupings and groupings for lexical matches
2 parents 5c3bd7c + 585107a commit 1c6bc7a

36 files changed

Lines changed: 2850835 additions & 318755 deletions

‎.github/workflows/qc.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ jobs:
1919
ontology_qc:
2020
# The type of runner that the job will run on
2121
runs-on: ubuntu-latest
22-
container: obolibrary/odkfull:v1.5.3
22+
container: obolibrary/odkfull:v1.5.4
2323

2424
# Steps represent a sequence of tasks that will be executed as part of the job
2525
steps:

‎.gitignore‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -248,3 +248,8 @@ src/ontology/upheno-test.db
248248
src/ontology/upheno-test.owl
249249
upheno-test.owl
250250
src/mappings/upheno-oba.kgx
251+
src/mappings/upheno-species-independent-eq.sssom.owl
252+
src/ontology/upheno-curated-with-sspo.owl
253+
src/ontology/upheno-curated-with-sspo.json
254+
src/ontology/upheno-curated-with-sspo.obo
255+
upheno-curated-with-sspo.*

‎reports/upheno-base.owl-obo-report.tsv‎

Lines changed: 1225 additions & 0 deletions
Large diffs are not rendered by default.

‎src/mappings/uberon.sssom.tsv‎

Lines changed: 21 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -12,11 +12,8 @@
1212
# FMA: http://purl.obolibrary.org/obo/FMA_
1313
# GO: http://purl.obolibrary.org/obo/GO_
1414
# HAO: http://purl.obolibrary.org/obo/HAO_
15-
# HsapDv: http://purl.obolibrary.org/obo/HsapDv_
1615
# MA: http://purl.obolibrary.org/obo/MA_
17-
# MmusDv: http://purl.obolibrary.org/obo/MmusDv_
1816
# NCIT: http://purl.obolibrary.org/obo/NCIT_
19-
# OlatDv: http://purl.obolibrary.org/obo/OlatDv_
2017
# SPD: http://purl.obolibrary.org/obo/SPD_
2118
# TADS: http://purl.obolibrary.org/obo/TADS_
2219
# TAO: http://purl.obolibrary.org/obo/TAO_
@@ -350,8 +347,6 @@ UBERON:0000066 fully formed stage semapv:crossSpeciesExactMatch WBls:0000041 sem
350347
UBERON:0000068 embryo stage skos:narrowMatch EV:0300001 semapv:UnspecifiedMatching
351348
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch FBdv:00005289 semapv:UnspecifiedMatching
352349
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch FMA:72652 semapv:UnspecifiedMatching
353-
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch HsapDv:0000002 semapv:UnspecifiedMatching
354-
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch MmusDv:0000002 semapv:UnspecifiedMatching
355350
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch WBls:0000003 semapv:UnspecifiedMatching
356351
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch WBls:0000092 semapv:UnspecifiedMatching
357352
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch WBls:0000102 semapv:UnspecifiedMatching
@@ -478,13 +473,8 @@ UBERON:0000101 lobe of lung semapv:crossSpeciesExactMatch FMA:7311 semapv:Unspec
478473
UBERON:0000101 lobe of lung semapv:crossSpeciesExactMatch MA:0003098 semapv:UnspecifiedMatching
479474
UBERON:0000102 lung vasculature semapv:crossSpeciesExactMatch FMA:73750 semapv:UnspecifiedMatching
480475
UBERON:0000104 life cycle semapv:crossSpeciesExactMatch FBdv:00000000 semapv:UnspecifiedMatching
481-
UBERON:0000104 life cycle semapv:crossSpeciesExactMatch HsapDv:0000001 semapv:UnspecifiedMatching
482-
UBERON:0000104 life cycle semapv:crossSpeciesExactMatch MmusDv:0000001 semapv:UnspecifiedMatching
483476
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch FBdv:00007012 semapv:UnspecifiedMatching
484477
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch FMA:24120 semapv:UnspecifiedMatching
485-
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch HsapDv:0000000 semapv:UnspecifiedMatching
486-
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch MmusDv:0000000 semapv:UnspecifiedMatching
487-
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch OlatDv:0000010 semapv:UnspecifiedMatching
488478
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch WBls:0000002 semapv:UnspecifiedMatching
489479
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch XAO:1000000 semapv:UnspecifiedMatching
490480
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch ZFS:0000000 semapv:UnspecifiedMatching
@@ -496,32 +486,21 @@ UBERON:0000106 zygote stage semapv:crossSpeciesExactMatch FBdv:00005288 semapv:U
496486
UBERON:0000106 zygote stage semapv:crossSpeciesExactMatch XAO:1000001 semapv:UnspecifiedMatching
497487
UBERON:0000106 zygote stage semapv:crossSpeciesExactMatch ZFS:0000001 semapv:UnspecifiedMatching
498488
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch FBdv:00000054 semapv:UnspecifiedMatching
499-
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch MmusDv:0000004 semapv:UnspecifiedMatching
500489
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch XAO:1000004 semapv:UnspecifiedMatching
501490
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch ZFS:0000046 semapv:UnspecifiedMatching
502-
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch HsapDv:0000006 semapv:UnspecifiedMatching
503-
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch MmusDv:0000007 semapv:UnspecifiedMatching
504491
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch WBls:0000005 semapv:UnspecifiedMatching
505492
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch XAO:1000003 semapv:UnspecifiedMatching
506493
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch ZFS:0000045 semapv:UnspecifiedMatching
507494
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch FBdv:00005317 semapv:UnspecifiedMatching
508-
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch HsapDv:0000010 semapv:UnspecifiedMatching
509-
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch MmusDv:0000013 semapv:UnspecifiedMatching
510495
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch WBls:0000010 semapv:UnspecifiedMatching
511496
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch XAO:1000005 semapv:UnspecifiedMatching
512497
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch ZFS:0000047 semapv:UnspecifiedMatching
513-
UBERON:0000110 neurula stage semapv:crossSpeciesExactMatch HsapDv:0000012 semapv:UnspecifiedMatching
514-
UBERON:0000110 neurula stage semapv:crossSpeciesExactMatch MmusDv:0000017 semapv:UnspecifiedMatching
515498
UBERON:0000110 neurula stage semapv:crossSpeciesExactMatch XAO:1000006 semapv:UnspecifiedMatching
516-
UBERON:0000111 organogenesis stage semapv:crossSpeciesExactMatch HsapDv:0000015 semapv:UnspecifiedMatching
517-
UBERON:0000111 organogenesis stage semapv:crossSpeciesExactMatch MmusDv:0000018 semapv:UnspecifiedMatching
518499
UBERON:0000112 sexually immature stage skos:narrowMatch EV:0300051 semapv:UnspecifiedMatching
519-
UBERON:0000112 sexually immature stage semapv:crossSpeciesExactMatch MmusDv:0000043 semapv:UnspecifiedMatching
520500
UBERON:0000112 sexually immature stage semapv:crossSpeciesExactMatch XAO:1000010 semapv:UnspecifiedMatching
521501
UBERON:0000112 sexually immature stage semapv:crossSpeciesExactMatch ZFS:0000051 semapv:UnspecifiedMatching
522502
UBERON:0000113 post-juvenile adult stage skos:narrowMatch EV:0300064 semapv:UnspecifiedMatching
523503
UBERON:0000113 post-juvenile adult stage skos:narrowMatch EV:0300070 semapv:UnspecifiedMatching
524-
UBERON:0000113 post-juvenile adult stage semapv:crossSpeciesExactMatch MmusDv:0000110 semapv:UnspecifiedMatching
525504
UBERON:0000113 post-juvenile adult stage semapv:crossSpeciesExactMatch XAO:1000093 semapv:UnspecifiedMatching
526505
UBERON:0000113 post-juvenile adult stage semapv:crossSpeciesExactMatch ZFS:0000044 semapv:UnspecifiedMatching
527506
UBERON:0000114 lung connective tissue semapv:crossSpeciesExactMatch EMAPA:35521 semapv:UnspecifiedMatching
@@ -18309,13 +18288,9 @@ UBERON:0007215 trabecula cranii semapv:crossSpeciesExactMatch ZFA:0001507 semapv
1830918288
UBERON:0007220 late embryonic stage skos:narrowMatch EV:0300011 semapv:UnspecifiedMatching
1831018289
UBERON:0007220 late embryonic stage semapv:crossSpeciesExactMatch FBdv:00005333 semapv:UnspecifiedMatching
1831118290
UBERON:0007220 late embryonic stage semapv:crossSpeciesExactMatch FMA:63631 semapv:UnspecifiedMatching
18312-
UBERON:0007220 late embryonic stage semapv:crossSpeciesExactMatch MmusDv:0000031 semapv:UnspecifiedMatching
1831318291
UBERON:0007221 neonate stage skos:narrowMatch EV:0300037 semapv:UnspecifiedMatching
18314-
UBERON:0007221 neonate stage semapv:crossSpeciesExactMatch HsapDv:0000082 semapv:UnspecifiedMatching
18315-
UBERON:0007221 neonate stage semapv:crossSpeciesExactMatch MmusDv:0000096 semapv:UnspecifiedMatching
1831618292
UBERON:0007222 late adult stage skos:narrowMatch EV:0300123 semapv:UnspecifiedMatching
1831718293
UBERON:0007222 late adult stage skos:narrowMatch NCIT:C16268 semapv:UnspecifiedMatching
18318-
UBERON:0007222 late adult stage semapv:crossSpeciesExactMatch HsapDv:0000093 semapv:UnspecifiedMatching
1831918294
UBERON:0007223 osseus cochlea semapv:crossSpeciesExactMatch EMAPA:35620 semapv:UnspecifiedMatching
1832018295
UBERON:0007223 osseus cochlea semapv:crossSpeciesExactMatch MA:0000239 semapv:UnspecifiedMatching
1832118296
UBERON:0007224 medial entorhinal cortex semapv:crossSpeciesExactMatch EMAPA:35545 semapv:UnspecifiedMatching
@@ -25132,4 +25107,25 @@ UBERON:8600111 right distal ureter semapv:crossSpeciesExactMatch FMA:15886 semap
2513225107
UBERON:8600112 left distal ureter semapv:crossSpeciesExactMatch FMA:15887 semapv:UnspecifiedMatching
2513325108
UBERON:8600113 right proximal ureter semapv:crossSpeciesExactMatch FMA:15884 semapv:UnspecifiedMatching
2513425109
UBERON:8600114 left proximal ureter semapv:crossSpeciesExactMatch FMA:15885 semapv:UnspecifiedMatching
25110+
UBERON:8600121 lumbar ganglion semapv:crossSpeciesExactMatch FMA:6472 semapv:UnspecifiedMatching
25111+
UBERON:8600122 sacral ganglion semapv:crossSpeciesExactMatch FMA:6473 semapv:UnspecifiedMatching
2513525112
UBERON:8850000 lumen of pulmonary alveolus semapv:crossSpeciesExactMatch FMA:62779 semapv:UnspecifiedMatching
25113+
UBERON:8920000 anterior ciliary artery semapv:crossSpeciesExactMatch FMA:49962 semapv:UnspecifiedMatching
25114+
UBERON:8920001 short posterior ciliary artery semapv:crossSpeciesExactMatch FMA:70777 semapv:UnspecifiedMatching
25115+
UBERON:8920002 long posterior ciliary artery semapv:crossSpeciesExactMatch FMA:70778 semapv:UnspecifiedMatching
25116+
UBERON:8920003 right marginal artery semapv:crossSpeciesExactMatch FMA:3818 semapv:UnspecifiedMatching
25117+
UBERON:8920004 segmental renal artery semapv:crossSpeciesExactMatch FMA:70494 semapv:UnspecifiedMatching
25118+
UBERON:8920005 superior segmental renal artery semapv:crossSpeciesExactMatch FMA:70499 semapv:UnspecifiedMatching
25119+
UBERON:8920006 anterior superior segmental renal artery semapv:crossSpeciesExactMatch FMA:70500 semapv:UnspecifiedMatching
25120+
UBERON:8920007 anterior inferior segmental renal artery semapv:crossSpeciesExactMatch FMA:70501 semapv:UnspecifiedMatching
25121+
UBERON:8920008 inferior segmental renal artery semapv:crossSpeciesExactMatch FMA:70502 semapv:UnspecifiedMatching
25122+
UBERON:8920009 posterior segmental renal artery semapv:crossSpeciesExactMatch FMA:70503 semapv:UnspecifiedMatching
25123+
UBERON:8920010 left marginal vein semapv:crossSpeciesExactMatch FMA:4708 semapv:UnspecifiedMatching
25124+
UBERON:8920011 stellate vein of kidney semapv:crossSpeciesExactMatch FMA:71635 semapv:UnspecifiedMatching
25125+
UBERON:8920013 anterior ciliary vein semapv:crossSpeciesExactMatch FMA:51798 semapv:UnspecifiedMatching
25126+
UBERON:8920014 left bronchial vein semapv:crossSpeciesExactMatch FMA:4837 semapv:UnspecifiedMatching
25127+
UBERON:8920015 right bronchial vein semapv:crossSpeciesExactMatch FMA:4942 semapv:UnspecifiedMatching
25128+
UBERON:8920016 right inferior pulmonary vein semapv:crossSpeciesExactMatch FMA:49911 semapv:UnspecifiedMatching
25129+
UBERON:8920017 left inferior pulmonary vein semapv:crossSpeciesExactMatch FMA:49913 semapv:UnspecifiedMatching
25130+
UBERON:8920018 right superior pulmonary vein semapv:crossSpeciesExactMatch FMA:49914 semapv:UnspecifiedMatching
25131+
UBERON:8920019 left superior pulmonary vein semapv:crossSpeciesExactMatch FMA:49916 semapv:UnspecifiedMatching

0 commit comments

Comments
 (0)