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Add manual groupings and groupings for lexical matches #68

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matentzn merged 34 commits into from
Jul 18, 2025
Merged

Add manual groupings and groupings for lexical matches #68

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3f3e07f
Update manual alignment files
matentzn Mar 30, 2025
1879113
Add upheno-ssspo-alignments-no-eq.tsv to ODK config
matentzn Mar 30, 2025
7248a03
Update ODK config with additional files
matentzn Mar 30, 2025
4b6ac5b
Add update_manual_alignments pipeline to makefile
matentzn Mar 30, 2025
e475188
Add python for manually aligned classes to upheno_build.py
matentzn Mar 30, 2025
e46493d
Update metadata.sparql
matentzn Mar 31, 2025
776f3fd
Update metadata.sparql
matentzn Mar 31, 2025
ba0fd38
Only write files if new stuff is found
matentzn Mar 31, 2025
522cd4e
Reformat templates and mapping files for automated grouping generation
matentzn Mar 31, 2025
1a85006
Add mapping justification in automated grouping
matentzn Mar 31, 2025
4535562
Update independent alignments
matentzn Mar 31, 2025
49d079f
Update upheno.Makefile
matentzn Mar 31, 2025
4f2479a
Reset manual phenotype grouping files
matentzn Apr 1, 2025
83eb6cb
Add fixed manual alignments
matentzn Apr 1, 2025
7524287
Updated cross-species mappings based on EQs
matentzn Apr 1, 2025
a19f97d
Update upheno-cross-species.sssom.tsv
matentzn Apr 1, 2025
6bc4c5e
Update upheno-species-independent-manual.sssom.tsv
matentzn Apr 1, 2025
b4b173b
First draft of non-eq based alignments
matentzn Apr 1, 2025
3da2ab8
Update metadata.sparql
matentzn Apr 1, 2025
0524550
Misc refactorings in lib, including r in regex expressions
matentzn Apr 1, 2025
d5e4efc
Add MGPO prefix to ODK config
matentzn Apr 1, 2025
9daccfd
Update upheno-species-independent.sssom.tsv
matentzn Apr 1, 2025
741d72e
Add sparql query to inject class declarations into mapping
matentzn Apr 5, 2025
62a5352
Ensure semapv:crossSpeciesExactMatch is correctly marked as a AP
matentzn Apr 5, 2025
58c8c12
Update cross species and species independent mapping set
matentzn Apr 5, 2025
b291d84
Upgrade qc.yml to ODK 1.5.4
matentzn Apr 5, 2025
25a9f0a
Add new mappings component to ODK setup
matentzn Apr 5, 2025
c0693d4
Update bridge and mapping components
matentzn Apr 5, 2025
acbc8e8
Add sssom metadata files to config
matentzn Apr 5, 2025
3db0e8d
Update Makefile with new release flavour upheno-curated-with-sspo.owl:
matentzn Apr 5, 2025
d4ac1f1
Removing mappings from bridge component
matentzn Apr 5, 2025
2d4e2a1
Update .gitignore
matentzn Apr 5, 2025
744c98d
Update .gitignore
matentzn Jul 11, 2025
585107a
misc changes
matentzn Jul 18, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/qc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5.3
container: obolibrary/odkfull:v1.5.4

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
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5 changes: 5 additions & 0 deletions .gitignore
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Expand Up @@ -248,3 +248,8 @@ src/ontology/upheno-test.db
src/ontology/upheno-test.owl
upheno-test.owl
src/mappings/upheno-oba.kgx
src/mappings/upheno-species-independent-eq.sssom.owl
src/ontology/upheno-curated-with-sspo.owl
src/ontology/upheno-curated-with-sspo.json
src/ontology/upheno-curated-with-sspo.obo
upheno-curated-with-sspo.*
1,225 changes: 1,225 additions & 0 deletions reports/upheno-base.owl-obo-report.tsv
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46 changes: 21 additions & 25 deletions src/mappings/uberon.sssom.tsv
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Expand Up @@ -12,11 +12,8 @@
# FMA: http://purl.obolibrary.org/obo/FMA_
# GO: http://purl.obolibrary.org/obo/GO_
# HAO: http://purl.obolibrary.org/obo/HAO_
# HsapDv: http://purl.obolibrary.org/obo/HsapDv_
# MA: http://purl.obolibrary.org/obo/MA_
# MmusDv: http://purl.obolibrary.org/obo/MmusDv_
# NCIT: http://purl.obolibrary.org/obo/NCIT_
# OlatDv: http://purl.obolibrary.org/obo/OlatDv_
# SPD: http://purl.obolibrary.org/obo/SPD_
# TADS: http://purl.obolibrary.org/obo/TADS_
# TAO: http://purl.obolibrary.org/obo/TAO_
Expand Down Expand Up @@ -350,8 +347,6 @@ UBERON:0000066 fully formed stage semapv:crossSpeciesExactMatch WBls:0000041 sem
UBERON:0000068 embryo stage skos:narrowMatch EV:0300001 semapv:UnspecifiedMatching
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch FBdv:00005289 semapv:UnspecifiedMatching
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch FMA:72652 semapv:UnspecifiedMatching
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch HsapDv:0000002 semapv:UnspecifiedMatching
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch MmusDv:0000002 semapv:UnspecifiedMatching
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch WBls:0000003 semapv:UnspecifiedMatching
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch WBls:0000092 semapv:UnspecifiedMatching
UBERON:0000068 embryo stage semapv:crossSpeciesExactMatch WBls:0000102 semapv:UnspecifiedMatching
Expand Down Expand Up @@ -478,13 +473,8 @@ UBERON:0000101 lobe of lung semapv:crossSpeciesExactMatch FMA:7311 semapv:Unspec
UBERON:0000101 lobe of lung semapv:crossSpeciesExactMatch MA:0003098 semapv:UnspecifiedMatching
UBERON:0000102 lung vasculature semapv:crossSpeciesExactMatch FMA:73750 semapv:UnspecifiedMatching
UBERON:0000104 life cycle semapv:crossSpeciesExactMatch FBdv:00000000 semapv:UnspecifiedMatching
UBERON:0000104 life cycle semapv:crossSpeciesExactMatch HsapDv:0000001 semapv:UnspecifiedMatching
UBERON:0000104 life cycle semapv:crossSpeciesExactMatch MmusDv:0000001 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch FBdv:00007012 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch FMA:24120 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch HsapDv:0000000 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch MmusDv:0000000 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch OlatDv:0000010 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch WBls:0000002 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch XAO:1000000 semapv:UnspecifiedMatching
UBERON:0000105 life cycle stage semapv:crossSpeciesExactMatch ZFS:0000000 semapv:UnspecifiedMatching
Expand All @@ -496,32 +486,21 @@ UBERON:0000106 zygote stage semapv:crossSpeciesExactMatch FBdv:00005288 semapv:U
UBERON:0000106 zygote stage semapv:crossSpeciesExactMatch XAO:1000001 semapv:UnspecifiedMatching
UBERON:0000106 zygote stage semapv:crossSpeciesExactMatch ZFS:0000001 semapv:UnspecifiedMatching
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch FBdv:00000054 semapv:UnspecifiedMatching
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch MmusDv:0000004 semapv:UnspecifiedMatching
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch XAO:1000004 semapv:UnspecifiedMatching
UBERON:0000107 cleavage stage semapv:crossSpeciesExactMatch ZFS:0000046 semapv:UnspecifiedMatching
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch HsapDv:0000006 semapv:UnspecifiedMatching
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch MmusDv:0000007 semapv:UnspecifiedMatching
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch WBls:0000005 semapv:UnspecifiedMatching
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch XAO:1000003 semapv:UnspecifiedMatching
UBERON:0000108 blastula stage semapv:crossSpeciesExactMatch ZFS:0000045 semapv:UnspecifiedMatching
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch FBdv:00005317 semapv:UnspecifiedMatching
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch HsapDv:0000010 semapv:UnspecifiedMatching
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch MmusDv:0000013 semapv:UnspecifiedMatching
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch WBls:0000010 semapv:UnspecifiedMatching
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch XAO:1000005 semapv:UnspecifiedMatching
UBERON:0000109 gastrula stage semapv:crossSpeciesExactMatch ZFS:0000047 semapv:UnspecifiedMatching
UBERON:0000110 neurula stage semapv:crossSpeciesExactMatch HsapDv:0000012 semapv:UnspecifiedMatching
UBERON:0000110 neurula stage semapv:crossSpeciesExactMatch MmusDv:0000017 semapv:UnspecifiedMatching
UBERON:0000110 neurula stage semapv:crossSpeciesExactMatch XAO:1000006 semapv:UnspecifiedMatching
UBERON:0000111 organogenesis stage semapv:crossSpeciesExactMatch HsapDv:0000015 semapv:UnspecifiedMatching
UBERON:0000111 organogenesis stage semapv:crossSpeciesExactMatch MmusDv:0000018 semapv:UnspecifiedMatching
UBERON:0000112 sexually immature stage skos:narrowMatch EV:0300051 semapv:UnspecifiedMatching
UBERON:0000112 sexually immature stage semapv:crossSpeciesExactMatch MmusDv:0000043 semapv:UnspecifiedMatching
UBERON:0000112 sexually immature stage semapv:crossSpeciesExactMatch XAO:1000010 semapv:UnspecifiedMatching
UBERON:0000112 sexually immature stage semapv:crossSpeciesExactMatch ZFS:0000051 semapv:UnspecifiedMatching
UBERON:0000113 post-juvenile adult stage skos:narrowMatch EV:0300064 semapv:UnspecifiedMatching
UBERON:0000113 post-juvenile adult stage skos:narrowMatch EV:0300070 semapv:UnspecifiedMatching
UBERON:0000113 post-juvenile adult stage semapv:crossSpeciesExactMatch MmusDv:0000110 semapv:UnspecifiedMatching
UBERON:0000113 post-juvenile adult stage semapv:crossSpeciesExactMatch XAO:1000093 semapv:UnspecifiedMatching
UBERON:0000113 post-juvenile adult stage semapv:crossSpeciesExactMatch ZFS:0000044 semapv:UnspecifiedMatching
UBERON:0000114 lung connective tissue semapv:crossSpeciesExactMatch EMAPA:35521 semapv:UnspecifiedMatching
Expand Down Expand Up @@ -18309,13 +18288,9 @@ UBERON:0007215 trabecula cranii semapv:crossSpeciesExactMatch ZFA:0001507 semapv
UBERON:0007220 late embryonic stage skos:narrowMatch EV:0300011 semapv:UnspecifiedMatching
UBERON:0007220 late embryonic stage semapv:crossSpeciesExactMatch FBdv:00005333 semapv:UnspecifiedMatching
UBERON:0007220 late embryonic stage semapv:crossSpeciesExactMatch FMA:63631 semapv:UnspecifiedMatching
UBERON:0007220 late embryonic stage semapv:crossSpeciesExactMatch MmusDv:0000031 semapv:UnspecifiedMatching
UBERON:0007221 neonate stage skos:narrowMatch EV:0300037 semapv:UnspecifiedMatching
UBERON:0007221 neonate stage semapv:crossSpeciesExactMatch HsapDv:0000082 semapv:UnspecifiedMatching
UBERON:0007221 neonate stage semapv:crossSpeciesExactMatch MmusDv:0000096 semapv:UnspecifiedMatching
UBERON:0007222 late adult stage skos:narrowMatch EV:0300123 semapv:UnspecifiedMatching
UBERON:0007222 late adult stage skos:narrowMatch NCIT:C16268 semapv:UnspecifiedMatching
UBERON:0007222 late adult stage semapv:crossSpeciesExactMatch HsapDv:0000093 semapv:UnspecifiedMatching
UBERON:0007223 osseus cochlea semapv:crossSpeciesExactMatch EMAPA:35620 semapv:UnspecifiedMatching
UBERON:0007223 osseus cochlea semapv:crossSpeciesExactMatch MA:0000239 semapv:UnspecifiedMatching
UBERON:0007224 medial entorhinal cortex semapv:crossSpeciesExactMatch EMAPA:35545 semapv:UnspecifiedMatching
Expand Down Expand Up @@ -25132,4 +25107,25 @@ UBERON:8600111 right distal ureter semapv:crossSpeciesExactMatch FMA:15886 semap
UBERON:8600112 left distal ureter semapv:crossSpeciesExactMatch FMA:15887 semapv:UnspecifiedMatching
UBERON:8600113 right proximal ureter semapv:crossSpeciesExactMatch FMA:15884 semapv:UnspecifiedMatching
UBERON:8600114 left proximal ureter semapv:crossSpeciesExactMatch FMA:15885 semapv:UnspecifiedMatching
UBERON:8600121 lumbar ganglion semapv:crossSpeciesExactMatch FMA:6472 semapv:UnspecifiedMatching
UBERON:8600122 sacral ganglion semapv:crossSpeciesExactMatch FMA:6473 semapv:UnspecifiedMatching
UBERON:8850000 lumen of pulmonary alveolus semapv:crossSpeciesExactMatch FMA:62779 semapv:UnspecifiedMatching
UBERON:8920000 anterior ciliary artery semapv:crossSpeciesExactMatch FMA:49962 semapv:UnspecifiedMatching
UBERON:8920001 short posterior ciliary artery semapv:crossSpeciesExactMatch FMA:70777 semapv:UnspecifiedMatching
UBERON:8920002 long posterior ciliary artery semapv:crossSpeciesExactMatch FMA:70778 semapv:UnspecifiedMatching
UBERON:8920003 right marginal artery semapv:crossSpeciesExactMatch FMA:3818 semapv:UnspecifiedMatching
UBERON:8920004 segmental renal artery semapv:crossSpeciesExactMatch FMA:70494 semapv:UnspecifiedMatching
UBERON:8920005 superior segmental renal artery semapv:crossSpeciesExactMatch FMA:70499 semapv:UnspecifiedMatching
UBERON:8920006 anterior superior segmental renal artery semapv:crossSpeciesExactMatch FMA:70500 semapv:UnspecifiedMatching
UBERON:8920007 anterior inferior segmental renal artery semapv:crossSpeciesExactMatch FMA:70501 semapv:UnspecifiedMatching
UBERON:8920008 inferior segmental renal artery semapv:crossSpeciesExactMatch FMA:70502 semapv:UnspecifiedMatching
UBERON:8920009 posterior segmental renal artery semapv:crossSpeciesExactMatch FMA:70503 semapv:UnspecifiedMatching
UBERON:8920010 left marginal vein semapv:crossSpeciesExactMatch FMA:4708 semapv:UnspecifiedMatching
UBERON:8920011 stellate vein of kidney semapv:crossSpeciesExactMatch FMA:71635 semapv:UnspecifiedMatching
UBERON:8920013 anterior ciliary vein semapv:crossSpeciesExactMatch FMA:51798 semapv:UnspecifiedMatching
UBERON:8920014 left bronchial vein semapv:crossSpeciesExactMatch FMA:4837 semapv:UnspecifiedMatching
UBERON:8920015 right bronchial vein semapv:crossSpeciesExactMatch FMA:4942 semapv:UnspecifiedMatching
UBERON:8920016 right inferior pulmonary vein semapv:crossSpeciesExactMatch FMA:49911 semapv:UnspecifiedMatching
UBERON:8920017 left inferior pulmonary vein semapv:crossSpeciesExactMatch FMA:49913 semapv:UnspecifiedMatching
UBERON:8920018 right superior pulmonary vein semapv:crossSpeciesExactMatch FMA:49914 semapv:UnspecifiedMatching
UBERON:8920019 left superior pulmonary vein semapv:crossSpeciesExactMatch FMA:49916 semapv:UnspecifiedMatching
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