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Added new metabolite terms #310

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merged 6 commits into from
Jan 12, 2024
Merged

Added new metabolite terms #310

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5f3f9eb
Added new metabolite terms
ar-ibrahim Jan 12, 2024
d85dca0
Delete src/patterns/data/default/.~lock.entity_attribute_location.tsv#
ar-ibrahim Jan 12, 2024
c4a266d
Fix omo import problem
rays22 Jan 12, 2024
72f4b7d
Update Makefile
rays22 Jan 12, 2024
62f1616
refreshed imports
ar-ibrahim Jan 12, 2024
6dc5ef0
Update dosdp patterns file
rays22 Jan 12, 2024
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9 changes: 5 additions & 4 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for oba
# Generated using ontology-development-kit
# ODK Version: v1.4.1
# ODK Version: v1.4.3
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use oba.Makefile instead

Expand Down Expand Up @@ -44,7 +44,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE)
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference
SPARQL_EXPORTS = basic-report
ODK_VERSION_MAKEFILE = v1.4.1
ODK_VERSION_MAKEFILE = v1.4.3

TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
Expand Down Expand Up @@ -464,8 +464,9 @@ mirror-pato: | $(TMPDIR)
.PHONY: mirror-omo
.PRECIOUS: $(MIRRORDIR)/omo.owl
mirror-omo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo/omo-base.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: hp
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4 changes: 2 additions & 2 deletions src/ontology/components/obsoletes.owl
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Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/oba/components/obsoletes.owl>
<http://purl.obolibrary.org/obo/oba/releases/2023-12-05/components/obsoletes.owl>
Annotation(owl:versionInfo "2023-12-05")
<http://purl.obolibrary.org/obo/oba/releases/2024-01-12/components/obsoletes.owl>
Annotation(owl:versionInfo "2024-01-12")

Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000037>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000039>))
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4 changes: 2 additions & 2 deletions src/ontology/components/synonyms.owl
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Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/oba/components/synonyms.owl>
<http://purl.obolibrary.org/obo/oba/releases/2023-12-05/components/synonyms.owl>
Annotation(owl:versionInfo "2023-12-05")
<http://purl.obolibrary.org/obo/oba/releases/2024-01-12/components/synonyms.owl>
Annotation(owl:versionInfo "2024-01-12")

Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0002546>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0002565>))
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6,849 changes: 5,357 additions & 1,492 deletions src/ontology/imports/merged_import.owl
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1 change: 0 additions & 1 deletion src/ontology/oba-odk.yaml
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Expand Up @@ -63,7 +63,6 @@ import_group:
- id: pato
use_base: True
- id: omo
use_base: True
- id: hp
use_base: True
- id: mondo
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62 changes: 62 additions & 0 deletions src/patterns/data/default/entity_attribute_location.tsv
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Expand Up @@ -5453,3 +5453,65 @@ OBA:2045448 attribute of response to heparin in plasma CHEBI:28304 heparin PATO:
OBA:2045449 plasma thyroxine level CHEBI:30660 thyroxine PATO:0000070 amount UBERON:0001969 blood plasma https://orcid.org/0000-0001-8314-2140
OBA:2045450 blood hemoglobin attribute CHEBI:35143 hemoglobin PATO:0000001 quality UBERON:0000178 blood blood haemoglobin attribute https://orcid.org/0000-0001-8314-2140
OBA:VT0010690 pericardial fat pad mass UBERON:0003916 fat pad PATO:0000125 mass UBERON:0035814 pericardial fat https://orcid.org/0000-0001-8314-2140
OBA:2050356 level of L-alloisoleucine in blood CHEBI:43433 L-alloisoleucine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050357 level of 5-bromotryptophan in blood CHEBI:133686 5-bromotryptophan PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050358 level of 1-arachidonoyl-sn-glycerol 3-phosphate(2-) in blood CHEBI:74938 1-arachidonoyl-sn-glycerol 3-phosphate(2-) PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050359 level of 5alpha-pregnane-3beta,20alpha-diol disulfate in blood CHEBI:133119 5alpha-pregnane-3beta,20alpha-diol disulfate PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050360 level of N-oxalylglycine in blood CHEBI:44482 N-oxalylglycine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050361 level of Leu-Ser in blood CHEBI:73523 Leu-Ser PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050362 level of His-Leu in blood CHEBI:5729 His-Leu PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050363 level of Isoleucyl-Threonine in blood CHEBI:177257 Isoleucyl-Threonine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050364 level of Leu-Glu in blood CHEBI:74531 Leu-Glu PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050365 level of Arg-Phe in blood CHEBI:73818 Arg-Phe PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050366 level of Leucyl-Asparagine in blood CHEBI:190378 Leucyl-Asparagine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050367 level of Ser-Leu in blood CHEBI:74815 Ser-Leu PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050368 level of Leu-Phe in blood CHEBI:73585 Leu-Phe PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050369 level of Tryptophyl-Asparagine in blood CHEBI:175077 Tryptophyl-Asparagine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050370 level of Gly-Trp in blood CHEBI:73921 Gly-Trp PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050371 level of His-Phe in blood CHEBI:141438 His-Phe PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050372 level of His-Val in blood CHEBI:74060 His-Val PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050373 level of Ile-Val in blood CHEBI:74327 Ile-Val PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050374 level of Lys-Leu in blood CHEBI:74561 Lys-Leu PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050375 level of glycerophosphoserine in blood CHEBI:35766 glycerophosphoserine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050376 level of 1-(1Z-hexadecenyl)-sn-glycero-3-phosphocholine in blood CHEBI:73850 1-(1Z-hexadecenyl)-sn-glycero-3-phosphocholine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050377 level of 1-(1Z-hexadecenyl)-2-linoleoyl-sn-glycero-3-phosphoethanolamine in blood CHEBI:84532 1-(1Z-hexadecenyl)-2-linoleoyl-sn-glycero-3-phosphoethanolamine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050378 level of 1-(1Z)-hexadecenyl-2-arachidonoyl-sn-glycero-3-phosphocholine in blood CHEBI:77292 1-(1Z)-hexadecenyl-2-arachidonoyl-sn-glycero-3-phosphocholine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050379 level of N-stearoylsphingosine-1-phosphocholine in blood CHEBI:83358 N-stearoylsphingosine-1-phosphocholine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050380 level of sphingomyelin d18:1/18:1 in blood CHEBI:85593 sphingomyelin d18:1/18:1 PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050381 level of N-icosanoylsphingosine-1-phosphocholine in blood CHEBI:83359 N-icosanoylsphingosine-1-phosphocholine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050382 level of 2-hydroxy-3-methylbutyrate in blood CHEBI:64669 2-hydroxy-3-methylbutyrate PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050383 level of dodecanedioic acid in blood CHEBI:4676 dodecanedioic acid PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050384 level of (R)-oleoylcarnitine in blood CHEBI:84651 (R)-oleoylcarnitine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050385 level of 1-stearoyl-sn-glycero-3-phosphocholine in blood CHEBI:73858 1-stearoyl-sn-glycero-3-phosphocholine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050386 level of tetradecanedioate(2-) in blood CHEBI:76281 tetradecanedioate(2-) PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050387 level of Gamma-glutamyl-Lysine in blood CHEBI:174623 Gamma-glutamyl-Lysine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050388 level of indole-3-carboxylic acid in blood CHEBI:24809 indole-3-carboxylic acid PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050389 level of kynurenic acid in blood CHEBI:18344 kynurenic acid PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050390 level of N-myristoylsphingosine-1-phosphocholine in blood CHEBI:64486 N-myristoylsphingosine-1-phosphocholine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050391 level of L-prolylglycine in blood CHEBI:61695 L-prolylglycine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050392 level of sarcosine in blood CHEBI:15611 sarcosine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050393 level of N(1)-acetylspermidine in blood CHEBI:17927 N(1)-acetylspermidine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050394 level of 1-oleoyl-2-linoleoyl-sn-glycerol in blood CHEBI:75450 1-oleoyl-2-linoleoyl-sn-glycerol PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050395 level of 1-palmitoyl-2-linoleoyl-sn-glycerol in blood CHEBI:82927 1-palmitoyl-2-linoleoyl-sn-glycerol PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050396 level of cholesterol ester 16:0 in blood CHEBI:191864 cholesterol ester 16:0 PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050397 level of CE(20:4) in blood CHEBI:183798 CE(20:4) PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050398 level of cholesteryl (5Z,8Z,11Z,14Z,17Z-eicosapentaenoate) in blood CHEBI:84969 cholesteryl (5Z,8Z,11Z,14Z,17Z-eicosapentaenoate) PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050399 level of N(2)-acetyl-L-lysine in blood CHEBI:35704 N(2)-acetyl-L-lysine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050400 level of N(1),N(12)-diacetylspermine in blood CHEBI:28101 N(1),N(12)-diacetylspermine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050401 level of N-acetylglucosamine in blood CHEBI:59640 N-acetylglucosamine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050402 level of N-acetylgalactosamine in blood CHEBI:28800 N-acetylgalactosamine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050403 level of 2-arachidonoyl-sn-glycero-3-phosphocholine in blood CHEBI:76079 2-arachidonoyl-sn-glycero-3-phosphocholine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050404 level of 1-palmitoyl-2-arachidonoyl-sn-glycerol in blood CHEBI:77096 1-palmitoyl-2-arachidonoyl-sn-glycerol PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050405 level of 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphoethanolamine in blood CHEBI:84846 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphoethanolamine PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050406 level of Glu-Glu in blood CHEBI:5390 Glu-Glu PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050407 level of fucose in blood CHEBI:33984 fucose PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050408 level of ribose in blood CHEBI:33942 ribose PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050409 level of pterin in blood CHEBI:26374 pterin PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050410 level of Ala-Leu in blood CHEBI:73770 Ala-Leu PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050411 level of Gly-Tyr in blood CHEBI:73517 Gly-Tyr PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050412 level of Thr-Phe in blood CHEBI:74862 Thr-Phe PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050413 level of Ethyl 2-ethylhexanoate in blood CHEBI:179548 Ethyl 2-ethylhexanoate PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050414 level of Gly-Pro in blood CHEBI:70744 Gly-Pro PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050415 level of indole-3-butyric acid in blood CHEBI:33070 indole-3-butyric acid PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050416 level of Phe-Gly in blood CHEBI:73635 Phe-Gly PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
OBA:2050417 level of Val-Leu in blood CHEBI:75013 Val-Leu PATO:0000070 amount UBERON:0000178 blood PMID:37253714 https://orcid.org/0000-0001-6757-4744
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