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Add some mp_efo_impc.sssom.tsv from IMPC #42

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Merged
matentzn merged 6 commits into from
Jun 14, 2025
Merged

Add some mp_efo_impc.sssom.tsv from IMPC #42

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1e5a083
Create mp_efo_impc.sssom.tsv
matentzn Jan 13, 2025
aeba14c
Update mappings/mp_efo_impc.sssom.tsv
matentzn Jan 13, 2025
0ca47d0
Update Makefile
matentzn May 22, 2025
aa26c27
Update mappings/mp_efo_impc.sssom.tsv
matentzn May 23, 2025
b9f601a
Replace obsolete EFO terms and update mapping set description
rays22 May 23, 2025
a7ede3a
Add missing prefix (OBA)
rays22 May 23, 2025
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46 changes: 45 additions & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -73,4 +73,48 @@ mappings/%_pistoia.sssom.tsv: sources/pistoia/calculated_output_%.rdf

.PHONY: mapping_set_%
mapping_set_%: mappings/%.sssom.tsv
echo "Build $<"
echo "Build $<"

##################################

EFO_OBA_URL=https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-efo.sssom.tsv

mappings/efo-oba.sssom.tsv:
wget "$(EFO_OBA_URL)" -O $@
.PRECIOUS: mappings/efo-oba.sssom.tsv

UPHENO_OBA_URL=https://github.com/obophenotype/upheno-dev/blob/master/src/ontology/reports/phenotype_trait.sssom.tsv

tmp/impc_traits.tsv:
wget https://raw.githubusercontent.com/obophenotype/upheno-dev/master/src/ontology/reports/impc_traits.tsv -O $@

tmp/gwas_traits.tsv:
wget https://raw.githubusercontent.com/obophenotype/upheno-dev/master/src/ontology/reports/gwas_traits.tsv -O $@

mappings/upheno-oba.tsv:
wget "$(UPHENO_OBA_URL)" -O $@
.PRECIOUS: mappings/mp-oba.sssom.tsv

mappings/mp-oba.sssom.tsv: mappings/upheno-oba.tsv
python python scripts/mh_mapping_commongs.py hp-oba $< > $@ mp-oba $< > $@
.PRECIOUS: mappings/mp-oba.sssom.tsv

mappings/hp-oba.sssom.tsv: mappings/upheno-oba.tsv
python scripts/mh_mapping_commons.py hp-oba $< > $@
.PRECIOUS: mappings/hp-oba.sssom.tsv

MP_EFO_URL=https://raw.githubusercontent.com/obophenotype/upheno-dev/master/src/ontology/reports/mp-efo.sssom.tsv
mappings/mp-efo.sssom.tsv:
wget "$(MP_EFO_URL)" -O $@

mappings/mp-hp.sssom.tsv: mappings/upheno-species-independent.sssom.tsv
python scripts/mh_mapping_commons.py mp-hp $< > $@

mappings/mp-efo.sssom.tsv: mappings/efo-oba.sssom.tsv \
mappings/mp-oba.sssom.tsv \
mappings/mp-hp.sssom.tsv \
mappings/mp-efo.sssom.tsv \
tmp/gwas_traits.tsv \
tmp/impc_traits.tsv
python3 scripts/mh_mapping_commons.py mappings/efo-oba.sssom.tsv mappings/mp-oba.sssom.tsv mappings/mp-impc.sssom.tsv > $@

99 changes: 99 additions & 0 deletions mappings/mp_efo_impc.sssom.tsv
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@@ -0,0 +1,99 @@
# comment: "Edit source: https://docs.google.com/spreadsheets/d/13_zoFywKXRFoa6VbqLYpjq1HJrO8zWMOTxZOCZ8s3Lw/edit"
# creator_id: orcid:0000-0001-8314-2140
# curie_map:
# MP: http://purl.obolibrary.org/obo/MP_
# EFO: http://www.ebi.ac.uk/efo/EFO_
# OBA: http://www.ebi.ac.uk/efo/OBA_
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# orcid: https://orcid.org/
# obo: http://purl.obolibrary.org/obo/
# semapv: https://w3id.org/semapv/vocab/
# license: https://creativecommons.org/publicdomain/zero/1.0/
# mapping_provider: https://www.mousephenotype.org
# mapping_set_description: 'Some Mammalian Phenotype Ontology (MP) to
# Experimental Factor Ontology (EFO) mappings initially curated by Violeta
# Munoz-Fuentes for The International Mouse Phenotyping Consortium (IMPC) and
# revised by orcid:0000-0001-8314-2140. This set of MP terms comprises those
# that have genotype-phenotype association data in the IMPC. The goal of this
# mapping is to help connect GWAS Catalog phenotypic trait association data
# (using EFO terms) with genotype-phenotype association data from the IMPC
# (using MP terms).'
# mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_efo_impc.sssom.tsv
subject_id subject_label predicate_id object_id object_label mapping_justification subject_source object_source confidence mapping_date author_id
MP:0000013 abnormal adipose tissue distribution skos:broadMatch EFO:0004341 body fat distribution semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000180 abnormal circulating cholesterol level skos:broadMatch EFO:0004574 total cholesterol measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000181 abnormal circulating LDL cholesterol level skos:broadMatch EFO:0004611 low density lipoprotein cholesterol measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000184 abnormal circulating HDL cholesterol level skos:broadMatch EFO:0008592 high density lipoprotein particle size measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000188 abnormal circulating glucose level skos:broadMatch EFO:0004468 glucose measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000199 abnormal circulating serum albumin level skos:broadMatch EFO:0004535 serum albumin measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000202 abnormal circulating alkaline phosphatase level skos:broadMatch EFO:0004533 alkaline phosphatase measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000203 abnormal circulating aspartate transaminase level skos:broadMatch EFO:0004736 aspartate aminotransferase measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0000226 abnormal mean corpuscular volume skos:broadMatch OBA:0003460 erythrocyte volume semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001259 abnormal body weight skos:broadMatch EFO:0004338 body weight semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001553 abnormal circulating free fatty acids level skos:broadMatch OBA:VT0010046 fatty acid amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001560 abnormal circulating insulin level skos:broadMatch OBA:VT0001560 blood insulin amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001562 abnormal circulating calcium level skos:broadMatch EFO:0004838 calcium measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001565 abnormal circulating phosphate level skos:broadMatch OBA:VT0001565 blood phosphate amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001565 abnormal circulating phosphate level skos:broadMatch EFO:0010972 blood phosphate measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001569 abnormal circulating bilirubin level skos:broadMatch EFO:0004570 bilirubin measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001573 abnormal circulating alanine transaminase level skos:broadMatch OBA:2050062 serum alanine aminotransferase amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001575 cyanosis skos:relatedMatch EFO:0009447 hypoxemia semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001586 abnormal erythrocyte cell number skos:broadMatch EFO:0004305 erythrocyte count semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001589 abnormal mean corpuscular hemoglobin skos:broadMatch EFO:0004527 mean corpuscular hemoglobin semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001771 abnormal circulating magnesium level skos:broadMatch EFO:0004845 magnesium measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001776 abnormal circulating sodium level skos:broadMatch EFO:0009282 sodium measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0001785 edema skos:exactMatch EFO:0009373 edema semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0002192 hydrops fetalis skos:broadMatch EFO:0009373 edema semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0002586 abnormal platelet volume skos:broadMatch OBA:0003277 platelet volume semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0002596 abnormal hematocrit skos:broadMatch EFO:0004348 hematocrit semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0002668 abnormal circulating potassium level skos:broadMatch EFO:0009283 potassium measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0002943 abnormal lactate dehydrogenase level skos:broadMatch EFO:0004808 L lactate dehydrogenase measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0003018 abnormal circulating chloride level skos:broadMatch OBA:1000959 chloride amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0004129 abnormal respiratory quotient skos:broadMatch EFO:0005189 respiratory quotient semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0004152 abnormal circulating iron level skos:relatedMatch OBA:2050055 serum iron amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005265 abnormal blood urea nitrogen level skos:broadMatch OBA:VT0005265 blood urea nitrogen amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005266 abnormal metabolism skos:broadMatch OBA:VT0002121 metabolism trait semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005278 abnormal cholesterol homeostasis skos:relatedMatch EFO:0020943 cholesterol:total lipids ratio semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005288 abnormal oxygen consumption skos:relatedMatch EFO:0004887 maximal oxygen uptake measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005291 abnormal glucose tolerance skos:broadMatch EFO:0004307 glucose tolerance test semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005328 abnormal circulating creatinine level skos:broadMatch OBA:2050096 serum creatinine amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch EFO:0004305 erythrocyte count semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch EFO:0004309 platelet count semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch EFO:0004348 hematocrit semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch EFO:0004509 hemoglobin measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch OBA:0003460 erythrocyte volume semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch EFO:0004527 mean corpuscular hemoglobin semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch EFO:0004528 mean corpuscular hemoglobin concentration semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch OBA:0003277 platelet volume semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch EFO:0007986 reticulocyte count semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005397 hematopoietic system phenotype skos:relatedMatch OBA:2045223 myeloid leukocyte count semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005448 abnormal energy homeostasis skos:relatedMatch EFO:0009374 energy intake measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005450 abnormal energy expenditure skos:relatedMatch OBA:VT0005450 energy expenditure trait semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005452 abnormal adipose tissue amount skos:broadMatch OBA:VT0005452 adipose amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005475 abnormal circulating thyroxine level skos:broadMatch OBA:1001010 thyroxine amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005563 abnormal hemoglobin content skos:broadMatch EFO:0004509 hemoglobin measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0005640 abnormal mean corpuscular hemoglobin concentration skos:broadMatch EFO:0004528 mean corpuscular hemoglobin concentration semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0008804 abnormal circulating amylase level skos:broadMatch EFO:0803343 amylase measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0008820 abnormal blood uric acid level skos:broadMatch EFO:0004761 uric acid measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0008961 abnormal basal metabolism skos:broadMatch EFO:0005115 metabolic rate measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0008962 abnormal carbon dioxide production skos:broadMatch OBA:1000957 carbon dioxide amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0010066 abnormal red blood cell distribution width skos:broadMatch EFO:0009188 Red cell distribution width semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0010086 abnormal circulating fructosamine level skos:broadMatch EFO:0009303 fructosamine measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0010089 abnormal circulating creatine kinase level skos:broadMatch EFO:0004534 creatine kinase measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0010163 hemolysis skos:exactMatch EFO:0009473 hemolysis semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011885 abnormal circulating lipase level skos:broadMatch OBA:2050069 serum lipase activity amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011888 abnormal circulating total protein level skos:broadMatch EFO:0004536 total blood protein measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011889 abnormal circulating ferritin level skos:broadMatch EFO:0004459 ferritin measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011892 abnormal circulating transferrin level skos:broadMatch EFO:0006341 transferrin measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011895 abnormal circulating unsaturated transferrin level skos:broadMatch EFO:0006334 total iron binding capacity semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011898 abnormal platelet cell number skos:broadMatch EFO:0004309 platelet count semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011898 abnormal platelet cell number skos:broadMatch OBA:VT0003179 platelet quantity semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011969 abnormal circulating triglyceride level skos:broadMatch EFO:0004530 triglyceride measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011970 abnormal circulating lactate dehydrogenase level skos:broadMatch EFO:0004808 L lactate dehydrogenase measurement semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0011973 abnormal circulating glycerol level skos:broadMatch OBA:1000966 glycerol amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140
MP:0013277 abnormal fasting circulating glucose level skos:broadMatch OBA:VT0000188 blood glucose amount semapv:ManualMappingCuration MP EFO 1 2025-05-23 orcid:0000-0001-8314-2140