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Add some mp_efo_impc.sssom.tsv from IMPC #42
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1e5a083
Create mp_efo_impc.sssom.tsv
matentzn aeba14c
Update mappings/mp_efo_impc.sssom.tsv
matentzn 0ca47d0
Update Makefile
matentzn aa26c27
Update mappings/mp_efo_impc.sssom.tsv
matentzn b9f601a
Replace obsolete EFO terms and update mapping set description
rays22 a7ede3a
Add missing prefix (OBA)
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| Original file line number | Diff line number | Diff line change |
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| # 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_ | ||
| # 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 MP-EFO mappings curated by Violeta Munoz-Fuentes for IMPC.' | ||
| # 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:closeMatch EFO:0007800 body fat percentage semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000180 abnormal circulating cholesterol level skos:narrowMatch EFO:0004574 total cholesterol measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000180 abnormal circulating cholesterol level skos:narrowMatch EFO:0004611 low density lipoprotein cholesterol measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000180 abnormal circulating cholesterol level skos:narrowMatch EFO:0008592 high density lipoprotein particle size measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000181 abnormal circulating LDL cholesterol level skos:exactMatch EFO:0004611 low density lipoprotein cholesterol measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
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| MP:0000184 abnormal circulating HDL cholesterol level skos:exactMatch EFO:0008592 high density lipoprotein particle size measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000188 abnormal circulating glucose level skos:exactMatch EFO:0004468 glucose measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000199 abnormal circulating serum albumin level skos:exactMatch EFO:0004535 serum albumin measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000202 abnormal circulating alkaline phosphatase level skos:exactMatch EFO:0004533 alkaline phosphatase measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000203 abnormal circulating aspartate transaminase level skos:exactMatch EFO:0004736 aspartate aminotransferase measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0000226 abnormal mean corpuscular volume skos:exactMatch EFO:0004526 mean corpuscular volume semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001259 abnormal body weight skos:exactMatch EFO:0004338 body weight semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001553 abnormal circulating free fatty acids level skos:broadMatch EFO:0005110 fatty acid measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001560 abnormal circulating insulin level skos:broadMatch EFO:0004467 insulin measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
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| MP:0001562 abnormal circulating calcium level skos:broadMatch EFO:0004838 calcium measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001565 abnormal circulating phosphate level skos:broadMatch EFO:0010968 phosphate measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001565 abnormal circulating phosphate level skos:exactMatch EFO:0010972 blood phosphate measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001569 abnormal circulating bilirubin level skos:broadMatch EFO:0004570 bilirubin measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001573 abnormal circulating alanine transaminase level skos:exactMatch EFO:0004735 serum alanine aminotransferase measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001575 cyanosis skos:exactMatch EFO:0009447 hypoxemia semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001586 abnormal erythrocyte cell number skos:exactMatch EFO:0004305 erythrocyte count semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001589 abnormal mean corpuscular hemoglobin skos:exactMatch EFO:0004527 mean corpuscular hemoglobin semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001771 abnormal circulating magnesium level skos:broadMatch EFO:0004845 magnesium measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001776 abnormal circulating sodium level skos:broadMatch EFO:0009282 sodium measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0001785 edema skos:exactMatch EFO:0009373 edema semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0002192 hydrops fetalis skos:broadMatch EFO:0009373 edema semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0002586 abnormal platelet volume skos:exactMatch EFO:0004584 mean platelet volume semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0002596 abnormal hematocrit skos:exactMatch EFO:0004348 hematocrit semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0002668 abnormal circulating potassium level skos:broadMatch EFO:0009283 potassium measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0002943 abnormal circulating lactate dehydrogenase level skos:broadMatch EFO:0004808 L lactate dehydrogenase measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0002943 abnormal lactate dehydrogenase level skos:exactMatch EFO:0004808 L lactate dehydrogenase measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0003018 abnormal circulating chloride level skos:broadMatch EFO:0009284 chloride measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0004129 abnormal respiratory quotient skos:exactMatch EFO:0005189 respiratory quotient semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0004152 abnormal circulating iron level skos:exactMatch EFO:0006332 serum iron measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005265 abnormal blood urea nitrogen level skos:exactMatch EFO:0004741 blood urea nitrogen measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005266 abnormal metabolism skos:narrowMatch EFO:0004887 maximal oxygen uptake measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005266 abnormal metabolism skos:narrowMatch EFO:0009374 energy intake measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005266 abnormal metabolism skos:narrowMatch EFO:0803345 carbon dioxide measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005278 abnormal cholesterol homeostasis skos:narrowMatch EFO:0020943 cholesterol:total lipids ratio semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005288 abnormal oxygen consumption skos:exactMatch EFO:0004887 maximal oxygen uptake measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005291 abnormal glucose tolerance skos:broadMatch EFO:0004468 glucose measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005291 abnormal glucose tolerance skos:exactMatch EFO:0004307 glucose tolerance test semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005328 abnormal circulating creatinine level skos:broadMatch EFO:0004518 creatinine measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004305 erythrocyte count semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004309 platelet count semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004348 hematocrit semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004509 hemoglobin measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004526 mean corpuscular volume semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004527 mean corpuscular hemoglobin semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004528 mean corpuscular hemoglobin concentration semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0004584 mean platelet volume semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0005192 red blood cell distribution width semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0007986 reticulocyte count semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0007988 myeloid white cell count semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005397 hematopoietic system phenotype skos:narrowMatch EFO:0009188 Red cell distribution width semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005448 abnormal energy homeostasis skos:narrowMatch EFO:0003939 energy intake semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005450 abnormal energy expenditure skos:narrowMatch EFO:0005115 metabolic rate measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005452 abnormal adipose tissue amount skos:narrowMatch EFO:0004764 adipose tissue measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005475 abnormal circulating thyroxine level skos:narrowMatch EFO:0005130 thyroxine measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005535 abnormal body temperature skos:narrowMatch EFO:0001702 temperature semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005563 abnormal hemoglobin content skos:exactMatch EFO:0004509 hemoglobin measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005640 abnormal mean corpuscular hemoglobin concentration skos:exactMatch EFO:0004527 mean corpuscular hemoglobin semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0005640 abnormal mean corpuscular hemoglobin concentration skos:exactMatch EFO:0004528 mean corpuscular hemoglobin concentration semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0008804 abnormal circulating amylase level skos:broadMatch EFO:0801371 alpha-amylase 1 measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0008820 abnormal blood uric acid level skos:broadMatch EFO:0004761 uric acid measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0008961 abnormal basal metabolism skos:broadMatch EFO:0005115 metabolic rate measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0008962 abnormal carbon dioxide production skos:broadMatch EFO:0803345 carbon dioxide measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0010066 abnormal red blood cell distribution width skos:exactMatch EFO:0005192 red blood cell distribution width semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0010086 abnormal circulating fructosamine level skos:broadMatch EFO:0009303 fructosamine measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0010089 abnormal circulating creatine kinase level skos:broadMatch EFO:0004534 creatine kinase measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0010163 hemolysis skos:exactMatch EFO:0009473 hemolysis semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011885 abnormal circulating lipase level skos:exactMatch EFO:0005849 serum lipase activity measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011888 abnormal circulating total protein level skos:exactMatch EFO:0004536 total blood protein measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011889 abnormal circulating ferritin level skos:broadMatch EFO:0004459 ferritin measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011892 abnormal circulating transferrin level skos:broadMatch EFO:0006341 transferrin measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 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 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011898 abnormal platelet cell number skos:exactMatch EFO:0004309 platelet count semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011969 abnormal circulating triglyceride level skos:broadMatch EFO:0004530 triglyceride measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 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 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011970 abnormal lactate dehydrogenase level skos:exactMatch EFO:0004808 L lactate dehydrogenase measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0011973 abnormal circulating glycerol level skos:broadMatch EFO:0010115 glycerol measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
| MP:0013277 abnormal fasting circulating glucose level skos:exactMatch EFO:0004465 fasting blood glucose measurement semapv:ManualMappingCuration MP EFO 1 2024-08-16 orcid:0000-0001-8314-2140 | ||
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Please add some more details to the description:
what is the use case for the mappings
how are you using the skos matches since these are not using the standard meaning
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I have added more details to the description. The use case is to help link mouse phenotype data from IMPC to GWAS traits (annotated with EFO terms).
I thought we are applying the standard skos definitions:
"The properties skos:broadMatch and skos:narrowMatch are used to state a hierarchical mapping link between two concepts."