WIP: Add LOINC PART mappings

.gitignore

@@ -5,4 +5,4 @@ tmp/
 .DS_Store
 mappings/*.sssom.tsv
 mappings/ttl
-data/
+data/

mappings/loinc2cl.sssom.tsv

@@ -0,0 +1,28 @@
+# curie_map:
+#   linkml: https://w3id.org/linkml/
+#   sempav: https://w3id.org/sempav
+#   loinc: https://loinc.org/
+#   CL: http://purl.obolibrary.org/obo/CL_
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   wikidata: https://www.wikidata.org/entity/
+#   orcid: https://orcid.org/
+# license: http://creativecommons.org/publicdomain/zero/1.0/
+# mapping_date: '2023-05-01'
+# mapping_set_id: http://w3id.org/mapping_commons/monarch/loinc2cl.sssom.tsv
+# issue_tracker: https://github.com/monarch-initiative/monarch-mapping-commons/issues
+# creator_label: "Monarch Initiative"
+# creator_id: wikidata:Q34645736
+# author_id: orcid:0000-0002-5316-1399
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification
+loinc:LP7536-8	RBC	skos:exactMatch	CL:0000232	erythrocyte	semapv:ManualMappingCuration
+loinc:LP30226-2	RBC^BPU	skos:exactMatch	CL:0000232	erythrocyte	semapv:ManualMappingCuration
+loinc:LP30227-0	Red Blood Cells^Donor	skos:exactMatch	CL:0000232	erythrocyte	semapv:ManualMappingCuration
+loinc:LP14304-7	Erythrocytes	skos:exactMatch	CL:0000232	erythrocyte	semapv:ManualMappingCuration
+loinc:LP7720-8	White blood cells	skos:exactMatch	CL:0000738	leukocyte	semapv:ManualMappingCuration
+loinc:LP14419-3	Leukocytes	skos:exactMatch	CL:0000738	leukocyte	semapv:ManualMappingCuration
+loinc:LP7234-0	Fibroblast	skos:exactMatch	CL:0000057	fibroblast	semapv:ManualMappingCuration
+loinc:LP14267-6	Neutrophils	skos:exactMatch	CL:0000775	neutrophil	semapv:ManualMappingCuration
+loinc:LP14540-6	Lymphocytes	skos:exactMatch	CL:0000542	lymphocyte	semapv:ManualMappingCuration
+loinc:LP14597-6	Platelets	skos:exactMatch	CL:0000233	platelet	semapv:ManualMappingCuration
+loinc:LP14539-8	Eosinophils	skos:exactMatch	CL:0000771	eosinophil	semapv:ManualMappingCuration
+loinc:LP18643-4	Granulocytes	skos:exactMatch	CL:0000094	granulocyte	semapv:ManualMappingCuration

mappings/loinc2go.sssom.tsv

@@ -0,0 +1,18 @@
+# curie_map:
+#   linkml: https://w3id.org/linkml/
+#   sempav: https://w3id.org/sempav
+#   loinc: https://loinc.org/
+#   GO: http://purl.obolibrary.org/obo/GO_
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   wikidata: https://www.wikidata.org/entity/
+#   orcid: https://orcid.org/
+# license: http://creativecommons.org/publicdomain/zero/1.0/
+# mapping_date: '2023-05-01'
+# mapping_set_id: http://w3id.org/mapping_commons/monarch/loinc2go.sssom.tsv
+# issue_tracker: https://github.com/monarch-initiative/monarch-mapping-commons/issues
+# creator_label: "Monarch Initiative"
+# creator_id: wikidata:Q34645736
+# author_id: orcid:0000-0002-5316-1399
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification
+loinc:LP14672-7	IgG	skos:exactMatch	GO:0071735	IgG immunoglobulin complex	semapv:ManualMappingCuration
+loinc:LP14674-3	IgM	skos:exactMatch	GO:0071753	IgM immunoglobulin complex	semapv:ManualMappingCuration

mappings/loinc2ncbitaxon.sssom.tsv

@@ -0,0 +1,28 @@
+# curie_map:
+#   linkml: https://w3id.org/linkml/
+#   sempav: https://w3id.org/sempav
+#   loinc: https://loinc.org/
+#   NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   wikidata: https://www.wikidata.org/entity/
+#   orcid: https://orcid.org/
+# license: http://creativecommons.org/publicdomain/zero/1.0/
+# mapping_date: '2023-05-01'
+# mapping_set_id: http://w3id.org/mapping_commons/monarch/loinc2ncbitaxon.sssom.tsv
+# issue_tracker: https://github.com/monarch-initiative/monarch-mapping-commons/issues
+# creator_label: "Monarch Initiative"
+# creator_id: wikidata:Q34645736
+# author_id: orcid:0000-0002-5316-1399
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	comment
+loinc:LP39606-6 Rickettsia typhi Ab	skos:relatedMatch	NCBITaxon:785	Rickettsia typhi	semapv:ManualMappingCuration	antibody vs bacteria
+loinc:LP29134-1	Yeast	skos:relatedMatch	NCBITaxon:4932	baker's yeast	semapv:ManualMappingCuration	antibody vs bacteria
+loinc:LP14082-9	Bacteria	skos:relatedMatch	NCBITaxon:2	bacteria	semapv:ManualMappingCuration	antibody vs bacteria
+loinc:LP14255-1	Cytomegalovirus	skos:exactMatch	NCBITaxon:10358	cytomegalovirus	semapv:ManualMappingCuration	antibody vs bacteria
+loinc:LP14413-6	Trichomonas vaginalis	skos:exactMatch	NCBITaxon:5722	trichomonas vaginalis	semapv:ManualMappingCuration	
+loinc:LP14316-1	Neisseria gonorrhoeae	skos:exactMatch	NCBITaxon:485	neisseria gonorrhoeae	semapv:ManualMappingCuration	
+loinc:LP14252-8	Toxoplasma gondii	skos:exactMatch	NCBITaxon:5811	toxoplasma gondii	semapv:ManualMappingCuration	
+loinc:LP39533-2	Rabies virus Ab	skos:relatedMatch	NCBITaxon:11292	Lyssavirus rabies	semapv:ManualMappingCuration	
+loinc:LP14405-2	Streptococcus agalactiae	skos:exactMatch	NCBITaxon:1311	streptococcus agalactiae	semapv:ManualMappingCuration	
+loinc:LP14061-3	Adenovirus	skos:exactMatch	NCBITaxon:10535	adenovirus	semapv:ManualMappingCuration	
+loinc:LP308326-0	enterobius vermicularis^2nd specimen	skos:exactMatch	NCBITaxon:51028	enterobius vermicularis	semapv:ManualMappingCuration	
+loinc:LP308327-8	enterobius vermicularis^3rd specimen	skos:exactMatch	NCBITaxon:51028	enterobius vermicularis	semapv:ManualMappingCuration	

mappings/loinc2ncit.sssom.tsv

@@ -0,0 +1,21 @@
+# curie_map:
+#   linkml: https://w3id.org/linkml/
+#   sempav: https://w3id.org/sempav
+#   loinc: https://loinc.org/
+#   NCIT: http://purl.obolibrary.org/obo/NCIT_
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   wikidata: https://www.wikidata.org/entity/
+#   orcid: https://orcid.org/
+# license: http://creativecommons.org/publicdomain/zero/1.0/
+# mapping_date: '2023-05-01'
+# mapping_set_id: http://w3id.org/mapping_commons/monarch/loinc2ncit.sssom.tsv
+# issue_tracker: https://github.com/monarch-initiative/monarch-mapping-commons/issues
+# creator_label: "Monarch Initiative"
+# creator_id: wikidata:Q34645736
+# author_id: orcid:0000-0002-5316-1399
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	comment
+loinc:LP7037-7	Aspirate	skos:exactMatch	NCIT:C13347	Aspirate	semapv:ManualMappingCuration	
+loinc:LP7096-3	Calculus (stone)	skos:exactMatch	NCIT:C35708	Stone	semapv:ManualMappingCuration	
+loinc:LP14492-0	Urea nitrogen	skos:exactMatch	NCIT:C919	Urea Nitrogen	semapv:ManualMappingCuration	
+loinc:LP15355-8	Amylase	skos:exactMatch	NCIT:C16284	Amylase	semapv:ManualMappingCuration	
+loinc:LP7370-2	Isolate	skos:exactMatch	NCIT:C53471	Isolate	semapv:ManualMappingCuration	

mappings/loinc2pr.sssom.tsv

@@ -0,0 +1,76 @@
+# curie_map:
+#   linkml: https://w3id.org/linkml/
+#   sempav: https://w3id.org/sempav
+#   loinc: https://loinc.org/
+#   PR: http://purl.obolibrary.org/obo/PR_
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   wikidata: https://www.wikidata.org/entity/
+#   orcid: https://orcid.org/
+# license: http://creativecommons.org/publicdomain/zero/1.0/
+# mapping_date: '2023-05-01'
+# mapping_set_id: http://w3id.org/mapping_commons/monarch/loinc2pr.sssom.tsv
+# issue_tracker: https://github.com/monarch-initiative/monarch-mapping-commons/issues
+# creator_label: "Monarch Initiative"
+# creator_id: wikidata:Q34645736
+# author_id: orcid:0000-0002-5316-1399
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	comment
+loinc:LP6118-6	Albumin	skos:exactMatch	PR:000003918	albumin	semapv:ManualMappingCuration	
+loinc:LP31978-7	Albumin	skos:exactMatch	PR:000003918	albumin	semapv:ManualMappingCuration	
+loinc:LP15033-1	Lactate dehydrogenase	skos:exactMatch	PR:000050331	lactate dehydrogenase complex	semapv:ManualMappingCuration	
+loinc:LP32142-9	Protein	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP15694-0	Lactoferrin	skos:exactMatch	PR:000009978	lactoferrin	semapv:ManualMappingCuration	
+loinc:LP14697-4	Thyroglobulin	skos:exactMatch	PR:000016283	thyroglobulin	semapv:ManualMappingCuration	
+loinc:LP306738-8	protein^1st specimen post dose sincalide	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307536-5	protein^1st tube	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307537-3	protein^2nd specimen	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP306739-6	protein^2nd specimen post dose sincalide	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307538-1	protein^2nd tube	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307539-9	protein^3rd specimen	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP306740-4	protein^3rd specimen post dose sincalide	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307540-7	protein^3rd tube	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307541-5	protein^4th specimen	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP306741-2	protein^4th specimen post dose sincalide	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307542-3	protein^4th tube	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307543-1	protein^5th specimen	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP306742-0	protein^5th specimen post dose sincalide	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307544-9	protein^6th specimen	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307545-6	protein^7th specimen	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307546-4	protein^8th specimen	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307547-2	protein^resting	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP307548-0	protein^upright	skos:exactMatch	PR:000000001	protein	semapv:ManualMappingCuration	
+loinc:LP306760-2	renin^1.5h post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306761-0	renin^100m post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306762-8	renin^10m post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306763-6	renin^1h post 25 mg captopril po	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306764-4	renin^1h post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306765-1	renin^1st specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306766-9	renin^20m post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306767-7	renin^2h post 25 mg captopril po	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306768-5	renin^2h post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306769-3	renin^2nd specimen	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306770-1	renin^2nd specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306771-9	renin^30m post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306772-7	renin^30m pre xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306773-5	renin^3h post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306774-3	renin^3rd specimen	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306775-0	renin^3rd specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306776-8	renin^4h post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306777-6	renin^4th specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306778-4	renin^5h post 600 ug furosemide po	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306779-2	renin^5h post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306780-0	renin^5th specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306781-8	renin^6th specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306782-6	renin^70m post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306783-4	renin^7th specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306784-2	renin^8th specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306785-9	renin^9th specimen post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306786-7	renin^baseline	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306787-5	renin^post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306788-3	renin^pre 600 ug furosemide po	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306789-1	renin^pre or post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP307550-6	renin^supine	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306790-9	renin^supine+30m post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP307551-4	renin^upright	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306791-7	renin^upright+1h post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP306792-5	renin^upright+30m post xxx challenge	skos:exactMatch	PR:000013883	renin	semapv:ManualMappingCuration	
+loinc:LP420755-3	thyroglobulin^post thyroglobulin antibody neutralization	skos:exactMatch	PR:000016283	thyroglobulin	semapv:ManualMappingCuration