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WIP: Add LOINC PART mappings #35

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WIP: Add LOINC PART mappings #35

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fd584c2
add loinc part mappings
drseb Nov 13, 2023
d56054a
Merge branch 'main' into upload-loinc-part-mappings
matentzn Nov 14, 2023
5375bc7
make some mappings broader/related
drseb Jan 27, 2024
670d045
use correct human curation relation
drseb Jan 27, 2024
24b56c9
fix comment column
drseb Jan 27, 2024
aab7b25
add creator
drseb Jan 27, 2024
c413630
rename files
drseb Jan 27, 2024
6e555de
Update mappings/loinc-part-obo/loinc2ncbitaxon.sssom.tsv
drseb Mar 8, 2024
b1aaf96
Update mappings/loinc-part-obo/loinc2go.sssom.tsv
drseb Mar 8, 2024
12384a5
Update mappings/loinc-part-obo/loinc2go.sssom.tsv
drseb Mar 8, 2024
760287c
Update mappings/loinc-part-obo/loinc2go.sssom.tsv
drseb Mar 8, 2024
19ce01e
Update mappings/loinc-part-obo/loinc2chebi_seb.sssom.tsv
drseb Mar 8, 2024
331c048
Update mappings/loinc-part-obo/loinc2ncit.sssom.tsv
drseb Mar 8, 2024
a68241e
Update mappings/loinc-part-obo/loinc2pr.sssom.tsv
drseb Mar 8, 2024
2a9afc6
Update mappings/loinc-part-obo/loinc2uberon.sssom.tsv
drseb Mar 8, 2024
eb2eb5a
Update mappings/loinc-part-obo/loinc2uberon.sssom.tsv
drseb Mar 8, 2024
4ee0846
Update mappings/loinc-part-obo/loinc2pr.sssom.tsv
drseb Mar 8, 2024
4b35266
move files to correct folder as requested by Nico
drseb Mar 8, 2024
fc164b1
rename files as requested by Nico
drseb Mar 8, 2024
4728824
change mapping set id and remove mapping tool as requested by Nico
drseb Mar 8, 2024
1d5726a
add author-id to all but one file (not the one from tim) as requested…
drseb Mar 8, 2024
a7421b3
fix formatting error in loinc-chebi meeting
drseb Mar 8, 2024
a51666d
fix formatting error in loinc-chebi mapping ( remove one header item)
drseb Mar 8, 2024
bfbcb9c
fix formatting error in one line - please god let the qc now pass
drseb Mar 8, 2024
06f302e
fix formatting errors in sssom: please any of you gods - let the qc n…
drseb Mar 8, 2024
23cbfcf
Merge branch 'main' into upload-loinc-part-mappings
drseb Mar 8, 2024
caaf453
add orcid in curie map - dear gh-actions, I give you 10 dollars if yo…
drseb Mar 8, 2024
ea1e8af
minor format changes - no more 10 dollars for you as promised in the …
drseb Mar 8, 2024
773a24f
rm swp files
drseb Mar 8, 2024
c9a6208
try with mp-file as template for creator
drseb Mar 8, 2024
c823c16
try again with creator
drseb Mar 8, 2024
3daa373
Merge branch 'main' into upload-loinc-part-mappings
matentzn Mar 9, 2024
b7ef0b9
Update metadata a bit
matentzn Mar 9, 2024
14c977d
Update loinc2uberon.sssom.tsv
matentzn May 16, 2024
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1,989 changes: 1,989 additions & 0 deletions mappings/loinc-part-obo/loinc2chebi_seb.sssom.tsv
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2,379 changes: 2,379 additions & 0 deletions mappings/loinc-part-obo/loinc2chebi_tim.sssom.tsv
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27 changes: 27 additions & 0 deletions mappings/loinc-part-obo/loinc2cl.sssom.tsv
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# 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#
# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
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# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
# license: http://creativecommons.org/publicdomain/zero/1.0/

# mapping_date: '2023-05-01'
# mapping_set_id: http://w3id.org/mapping_commons/disease-mappings/onto-icd10
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# mapping_set_id: http://w3id.org/mapping_commons/disease-mappings/onto-icd10
# mapping_set_id: http://w3id.org/mapping_commons/monarch/loincpart2cl.sssom.tsv

# mapping_tool: https://github.com/mapping-commons/sssom-py
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# mapping_tool: https://github.com/mapping-commons/sssom-py

# creator_label: "monarch-initiative"
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



14 changes: 14 additions & 0 deletions mappings/loinc-part-obo/loinc2go.sssom.tsv
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# 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#
# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
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# mapping_date: '2023-05-01'
# mapping_set_id: http://w3id.org/mapping_commons/disease-mappings/onto-icd10
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# mapping_tool: https://github.com/mapping-commons/sssom-py
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# creator_label: "monarch-initiative"
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
25 changes: 25 additions & 0 deletions mappings/loinc-part-obo/loinc2ncbitaxon.sssom.tsv
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# 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#
# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
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# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
# license: http://creativecommons.org/publicdomain/zero/1.0/

# mapping_date: '2023-05-01'
# mapping_set_id: http://w3id.org/mapping_commons/disease-mappings/onto-icd10
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# mapping_set_id: http://w3id.org/mapping_commons/disease-mappings/onto-icd10
# mapping_set_id: http://w3id.org/mapping_commons/monarch/loincpart2ncbitaxon.sssom.tsv

# mapping_tool: https://github.com/mapping-commons/sssom-py
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# creator_label: "monarch-initiative"
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

17 changes: 17 additions & 0 deletions mappings/loinc-part-obo/loinc2ncit.sssom.tsv
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# 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#
# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
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# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
# license: http://creativecommons.org/publicdomain/zero/1.0/

# mapping_date: '2023-05-01'
# mapping_set_id: http://w3id.org/mapping_commons/disease-mappings/onto-icd10
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# mapping_tool: https://github.com/mapping-commons/sssom-py
# creator_label: "monarch-initiative"
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
72 changes: 72 additions & 0 deletions mappings/loinc-part-obo/loinc2pr.sssom.tsv
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# 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#
# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
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Suggested change
# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
# license: http://creativecommons.org/publicdomain/zero/1.0/

# mapping_date: '2023-05-01'
# mapping_set_id: http://w3id.org/mapping_commons/disease-mappings/onto-icd10
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# mapping_tool: https://github.com/mapping-commons/sssom-py
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# creator_label: "monarch-initiative"
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
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