From 340a87d352d7703847cb744c93f286cad5848c72 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 23 Aug 2023 16:06:24 +0200 Subject: [PATCH] CVX and MeSH mappings (#147) CPT mappings to MeSH were problematic since CPT names its things without the word "vaccine", so it will require a more custom script to make good predictions. I did several curations, and left 48 left for later. --- scripts/generate_vaccine_mappings.py | 42 ++++++++++++++++++++ src/biomappings/resources/incorrect.tsv | 9 +++++ src/biomappings/resources/mappings.tsv | 41 +++++++++++++++++++ src/biomappings/resources/predictions.tsv | 48 +++++++++++++++++++++++ src/biomappings/resources/unsure.tsv | 1 + 5 files changed, 141 insertions(+) create mode 100644 scripts/generate_vaccine_mappings.py diff --git a/scripts/generate_vaccine_mappings.py b/scripts/generate_vaccine_mappings.py new file mode 100644 index 00000000..6fa47528 --- /dev/null +++ b/scripts/generate_vaccine_mappings.py @@ -0,0 +1,42 @@ +"""Generate vaccine mappings.""" + +import click +from pyobo.sources.cpt import iter_terms + +from biomappings import PredictionTuple +from biomappings.gilda_utils import append_gilda_predictions, get_grounder +from biomappings.resources import append_prediction_tuples +from biomappings.utils import get_script_url + + +@click.command() +def main(): + """Generate vaccine mappings.""" + provenance = get_script_url(__file__) + append_gilda_predictions("cvx", ["mesh", "cpt", "vo"], provenance=provenance) + append_gilda_predictions("cpt", ["mesh", "vo"], provenance=provenance) + + preds = [] + grounder = get_grounder(["mesh", "vo"], versions=["2023", None]) + for term in iter_terms(): + texts = [term.name, *(s.name for s in term.synonyms)] + for text in texts: + for scored_match in grounder.ground(text + " vaccine"): + pred = PredictionTuple( + source_prefix=term.prefix, + source_id=term.identifier, + source_name=term.name, + relation="skos:exactMatch", + target_prefix=scored_match.term.db, + target_identifier=scored_match.term.id, + target_name=scored_match.term.entry_name, + type="semapv:LexicalMatching", + confidence=0.9, + source=provenance, + ) + preds.append(pred) + append_prediction_tuples(preds) + + +if __name__ == "__main__": + main() diff --git a/src/biomappings/resources/incorrect.tsv b/src/biomappings/resources/incorrect.tsv index 7eb7d17f..1e40cf4d 100644 --- a/src/biomappings/resources/incorrect.tsv +++ b/src/biomappings/resources/incorrect.tsv @@ -211,6 +211,15 @@ clo 0037261 3T3-derived cell skos:exactMatch mesh D016475 3T3 Cells semapv:Manua clo 0037287 COR123 cell skos:exactMatch efo 0002142 CORL23 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:UnspecifiedMatching clo 0.8 clo 0051004 RCB0256 cell skos:exactMatch cellosaurus CVCL_1075 BALL-1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:UnspecifiedMatching clo 0.8 clo 0051005 RCB1882 cell skos:exactMatch cellosaurus CVCL_1075 BALL-1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:UnspecifiedMatching clo 0.8 +cpt 90389 TIG skos:exactMatch vo 0010969 Tig semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.762 +cpt 90581 anthrax skos:exactMatch mesh D000881 Anthrax semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cpt 90585 BCG skos:exactMatch mesh D009163 Mycobacterium bovis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.556 +cpt 90665 Lyme disease skos:exactMatch mesh D008193 Lyme Disease semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.772 +cpt 90704 mumps skos:exactMatch mesh D009107 Mumps semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cpt 90705 measles skos:exactMatch mesh D008457 Measles semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cpt 90706 rubella skos:exactMatch mesh D012409 Rubella semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cpt 90716 varicella skos:exactMatch mesh D002644 Chickenpox semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.54 +cpt 90727 plague skos:exactMatch mesh D010930 Plague semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 doid DOID:0001816 angiosarcoma skos:exactMatch mesh D006394 Hemangiosarcoma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 doid DOID:0001816 angiosarcoma skos:exactMatch umls C0018923 Hemangiosarcoma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 doid DOID:0001816 angiosarcoma skos:exactMatch umls C0278592 Adult Angiosarcoma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index 9410f984..8dacf6b6 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -3059,6 +3059,47 @@ clo 0037230 Ishikawa 3-H-12 cell skos:exactMatch cellosaurus CVCL_D199 Ishikawa clo 0037291 MDAMB231 cell skos:exactMatch mesh D000092302 MDA-MB-231 Cells semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/746fde/scripts/generate_clo_mesh_mappings.py 0.549 clo 0037300 BALL-1 cell skos:exactMatch cellosaurus CVCL_1075 BALL-1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:UnspecifiedMatching clo 0.8 clo 0037339 tissue donor skos:exactMatch mesh D014019 Tissue Donors semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/746fde/scripts/generate_clo_mesh_mappings.py 0.54 +cpt 90287 botulinum antitoxin skos:exactMatch mesh D001904 Botulinum Antitoxin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cpt 90287 botulinum antitoxin skos:exactMatch vo 0006001 botulinum antitoxin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.778 +cpt 90291 CMVIG skos:exactMatch mesh C045781 cytomegalovirus-specific hyperimmune globulin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.556 +cpt 90296 diphtheria antitoxin skos:exactMatch mesh D004166 Diphtheria Antitoxin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cpt 90296 diphtheria antitoxin skos:exactMatch vo 0006005 diphtheria antitoxin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.778 +cpt 90371 HBIG skos:exactMatch mesh C045213 hepatitis B hyperimmune globulin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.556 +cpt 90396 VZIG skos:exactMatch mesh C030799 varicella-zoster immune globulin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.556 +cpt 90581 anthrax skos:exactMatch mesh D022122 Anthrax Vaccines semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90585 BCG skos:exactMatch mesh D001500 BCG Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90585 BCG skos:exactMatch vo 0000771 BCG vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.9 +cpt 90665 Lyme disease skos:exactMatch mesh D022123 Lyme Disease Vaccines semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90665 Lyme disease skos:exactMatch vo 0000764 Lyme disease vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.9 +cpt 90685 Influenza, injectable,quadrivalent, preservative free, pediatric skos:exactMatch vo 0005462 Influenza, injectable,quadrivalent, preservative free, pediatric semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.778 +cpt 90700 DTaP skos:exactMatch mesh D022681 Diphtheria-Tetanus-acellular Pertussis Vaccines semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90701 DTP skos:exactMatch mesh D015721 Diphtheria-Tetanus-Pertussis Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90704 mumps skos:exactMatch mesh D009108 Mumps Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90705 measles skos:exactMatch mesh D008458 Measles Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90706 rubella skos:exactMatch mesh D012411 Rubella Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90707 MMR skos:exactMatch mesh D022542 Measles-Mumps-Rubella Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90710 MMRV skos:exactMatch mesh C050102 measles, mumps, rubella, varicella vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90715 Tdap skos:exactMatch vo 0003180 TDAP semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.762 +cpt 90716 varicella skos:exactMatch mesh D019433 Chickenpox Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90720 DTP-Hib skos:exactMatch mesh C080881 diphtheria-tetanus-pertussis-haemophilus b conjugate vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90727 plague skos:exactMatch mesh D010931 Plague Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90728 BCG skos:exactMatch mesh D001500 BCG Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/6301b7/scripts/generate_vaccine_mappings.py 0.9 +cpt 90728 BCG skos:exactMatch vo 0000771 BCG vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.9 +cpt 90756 Influenza, injectable, MDCK, quadrivalent, preservative skos:exactMatch vo 0005463 Influenza, injectable, MDCK, quadrivalent, preservative semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py 0.778 +cvx 10 poliovirus vaccine, inactivated skos:exactMatch mesh D011054 Poliovirus Vaccine, Inactivated semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.725 +cvx 103 meningococcal C conjugate vaccine skos:exactMatch mesh C410218 serogroup C meningococcal conjugate vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.556 +cvx 11 pertussis vaccine skos:exactMatch mesh D010567 Pertussis Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cvx 12 diphtheria antitoxin skos:exactMatch mesh D004166 Diphtheria Antitoxin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cvx 19 Bacillus Calmette-Guerin vaccine skos:exactMatch mesh D001500 BCG Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.54 +cvx 23 plague vaccine skos:exactMatch mesh D010931 Plague Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cvx 24 anthrax vaccine skos:exactMatch mesh D022122 Anthrax Vaccines semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.54 +cvx 27 botulinum antitoxin skos:exactMatch mesh D001904 Botulinum Antitoxin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cvx 37 yellow fever vaccine skos:exactMatch mesh D022341 Yellow Fever Vaccine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.762 +cvx 64 leishmaniasis vaccine skos:exactMatch mesh D054332 Leishmaniasis Vaccines semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.54 +cvx 66 Lyme disease vaccine skos:exactMatch mesh D022123 Lyme Disease Vaccines semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.549 +cvx 67 malaria vaccine skos:exactMatch mesh D017780 Malaria Vaccines semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.54 +cvx 801 AS03 Adjuvant skos:exactMatch mesh C550253 AS03 adjuvant semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.772 +cvx 87 immune globulin, intravenous skos:exactMatch mesh D016756 Immunoglobulins, Intravenous semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.502 doid DOID:0040002 aspirin allergy skos:exactMatch umls C0004058 Allergy to aspirin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 doid DOID:0040004 amoxicillin allergy skos:exactMatch umls C0571417 Allergy to amoxicillin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 doid DOID:0040005 ceftriaxone allergy skos:exactMatch umls C0571463 Allergy to ceftriaxone semapv:ManualMappingCuration orcid:0000-0003-4423-4370 diff --git a/src/biomappings/resources/predictions.tsv b/src/biomappings/resources/predictions.tsv index 5878ea00..e818e515 100644 --- a/src/biomappings/resources/predictions.tsv +++ b/src/biomappings/resources/predictions.tsv @@ -9460,6 +9460,54 @@ clo 0037372 HEK293T cell skos:exactMatch cellosaurus CVCL_0063 HEK293T semapv:Un clo 0050405 RCB2280 cell skos:exactMatch cellosaurus CVCL_1272 HCE-T semapv:UnspecifiedMatching 0.8 clo clo 0050406 RCB1384 cell skos:exactMatch cellosaurus CVCL_1272 HCE-T semapv:UnspecifiedMatching 0.8 clo clo 0050894 RCB2202 cell skos:exactMatch cellosaurus CVCL_0063 HEK293T semapv:UnspecifiedMatching 0.8 clo +cvx 02 trivalent poliovirus vaccine, live, oral skos:exactMatch vo 0005469 trivalent poliovirus vaccine, live, oral semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 05 measles virus vaccine skos:exactMatch vo 0000654 Measles virus vaccine semapv:LexicalMatching 0.772 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 06 rubella virus vaccine skos:exactMatch vo 0010637 Rubella virus vaccine semapv:LexicalMatching 0.772 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 07 mumps virus vaccine skos:exactMatch vo 0000656 Mumps virus vaccine semapv:LexicalMatching 0.772 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 09 tetanus and diphtheria toxoids, adsorbed, preservative free, for adult use (2 Lf of tetanus toxoid and 2 Lf of diphtheria toxoid) skos:exactMatch vo 0005466 tetanus and diphtheria toxoids, adsorbed, preservative free, for adult use (2 Lf of tetanus toxoid and 2 Lf of diphtheria toxoid) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 103 meningococcal C conjugate vaccine skos:exactMatch vo 0006033 meningococcal C conjugate vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 107 diphtheria, tetanus toxoids and acellular pertussis vaccine, unspecified formulation skos:exactMatch vo 0005459 Diphtheria, tetanus toxoids and acellular pertussis vaccine, unspecified formulation semapv:LexicalMatching 0.734 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 117 varicella zoster immune globulin (Investigational New Drug) skos:exactMatch vo 0005455 varicella zoster immune globulin (Investigational New Drug) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 12 diphtheria antitoxin skos:exactMatch vo 0006005 diphtheria antitoxin semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 13 tetanus immune globulin skos:exactMatch vo 0005452 tetanus immune globulin semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 131 Historical record of a typhus vaccination skos:exactMatch vo 0006019 Historical record of a typhus vaccination semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 138 tetanus and diphtheria toxoids, not adsorbed, for adult use skos:exactMatch vo 0005468 tetanus and diphtheria toxoids, not adsorbed, for adult use semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 14 immune globulin, unspecified formulation skos:exactMatch vo 0005446 immune globulin, unspecified formulation semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 146 Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed, Inactivated Poliovirus, Haemophilus b Conjugate (Meningococcal Protein Conjugate), and Hepatitis B (Recombinant) Vaccine. skos:exactMatch vo 0005470 Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed, Inactivated Poliovirus, Haemophilus b Conjugate (Meningococcal Protein Conjugate), and Hepatitis B (Recombinant) Vaccine. semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 157 Rho(D) Immune globulin - IM skos:exactMatch vo 0005449 Rho(D) Immune globulin - IM semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 159 Rho(D) Unspecified formulation skos:exactMatch vo 0005451 Rho(D) Unspecified formulation semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 161 Influenza, injectable,quadrivalent, preservative free, pediatric skos:exactMatch vo 0005462 Influenza, injectable,quadrivalent, preservative free, pediatric semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 167 meningococcal vaccine of unknown formulation and unknown serogroups skos:exactMatch vo 0006034 meningococcal vaccine of unknown formulation and unknown serogroups semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 175 Human Rabies vaccine from human diploid cell culture skos:exactMatch vo 0006021 Human Rabies vaccine from human diploid cell culture semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 178 Non-US bivalent oral polio vaccine (types 1 and 3) skos:exactMatch vo 0005464 Non-US bivalent oral polio vaccine (types 1 and 3) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 179 Non-US monovalent oral polio vaccine, unspecified formulation skos:exactMatch vo 0005465 Non-US monovalent oral polio vaccine, unspecified formulation semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 180 tetanus immune globulin skos:exactMatch vo 0005452 tetanus immune globulin semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 190 Typhoid conjugate vaccine (non-US) skos:exactMatch vo 0006082 Typhoid conjugate vaccine (non-US) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 191 meningococcal A polysaccharide vaccine (non-US) skos:exactMatch vo 0006029 meningococcal A polysaccharide vaccine (non-US) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 192 meningococcal AC polysaccharide vaccine (non-US) skos:exactMatch vo 0006030 meningococcal AC polysaccharide vaccine (non-US) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 196 tetanus and diphtheria toxoids, adsorbed, preservative free, for adult use, Lf unspecified skos:exactMatch vo 0005467 tetanus and diphtheria toxoids, adsorbed, preservative free, for adult use, Lf unspecified semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 208 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 30 mcg/0.3mL dose skos:exactMatch vo 0005437 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 30 mcg/0.3mL dose semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 22 DTP-Haemophilus influenzae type b conjugate vaccine skos:exactMatch vo 0005460 DTP--Haemophilus influenzae type b conjugate vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 27 botulinum antitoxin skos:exactMatch vo 0006001 botulinum antitoxin semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 34 rabies immune globulin skos:exactMatch vo 0005447 rabies immune globulin semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 36 varicella zoster immune globulin skos:exactMatch vo 0005454 varicella zoster immune globulin semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 504 SARS-COV-2 COVID-19 Viral Vector Non-replicating Non-US Vaccine Product (Sputnik Light) skos:exactMatch vo 0006075 SARS-COV-2 COVID-19 Viral Vector Non-replicating Non-US Vaccine Product (Sputnik Light) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 508 SARS-COV-2 COVID-19 Protein Subunit Non-US Vaccine Product (Jiangsu Province Centers for Disease Control and Prevention) skos:exactMatch vo 0006071 SARS-COV-2 COVID-19 Protein Subunit Non-US Vaccine Product (Jiangsu Province Centers for Disease Control and Prevention) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 520 SARS-COV-2 COVID-19 mRNA, bivalent, original/Omicron BA.1, Non-US Vaccine Product (Comirnaty Bivalent), Pfizer-BioNTech skos:exactMatch vo 0005435 SARS-COV-2 COVID-19 mRNA, bivalent, original/Omicron BA.1, Non-US Vaccine Product (Comirnaty Bivalent), Pfizer-BioNTech semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 57 hantavirus vaccine skos:exactMatch vo 0012167 Hantavirus vaccine semapv:LexicalMatching 0.772 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 58 hepatitis C vaccine skos:exactMatch vo 0006016 hepatitis C vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 59 hepatitis E vaccine skos:exactMatch vo 0006017 hepatitis E vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 61 human immunodeficiency virus vaccine skos:exactMatch vo 0000295 human immunodeficiency virus vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 63 Junin virus vaccine skos:exactMatch vo 0006027 Junin virus vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 65 leprosy vaccine skos:exactMatch vo 0006028 leprosy vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 66 Lyme disease vaccine skos:exactMatch vo 0000764 Lyme disease vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 67 malaria vaccine skos:exactMatch vo 0000761 malaria vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 68 melanoma vaccine skos:exactMatch vo 0000422 melanoma vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 69 parainfluenza-3 virus vaccine skos:exactMatch vo 0000451 Parainfluenza 3 virus vaccine semapv:LexicalMatching 0.762 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 72 rheumatic fever vaccine skos:exactMatch vo 0006049 rheumatic fever vaccine semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 77 Tick-borne encephalitis vaccine (non-US) skos:exactMatch vo 0006078 Tick-borne encephalitis vaccine (non-US) semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 86 immune globulin, intramuscular skos:exactMatch vo 0005444 immune globulin, intramuscular semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py +cvx 87 immune globulin, intravenous skos:exactMatch vo 0005445 immune globulin, intravenous semapv:LexicalMatching 0.778 https://github.com/biomappings/biomappings/blob/e55031/scripts/generate_vaccine_mappings.py doid DOID:0050041 Astrakhan spotted fever skos:exactMatch umls C0549160 North Asian Tick Typhus semapv:LexicalMatching 0.5555555555555556 https://github.com/biomappings/biomappings/blob/f293d0/scripts/generate_doid_mappings.py doid DOID:0050042 Indian tick typhus skos:exactMatch umls C0343768 India tick typhus semapv:LexicalMatching 0.5555555555555556 https://github.com/biomappings/biomappings/blob/f293d0/scripts/generate_doid_mappings.py doid DOID:0050134 cutaneous mycosis skos:exactMatch umls C0011630 Dermatomycoses semapv:LexicalMatching 0.5555555555555556 https://github.com/biomappings/biomappings/blob/f293d0/scripts/generate_doid_mappings.py diff --git a/src/biomappings/resources/unsure.tsv b/src/biomappings/resources/unsure.tsv index d7e0cf8d..ab999e98 100644 --- a/src/biomappings/resources/unsure.tsv +++ b/src/biomappings/resources/unsure.tsv @@ -32,6 +32,7 @@ chebi CHEBI:68540 teriflunomide skos:exactMatch mesh C072876 A 771726 semapv:Man chebi CHEBI:8416 Pristimerin skos:exactMatch mesh C009043 pristimerin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95 cl CL:0000798 gamma-delta T cell skos:exactMatch mesh D000075942 Intraepithelial Lymphocytes semapv:ManualMappingCuration orcid:0000-0001-9439-5346 cl CL:0000816 immature B cell skos:exactMatch mesh D054448 Precursor Cells, B-Lymphoid semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +cpt 90728 BCG skos:exactMatch mesh D009163 Mycobacterium bovis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/8d4bd2/scripts/generate_vaccine_mappings.py 0.556 doid DOID:0050025 human granulocytic anaplasmosis skos:exactMatch mesh D000712 Anaplasmosis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 doid DOID:0050035 African tick-bite fever skos:exactMatch mesh D000073605 Spotted Fever Group Rickettsiosis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 doid DOID:0050061 erysipeloid skos:exactMatch umls C0014736 Erysipelothrix infection semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/f293d0/scripts/generate_doid_mappings.py 0.5400948258091115