From e550313fa71f21701eac0d9718a7b5079739da3f Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 18 Aug 2023 14:43:47 +0200 Subject: [PATCH] Curate engineered --- scripts/generate_vaccine_mappings.py | 31 +++++++++++++++++++++++--- src/biomappings/resources/mappings.tsv | 14 ++++++++++++ 2 files changed, 42 insertions(+), 3 deletions(-) diff --git a/scripts/generate_vaccine_mappings.py b/scripts/generate_vaccine_mappings.py index 81954386..052f9da3 100644 --- a/scripts/generate_vaccine_mappings.py +++ b/scripts/generate_vaccine_mappings.py @@ -2,16 +2,41 @@ import click -from biomappings.gilda_utils import append_gilda_predictions +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 +from pyobo.sources.cpt import iter_terms + @click.command() def main(): """Generate vaccine mappings.""" provenance = get_script_url(__file__) - append_gilda_predictions("cvx", ["mesh", "cpt"], provenance=provenance) - append_gilda_predictions("cpt", ["mesh"], provenance=provenance) + # append_gilda_predictions("cvx", ["mesh", "cpt"], provenance=provenance) + # append_gilda_predictions("cpt", ["mesh"], provenance=provenance) + + preds = [] + grounder = get_grounder("mesh", versions="2023") + 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="mesh", + 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__": diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index ab6c8484..c3327de0 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -3064,6 +3064,20 @@ cpt 90291 CMVIG skos:exactMatch mesh C045781 cytomegalovirus-specific hyperimmun 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 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 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 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 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 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