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Curate engineered
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@cthoyt
cthoyt committed Aug 18, 2023
1 parent 6301b7f commit e550313
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31 changes: 28 additions & 3 deletions scripts/generate_vaccine_mappings.py
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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__":
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14 changes: 14 additions & 0 deletions src/biomappings/resources/mappings.tsv
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Expand Up @@ -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
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