Skip to content

Commit

Permalink
Changes were made in the scripts to resolve errors in the data cleani…
Browse files Browse the repository at this point in the history
…ng and formatting of the PharmGKB CSV+tMCF pairs. It also breaks out the phenotypes to distinguish that one is a MeSHQualifier and seven are MeSHSupplementaryConceptRecords, unlike the rest of the phenotypes which are MeSHDescriptors. Therefore these were separated into 3 CSV+tMCF pairs. In particular, the links to the enums and between entity types were fixed. This was done by initializing all nodes referenced and then pointing to them within the tMCF. Because of this any existence missing errors in the json reports can be ignored. The changes to the scripts, tMCF files, and documentation (README.md) for this import are part of GitHub PR 1056 datacommonsorg/data#1056

Schema Changes:
- Add CPICLevelEnum, DosageGuidelineSourceCpicNoRecommendation, DrugTypeEnum, PGxLevelEnum, PharmacogeneticAssociationEnum.
- Add properties for clinicalAnnotationCount, clinicalAnnotationCountLevel1_2, clinicalGuidelineAnnotationCount, dosageGuideline, drugHasPrescribingInfo, drugLabelAnnotationCount, drugType, fdaTopPharmacogeneticLevel, geneticVariantAnnotationCount, hasCpicDosingGuideline, hasGenomicCoordinates, hasGeneticVariantAnnotation, hasPrescribingInfo, medicalDictionaryForRegulatoryActivitiesId, metabolicPathwayCount, pharmageneticAssociation, topClinicalAnnotationLevel, topCpicLevel, topPharmacogeneticLevel, veryImportantPharmacogeneCount.
- Remove properties for fdaTopPGxLevel, mintID, nationalClinicalTrialNumber, nationalDrugCode, nationalDrugFileReferenceTerminologyCode, neuroMabID, patentID,pharmGkbClinicalAnnotationCount,pharmGkbPathwayCount, pkgbTags.

PiperOrigin-RevId: 655002332
  • Loading branch information
spiekos authored and copybara-github committed Jul 23, 2024
1 parent c8f1ebe commit 9731b2c
Show file tree
Hide file tree
Showing 2 changed files with 328 additions and 108 deletions.
Loading

0 comments on commit 9731b2c

Please sign in to comment.