New Relationships File Available

PharmGKB has a new relationships file available for download. This file catalogs all the current relationships between drugs, genes, diseases, variants, and haplotypes in PharmGKB. These relationships are based on annotations generated by our curators.

The new relationships file replaces and improves on the old relationships file. The entries in the old relationships file were based on co-occurence of gene, drug, and disease names within literature (primarily abstracts) and did not necessarily represent direct, curated relationships between entities.

The relationships file has quite a few new features.

  • Includes relationships from our new annotations like clinical annotations, dosing guidelines, and drug label annotations
  • Each relationship indicates what types of annotation it comes from in the “Evidence” field.
  • PMIDs are now listed for relationships when available in the “PMIDs” field. This is a semi-colon(;) delimited list of PMIDs used to support the annotation.
  • The “Association” field gives a sense of whether an association is positive, negative, or ambiguous. Please see note below regarding associations in disease relationships.
  • Haplotype annotations are now included.
  • PK/PD flags for pharmacokinetic or pharmacodynamic relationships have been added back in.

To get a copy of this file please sign into the site, agree to the PharmGKB Relationship Agreement on the Downloads page, and a copy of the file with supporting documentation will be sent to you.

NOTE: Disease associations derived from a VariantAnnotation or ClinicalAnnotation are really referring to a variant that has an annotation with that “Disease” tag.  These associations can be misleading because they are not necessarily indications that a variant is directly associated with a disease phenotype.

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