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.
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.