Adding disease context qualifier to Biolink

[codewarrior2000]

Is your feature request related to a problem? Please describe.

• We are ingesting drug-phenotype associations from PharmGKB entities and we want a new qualifier to be used for phenotypes

What working group (or team) did this request originate from?
The need for representing this type of data originated from MolePro

Note: This may be relevant for members of NCATS Translator.

Describe the solution you'd like
Add to Biolink a disease context qualifier ‘https://www.pharmgkb.org/disease/PA445208’ (e.g., the “Pain phenotype” for oxycodone)

Tag relevant members for discussion
@sierra-moxon @vdancik

[codewarrior2000]

Also, should the value of the disease context qualifier be a CURIE or would just the disease name suffice?

[sierra-moxon]

Hi @codewarrior2000 -

Let me know if either of these examples represent the statements you want to make? These are completely out of my head to try and capture what it is you're trying to say (they may be a bit nonsensical -- e.g. the first one).

subject: oxycodon 
predicate: treats
object: liver disease
disease_or_phenotypic_feature_context_qualifier: Pain

or

subject: oxycodone
predicate: treats
object: pain phenotype

or

subject: oxycodone
predicate: affects
qualified_predicate: causes
object: pain phenotype
object_direction_qualifier: decreased

or something different?

Note we have subject and object_context_qualifier that might help?

[codewarrior2000]

Hi @sierra-moxon

Thank you for asking. We are creating a knowledge graph that looks like the following with real PharmGKB data:

          subject: methotrexate
          predicate: affects
          object: ABCB1
          object_form_or_variant_qualifier: DBSNP:rs868755
          disease_or_phenotypic_feature_context_qualifier: Arthritis, Rheumatoid
          disease_or_phenotypic_feature_context_qualifier: Precursor Cell Lymphoblastic Leukemia-Lymphoma
          disease_or_phenotypic_feature_context_qualifier: Lymphoma, T-Cell