Load variant assestions from the Molecular Oncology Almanac1.
node bin/load.js api moa- A specific drug ontology is not used/given and therefore drugs are matched by name
- A specific gene ontology is not specified and therefore we default to using Entrez genes as they are popular amongst other knowledge bases
- When given, diseases are preferentially matched to their OncoTree term by both name and code. This falls back to matching by name when the oncotree term/code is not given
The mapping of relevance terms to their GraphKB equivalent is given below
| MOA field | MOA term | GraphKB relevance |
|---|---|---|
.therapy_resistance |
true | resistance |
.therapy_sensitivity |
true | sensitivity |
.therapy_sensitivity |
false | no sensitivity |
.favorable_prognosis |
true | favorable prognosis |
.favorable_prognosis |
false | unfavorable prognosis |
.features[].attributes[].pathogenic |
"1.0" | pathogenic |
We have linked the predictive_implication from MOA to specific evidence levels in GraphKB
| MOA | AMP | CIViC | IPR |
|---|---|---|---|
| Clinical evidence | Level B (Tier II) | B | B |
| Clinical trial | Level B (Tier II) | B | B |
| FDA-Approved | Level A (Tier I) | A | A |
| Guideline | Level A (Tier I) | A | A |
| Preclinical | Level D (Tier II) | D | D |
| Inferential | E | E |
Specific MOA variant types are mapped as category variants in GraphKB:
| MOA feature_type | MOA field | MOA field value | GraphKB reference1 class | GraphKB reference1 | GraphKB type |
|---|---|---|---|---|---|
| microsatellite_stability | status | MSI-High | Signature | microsatellite instability | high signature |
| mutational_signature | cosmic_signature_number | # | Signature | SBS# | signature present |
| knockdown | n/a | <gene name> |
Feature | <gene name> |
knockdown |
Footnotes
-
Reardon, B. et al. Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. Nature Cancer 2, 1102–1112 (2021) ↩