obophenotype / obophenotype/chiro
Align roles with MESH and other descriptor vocabularies used in DrugBank etc
@cmungall is already working on this.
Since Jul 1, 2019.
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Description
Example MESH descriptors for Imatinib in DrugBank:
| ID | Label |
|---|---|
| id:mesh/D000146 | Acids, Carbocyclic |
| id:mesh/D000577 | Amides |
| id:mesh/D000970 | Antineoplastic Agents |
| id:mesh/D001549 | Benzamides and benzamide derivatives |
| id:mesh/D001555 | Benzene Derivatives |
| id:mesh/D001565 | Benzoates |
| id:mesh/D002264 | Carboxylic Acids |
| id:mesh/D004791 | Enzyme Inhibitors |
| id:mesh/D006571 | Heterocyclic Compounds |
| id:mesh/D006573 | Heterocyclic Compounds, 1-Ring |
| id:mesh/D006838 | Hydrocarbons |
| id:mesh/D006841 | Hydrocarbons, Aromatic |
| id:mesh/D006844 | Hydrocarbons, Cyclic |
| id:mesh/D007166 | Immunosuppressive Agents |
| id:mesh/D010879 | Piperazines |
| id:mesh/D011743 | Pyrimidines |
| id:mesh/D047428 | Protein Kinase Inhibitors |
| id:mesh/D065607 | Cytochrome P-450 Enzyme Inhibitors |
| id:mesh/D065690 | Cytochrome P-450 CYP2D6 Inhibitors |
| id:mesh/D065692 | Cytochrome P-450 CYP3A Inhibitors |
| id:mesh/D065692 | Cytochrome P-450 CYP3A4 Inhibitors |
| id:mesh/D065692 | Cytochrome P-450 CYP3A5 Inhibitors |
| id:mesh/D065692 | Cytochrome P-450 CYP3A7 Inhibitors |
I believe many/all could be mapped to CHEBI roles. This would be very powerful as it would allow us to (a) compare role assignments in CHEBI with role assignments in other databases like DrugBank (b) GO from DrugBank drugs to OBO classes, e.g. Imatinib-[inhibits]->GO:kinase activity. cc @cbizon @balhoff
We could also include these in mychem cc @newgene
I think these will be useful for IDG cc @pnrobinson @realmarcin @deepakunni3
btw, I am getting the drugbank-to-mesh associations via the Dumontierlab biolink-compliant triplestore http://graphdb.dumontierlab.com/repositories/ncats-red-kg provided by @vemonet
Example query:
SELECT ?x ?y ?g ?v0 ?v1 ?v2 WHERE {?x <http://w3id.org/biolink/vocab/name> ?v3 . FILTER (?v3 = "Imatinib") . GRAPH ?g {?x <http://w3id.org/biolink/vocab/category> ?y} . OPTIONAL {?x <http://w3id.org/biolink/vocab/name> ?v0} . OPTIONAL {?y <http://w3id.org/biolink/vocab/name> ?v1} . OPTIONAL {?g <http://w3id.org/biolink/vocab/name> ?v2}}
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