Closed chunyuma closed 3 years ago
Personally, I think we should treat any child of chemical substance as a drug. Recall the example of cyclic vomiting being treated with ethanol; so I would assume that we shouldn’t exclude food additives, nutrients, etc. from drug repurposing targets. Better to cast a wide net in the beginning, and then after potential repurposing targets are found, figure out if it would actually be viable to use as a drug.
Hi @dkoslicki, theoretically, it is true that all children of chemical substance can be treated as a drug. But in practice, we might not be able to do this because of the training data. Currently, the training data we used for DTD model are mainly from MyChem
, semeddb
and NDF
. The MyChem
training data are mainly the curies with prefix CHEMBL.COMPOUND
; the semeddb
data are mainly the curies with prefix CHEBI
, CHEMBL.COMPOUND
and MESH
; the NDF
data are also CHEMBL.COMPOUND
. If we want to include food additives, nutrients, etc as a drug, we have to also include them in our training data. Otherwise, the model can't learn the features from these children of chemical substance.
I don't know if our training data MyChem
, semeddb
and NDF
have already contains the pairs of food additives, nutrients with disease since currently kg2.5.2 don't have these categories yet. But I checked the provider source distribution of biolink:Metabolite
based on kg2.5.2c, they are mainly KEGG
. In our training data, we don't have KEGG
.
To validate whether the model has the predictive power for the curies outside biolink:Drug
and biolink:ChemicalSubstance
, we need to add a set of drug-disease pairs for the curies outside biolink:Drug
and biolink:ChemicalSubstance
in this plot:
Thanks to @dkoslicki's suggestion, in the next version of DTD
model, we decide to treat biolink:Metabolite
, biolink:ChemicalSubstance
and biolink:Drug
as general drugs in DTD model. So this issue can be closed
This question is raised from issue #1321.
The biolink:Metabolite is a direct child of biolink:ChemicalSubstance but biolink:ChemicalSubstance has many other children such as FoodAdditive, Nutrient, ProcessedMaterial, etc. See Children at https://biolink.github.io/biolink-model/docs/ChemicalSubstance.html
Here is an example: Glycyl-Histidine (HMDB0028843) is a metabolite so it should be a chemical too. Although it might not be directly used as drug but it does involves some biological actions like physiological or cell-signaling effect.