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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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Should we ETL "SMILE" information for small molecule compounds, into KG2pre? #401

Open saramsey opened 4 months ago

saramsey commented 4 months ago

@chunyuma was asking about this at today,'s Expander Agent all-hands meeting. I'll let @chunyuma fill in the use-case details here.

saramsey commented 4 months ago

This is assuming we don't already have SMILE information in KG2pre. I don't think we do, but I am not 100% sure. @ecwood can you confirm that is the case?

ecwood commented 4 months ago

We currently extract the SMILES information from DrugBank and HMDB. In KG2.10.0pre, it looks like this is saved under the property has_biological_sequence. This was explored in this issue, several years back: https://github.com/RTXteam/RTX/issues/1273. I'm not sure if we want to expand this to more sources though, or keep better records of that field.

chunyuma commented 4 months ago

Thank you @saramsey and @ecwood. Could you please tell me where I can access the KG2.10.0pre?