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Should we ETL "SMILE" information for small molecule compounds, into KG2pre? #401

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saramsey opened this issue Jul 17, 2024 · 3 comments
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Should we ETL "SMILE" information for small molecule compounds, into KG2pre? #401

saramsey opened this issue Jul 17, 2024 · 3 comments
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@saramsey
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@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 saramsey added the question Further information is requested label Jul 17, 2024
@saramsey
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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
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ecwood commented Jul 17, 2024

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: RTXteam/RTX#1273. I'm not sure if we want to expand this to more sources though, or keep better records of that field.

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

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@saramsey @chunyuma @ecwood