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Signor processor error #1419

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kkaris opened this issue Sep 8, 2023 · 2 comments · Fixed by #1423
Closed

Signor processor error #1419

kkaris opened this issue Sep 8, 2023 · 2 comments · Fixed by #1423

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@kkaris
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kkaris commented Sep 8, 2023

When running sources.signor.api.process_from_web an InvalidIdentifier error is raised:

InvalidIdentifier: Invalid identifier: SID:135317436 for PUBCHEM pattern ^\d+$

To re-create the error:

from indra.sources.signor import process_from_web
sp = process_from_web()
@kkaris kkaris mentioned this issue Sep 11, 2023
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@cthoyt
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cthoyt commented Sep 12, 2023

PubChem has two databases - compounds and substances. SID would correspond to a substance ID, which with some api calls can probably be resolved to a proper CID (compound ID)

@kkaris
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kkaris commented Sep 18, 2023

Resolved by #1423

@kkaris kkaris linked a pull request Sep 18, 2023 that will close this issue
Db sources updates #1423
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Db sources updates sorgerlab/indra
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@kkaris @cthoyt