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sorgerlab / indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
http://indra.bio
BSD 2-Clause "Simplified" License
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Signor processor error #1419

Closed kkaris closed 1 year ago

kkaris commented 1 year ago

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()
cthoyt commented 1 year ago

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 commented 1 year ago

Resolved by #1423