Found unstandardized references while building DUB portal

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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Found unstandardized references while building DUB portal #1350

Closed cthoyt closed 2 years ago

cthoyt commented 2 years ago

Looks like there is a problem with standardizing ChEBI identifiers floating around somewhere:

INFO: [2021-11-10 14:13:56] indra.assemblers.html.assembler - Removing CHEBI from refs due to too many matches: {'CHEBI:131902', '131902'}

bgyori commented 2 years ago

Those come from the DB, we would have to include post-processing in the given application to clean those up.

cthoyt commented 2 years ago

In the DUB portal this only happens like 3 times, so it's not a big deal, but just wanted to make sure you aware

bgyori commented 2 years ago

Thanks, these have been fixed over time in INDRA and the indra.tools.fix_invalidities(https://indra.readthedocs.io/en/latest/modules/tools/index.html#module-indra.tools.fix_invalidities) module allows post-processing in cases where previously generated and saved statements have to be fixed up.