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
171 stars 65 forks source link

RLIMS-P invalid statement error #1422

Closed kkaris closed 9 months ago

kkaris commented 11 months ago

Running the processor on the latest available data (see https://hershey.dbi.udel.edu/textmining/export/), there are two errors when processing the medline file and they are both about the idString in the id_dict when getting agents containing a badly formatted identifier, both of the form <identifier>;<decimal>', and in both cases MESH identifiers.

Right now the error occurs first at the stage where the statements are checked in the processor with assert_valid_statements.

Suggestions:

bgyori commented 11 months ago

I fixed this in the processor

kkaris commented 11 months ago

Resolved by #1423