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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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Remove mesh cycle from bio-ontology #1433

Closed kkaris closed 7 months ago

kkaris commented 7 months ago

This PR adds functionality to remove edges from the bio ontology and does that for one edge in the MeSH 2024 data. The edge removed is MESH:D015835 -[isa]-> MESH:D013285 which prevents a circular hierarchy structure since MESH:D013285 -[isa]-> MESH:D015835 is already a relation. See https://meshb.nlm.nih.gov/record/ui?ui=D015835 under the MeSH Tree Structure tab then check the branch for Nervous System Diseases [C10] where the hierarchical path MESH:D015835 -> MESH:D013285 -> MESH:D015835 is present, creating an is_a/partof cycle.

The bio ontology version is bumped to 1.32 with this PR.

kkaris commented 7 months ago

All the failing tests are related to 404 errors from the cbio client