Bump Reactome graph DB to Release97#52
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Diagrams (~/reactome-diagrams/97) are Release 97 but the compose pinned the DB to Release96, so ~85 diagram 'following' pairs referenced R97 reactions absent from the R96 DB (e.g. R-HSA-9980233 "PIP3 activates mTORC2") — a version-skew gap, not the diagram encoding connectivity the DB lacks. At matching release, diagram following == neo4j precedingEvent exactly (0 diagram-only pairs). The DB is baked into the image at /var/lib/neo4j/data; the neo4j_data:/data volume is vestigial (empty), so the tag bump serves R97 with no volume changes. Version sentinel test reports v97. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Pin the graph DB image to Release 97 to match the diagram files (
~/reactome-diagrams/97) and current Reactome.Why
The diagrams are Release 97 but the DB was pinned to Release 96. That skew made ~85 diagram
following(preceding-event) pairs look "missing from Neo4j" — but 95% of them reference R97 reactions that simply don't exist in the R96 DB (e.g.R-HSA-9980233"PIP3 activates mTORC2"). It was a version gap, not the diagram holding connectivity the database lacks.Verified: with the DB on R97, diagram
followingpairs == Neo4jprecedingEventexactly — 0 diagram-only pairs (was 85 at R96). So no diagram-parsing is needed to recover preceding events; matching the release closes the gap.Mechanics
The DB is baked into the image at
/var/lib/neo4j/data; theneo4j_data:/datavolume is vestigial (mounted at the wrong path, 12K empty). So the tag bump +docker compose up -d --force-recreate neo4jserves R97 with no volume surgery. Version sentinel test (test_reactome_version.py) now reports v97 and passes; full non-Neo4j suite: 923 passed.Note
Previously-generated catalogs (
output/, MP-BioPath refs) are R96-based — regenerate against R97 if the networks should track the current release.🤖 Generated with Claude Code