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A multi-source kg transform accumulates memory across sources, so a later transform that forks a Pool inherits a ~10 GB parent and thrashes

Status: Open.

#1046 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 11, 2026

kg transform -s ontologies silently depends on the network for Biolink 2.2.5's context.jsonld, and a DNS blip kills the longest step plus six dependents

Status: Open.

#1045 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 11, 2026

The unified name index carries MediaDive recipe instructions as entity names

Status: Open.

#1009 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 9, 2026

kg-model-review --merged can only read merged-kg.tar.gz, so a variant merge (merge.noprego.yaml) cannot be reviewed without staging it under the canonical name

Status: Open.

#992 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 8, 2026

ontologies_stubs calls ROBOT directly, bypassing robot_utils' atomic output guarantee

Status: Open.

#989 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 8, 2026

LPSN and BacDive can disagree on a deposit's name; KGX merge then turns name into a list

Status: Open.

#984 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 7, 2026

Transform.__init__ deletes and recreates data/raw/nlp/* on construction; side effects belong in run()

Status: Open.

#980 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 7, 2026

kgm.name subject_label is the ASCII-min surface form, so a new capitalisation variant relabels the row

Status: Open.

#979 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 7, 2026

The exporter fingerprint covers the script but not the code it imports

Status: Open.

#974 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 7, 2026

Nothing checks the committed mappings artifact was produced by the exporter in the tree

Status: Open.

#973 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 7, 2026

semsql 0.4.0 (the latest release) still downloads prebuilt DBs from the retired bbop-sqlite bucket

Status: Open.

#964 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 6, 2026

No test covers main(--dry-run) end to end, or the complex_ingredients dry-run path

Status: Open.

#954 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Sep 6, 2026