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Add rhea and EC curie prefixes to neo4j2owl config - #20

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Robbie1977 merged 1 commit into
pdb-v4_2from
dumps-curie-rhea-ec
Oct 6, 2026
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Robbie1977 merged 1 commit into
pdb-v4_2from
dumps-curie-rhea-ec

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The dumps pipeline logs thousands of lines like:

A namespace does not have a legal namespace ... http://rdf.rhea-db.org/70411
Adding NS: http://rdf.rhea-db.org/70411 to ns2287

Rhea reaction IRIs (http://rdf.rhea-db.org/NNNNN) and UniProt enzyme IRIs
(http://purl.uniprot.org/enzyme/N.N.N.N) end in a bare number, so neo4j2owl
cannot derive a namespace and mints a throwaway nsNNNN prefix for every IRI
(ns2287 to ns2505 in the 5-6 Oct run).

This adds two curie_map entries:

rhea: http://rdf.rhea-db.org/
EC: http://purl.uniprot.org/enzyme/

Effects:

  • The "no legal namespace" / "Adding NS" lines for these IRIs go away.
  • The per-entity prefix list stops growing by one entry per Rhea/EC IRI.
  • short_form / curie for these nodes become stable (rhea_70411) instead of
    depending on processing order (ns2287:http___rdf_rhea_db_org_70411).

Note: this changes short_form and curie values for Rhea/EC nodes in the KB.
Nothing in this repo keys on the old values, but worth a glance before the
next load. The config is fetched from virtualflybrain.org/config/, so the file
needs publishing there for dumps to pick it up.

Not covered here: the "starts with a digit" messages (neo4j2owl change, held
back) and the mangled http://purl.oboInOwllibrary.org/oboInOwl/uberon/core#
namespace, which looks like an upstream data issue.

@Robbie1977
Robbie1977 merged commit bb446ee into pdb-v4_2 Oct 6, 2026
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