subClassOf cycles in nmdco-classes.json breaks the nmdc-server ingest

[turbomam]

In recent builds of nmdco-classes.json, there has been a cycle between ChEBI's role CHEBI:50906 and BFO's role BFO:0000023. See image below.

This can be observed by configuring and starting the nmdc-server Docker environment, accessing the backend container's shell and running

nmdc-server ingest

The relevant error here is

Updating NMDC functions for the active database. ... File "/app/nmdc_server/ingest/envo.py", line 29, in populate_envo_ancestor raise Exception(f"Cyclic graph detected ({node})") Exception: Cyclic graph detected (CHEBI:50906)

And comes from https://github.com/microbiomedata/nmdc-server/blame/10cdc936387b7be890890d225b59875f0a83718e/nmdc_server/ingest/envo.py#L16-L29

I believe I found the most recent nmdco-classes.json that does parse, and I retroactively made a release

https://raw.githubusercontent.com/microbiomedata/nmdc-ontology/2024-02-16/nmdco-classes.json

[turbomam]

Moving parts:

• the content in the legacy imports will certainly change over time. See https://github.com/microbiomedata/nmdc-ontology/blob/main/src/ontology/Makefile#L47C1-L47C117
  • EnvO
  • PO
  • RO
• the build processes used by those ontologies may change over time, like the change from Elk 0,4,3 too 0.5.0 reasoning in the EnvO release product
• I have removed the use of relation-graph from the nmdco build process
• I have added an extract of Uberon that requests 2 classes (but gets a lot of other stuff with it)