Standardize node identifiers and improve provenance - Githubissues

Knowledge-Graph-Hub / kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub

https://knowledge-graph-hub.github.io/kg-obo/getting_started.html

GNU General Public License v3.0

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Standardize node identifiers and improve provenance #172

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

During each transform:

[x] Standardize node prefixes to those in Bioregistry and elsewhere in OBO Foundry using the curies package
[x] Re-map remaining CURIE/IRI prefixes not handled above to appropriate, consistent prefix
[x] Remove 'ghost' nodes (bnodes without any content)
[x] Assign knowledge source values through KGX transform

caufieldjh commented 2 years ago

See https://github.com/linkml/prefixmaps

caufieldjh commented 2 years ago

Several OBOs are not transforming from JSON -> TSV correctly. Only the header is written. Examples: mpath, rxno, wbphenotype.

caufieldjh commented 2 years ago

Also keep seeing this error when getting stats:

Encountered unresolvable error while generating stats: <class 'ImportError'> - cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)

caufieldjh commented 2 years ago

Also, transform of ero fails silently