Comments (3)
deepakunni3
commented on August 16, 2024
Would it make sense to just generate a UUID for every edge added into the networkx MultiDiGraph?
I did play around with assigning unique edge IDs, when not available, in NeoTransformer. Not sure if there is more to the specification.
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deepakunni3
commented on August 16, 2024
Currently KGX has edge IDs via a key of subject-predicate-object. Of course this is less than ideal.
The most accommodating would be to have a UUID for each edge. The disadvantage here is that there will be no merging of edges since each edge is treated as unique. Perhaps this is not a problem at all.
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deepakunni3
commented on August 16, 2024
IDs for edges can be seen as serving two purposes:
- uniquely locating an edge
- merging edges between graphs
We now generate UUIDs for edges. Addressed as part of #214
But we still merge edges based on a criteria of SPO. This criteria can be made configurable in future iterations.
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Related Issues (20)
- add documentation to the kgx merge doc that shows when to use cat-merge as well as a set of steps to use merge config
- Dynamic configuration of Biolink Model semantics in KGX validation
- Knowledge Graph Exchange (KGE) Archive Download
- neo_sink.py constraints not created in neo4j v5+
- Do the KGX serialization formats support representation of Biolink qualifiers? HOT 2
- Error occurs when specifying a version starting with "v" in get_biolink_model_schema method HOT 1
- remove pinning of docutils==0.16.0 so that downstream users can also use sphinx
- Option to add un-prefixed labels in neo4j labels
- Automate mapping of infores in primary_knowledge_source HOT 1
- Fetching biolink-model for validate is confused by `v` in biolink version HOT 1
- run kgx validate from inside the project - need scripts defined in pyproject.toml HOT 2
- kgx validate `-o` option writes an empty file, output goes to stderr rather than stdout
- log_error in validation scales poorly HOT 1
- add SQL sink
- When translating kgx tsvs to ntriples, type assertions are wrong
- update KGX to optionally provide "retrieval_source_ids" attribute to collect information retrieval properties
- Relax KGX's `pandas` version dependency.
- KGX merge overwrites "provided_by" property
- Obsolete/Deprecated property is not populated when converting from obojson HOT 15
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