Richard Bruskiewich

Add additional description property values to Biolink Model classes as required to better inform the user of the model

2

Several Biolink Model classes (perhaps, slots, types and mixins as well) could use better `description` properties

Where do we officially document, with indexing, Biolink modelling for specific scientific use cases?

1

Our primary Biolink Model documentation is extremely helpful, but we (yet) seem to have a systematic repository of examples of using the Biolink Model for specific scientific use cases. This...

Perhaps KGX files should be somewhat self documenting with respect to key parameters like their Biolink Model version

1

Given a KGX file, semantics constraints for its interpretation are not always known _a priori_. In particular, the Biolink Model Version to which the KGX data complies is not documented...

Neo4j Sink (neo_sink.py) CACHE flushing may result in information loss to the graph

1

The observed node and edge counts in target graphs seems smaller than expected with large graphs. This may relate to the number of node records exceeding CACHE_SIZE (set to 100,000...

Integrate JSON _attributes into KGX

3

We wish to integrate JSON "blob" attributes into KGX. The proposed syntax and content is the TRAPI JSON Attribute (https://github.com/NCATSTranslator/ReasonerAPI/blob/v1.1.2/TranslatorReasonerAPI.yaml#L538). One key use case is the [representation of EPC attributes...

Unlike the TSV source module, the JSON lines `source` module doesn't seem to recognize the internal _nodes_ and `edges` jsonlines formatted files (i.e. with file extension `.jsonl`) of an aggregated...

Remove legacy Biolink Model fields like 'relation'

1

KGX needs to be updated to align with the latest Biolink Model standards? See https://github.com/biolink/biolink-model/issues/922 Do we need to keep legacy support of older Biolink Model slots, like `relation`?

Duplication of identifiers in pipe-delimited slot value lists

1

It is (possibly) noted that some fields - e.g. provided_by slot - in KGX sometimes tend to accumulate duplicate (CURIE) identifiers. Rather, such lists should be managed internally as proper...

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