Sebastian Lobentanzer

There are two tasks that can take a while in creating a BioCypher KG: - tree visualisation (endless loop) - ontology adapter creation (issue with slow response from identifiers.org) While...

Downstream reasoning and interpretation are dependent on having information regarding the structure of ontology underlying each specific graph. Convert the ontological structure derived from the configuration YAML to a subnetwork...

If we have multiple concatenated source types that should be merged to one target type, such as the host of protein_protein_... interactions in the OTAR graph; should we allow using...

Resource adapters should provide a harmonised (ontology) overview of the resource contents, and if two resources overlap in a node or edge content, there should be an alert.

We can download files, compressed files, lists of files; a great addition would be to cache the results of API requests.

User does not need to specify the file prefix in the standard use case. https://biocypher.org/neo4j.html

Could add parameter to resource url spec

I remove those nodes in https://github.com/biocypher/biocypher/blob/06389f5c96675cb19700f4abb9aee5af8e18ca52/biocypher/_ontology.py#L255, but it would still be interesting where they come from and whether they can be prevented.