monarch-initiative / ontogpt

LLM-based ontological extraction tools, including SPIRES
https://monarch-initiative.github.io/ontogpt/
BSD 3-Clause "New" or "Revised" License
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add option to export KGX TSV #138

Open justaddcoffee opened 1 year ago

justaddcoffee commented 1 year ago

per convo in hackathon with @hrshdhgd @caufieldjh @AgranyaGitHub

We could/should consider adding an option to export KGX TSV

This will be useful for the literature -> KG workflow

cmungall commented 1 year ago

This is for any schema or just ones that are biolink compatible.

the general plan is for the core linkml framework to have a generic kgx-like output for any classes that are annotated as being nodes or edges

caufieldjh commented 1 year ago

At minimum, this should be for any schema - so it could rely on linkml functionality for yielding nodes + edges. Adding additional maps for Biolink types, slots, etc. (or maybe these can just be provided as annotations, too) would be very convenient for compatibility but not strictly necessary for now.