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Planteome / plant-ontology

Repository for the Plant Ontology
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Getting ontology as LinkML schema? #721

Open serenalotreck opened 8 months ago

serenalotreck commented 8 months ago

I'm trying to use OntoGPT for information extraction, which is a tool that requires a schema input in LinkML format. I'd love to use PO, but I've been unable to figure out how to convert from OWL to LinkML. It seems straightforward to do in the other direction, but no amount of googling has helped me figure out how to go from OWL --> LinkML. My understanding of different ontology specification formats is limited, but I suspect it may be because OWL encodes data beyond just the schema -- however, I'm not sure why that would preclude the schema from being pulled out of an OWL ontology and put into LinkML format.

Wondering if your team has any insights for how to go about doing this?

cmungall commented 8 months ago

Hi @serenalotreck

It's probably best to take this to the OntoGPT tracker. If you want to use PO to ground concepts using OntoGPT then you don't need to convert to LinkML. LinkML is a schema language and PO isn't a schema.

A schema would describe the structure of the objects you want to extract. For example, a schema to extract gene-tissue associations from abstracts would have a GeneExpression class with fields for gene and tissue, the latter configured to use PO.