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Chris Mungall
@cmungall.bsky.social
Berkeley Lab, Environmental Genomics and Systems Biology division. #GeneOntology #MonarchInitiative #AllianceGenome #NationalMicrobimeDataCollaborative #OBOFoundry.
74 followers145 following2 posts
CMcmungall.bsky.social

Glad to see our OntoGPT/SPIRES paper finally out in Bioinformatics! academic.oup.com/bioinformati.... Great work from Harry Caufield who led the study, and all the authors. SPIRES uses a schema and ontology driven approach to extract complex knowledge nuggets from text.

Depiction of schema and ontology-driven workflow of SPIRES. Inputs are a LinkML schema and Text. OntoGPT will recurse through the schema iteratively parsing using an LLM and finally grounding using ontologies specified by LinkML value sets.
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CMcmungall.bsky.social

Our manuscript on using Large Language Models for generating ontology terms is up on arxiv! arxiv.org/abs/2312.10904genomic.social/@Cmungall/11...www.linkedin.com/feed/update/...

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CM
Chris Mungall
@cmungall.bsky.social
Berkeley Lab, Environmental Genomics and Systems Biology division. #GeneOntology #MonarchInitiative #AllianceGenome #NationalMicrobimeDataCollaborative #OBOFoundry.
74 followers145 following2 posts