v0.3.15

Highlights

• Four new templates: alz_treat, gene_extraction, storms, and onto_usage - see below for more details.
• The pubmed-extract and pubmed-annotate commands now allow setting the text segment size (in number of characters) with the max-text-length option. Many LLMs now allow for large contexts, so set this to 100000 or so to parse the full text of a scientific article (along with the --get-pmc option).
  • Example: ontogpt -vvv pubmed-annotate -t storms --get-pmc --model gpt-4o --limit 1 --max-text-length 100000 -o storms_test.yaml "36598999"

What's Changed

• Add template for alternate gene symbol extraction strategy by @caufieldjh in #390
• Template for Alzheimer's Disease extractions from literature; expose the max-text-length option for pubmed_annotate by @caufieldjh in #392
• Add ontology usage extraction template by @caufieldjh in #393
• Fixes #396 by @cmungall in #397
• Adding STORMS checklist by @cmungall in #395
• Bump version to 0.3.15 by @caufieldjh in #398

Full Changelog: v0.3.14...v0.3.15