The NLP4Biocuration Working Group was formed in March 2025 to evaluate, prototype, and coordinate the integration of natural-language-processing (NLP) and large language model (LLM) tools to support scalable, ontology-driven literature curation across agricultural genomics databases. This effort is conducted under the umbrella of the AgBioData Consortium and is supported by the NSF Research Coordination Network award #2126334, a shared community resource initiative that promotes interoperable informatics solutions. Over the past eight months, working group members performed a coordinated assessment of AI-assisted literature tools, developed shared benchmarking practices, and explored infrastructure options for cross-database deployment. Tools evaluated include BioBERT, Elicit, Textpresso, OntoGPT, and early agentic-AI frameworks, with attention to their utility for named entity recognition, relationship extraction, summarization, and paper prioritization for plant and crop species. Several members implemented pilot pipelines comparing AI-generated literature sets with manually curated datasets, providing practical insights into recall, precision, and model behavior within agriculture-specific contexts. To facilitate shared learning and reproducibility, the group established a structured "tool review" framework and a community repository of test cases, datasets, and documented workflows. A major milestone is the ongoing organization of a Textpresso proof-of-concept deployment tailored for agricultural species. Participating AgBioData resources, including SorghumBase, MaizeGDB, GDR, SoyBase, GrainGenes, and others, are assembling FAIR-compliant gene lists, entity vocabularies, and open-access corpora, and are coordinating with the Alliance of Genome Resources team on compute requirements for a shared AWS-based test environment. In parallel, the group distributed a survey across AgBioData member databases to capture literature volume, workflows, AI adoption, and technical barriers; survey findings are guiding both a manuscript currently in development and continued infrastructure planning. Aligned with FAIR principles, the AgBioData consortium advances sustainable informatics infrastructure. By aligning NLP4Biocuration activities with these principles, the working group is helping establish sustainable informatics infrastructure and analytics-driven methods that benefit the entire agricultural genomics community.
This presentation will cover the AgBioData implementation of Textpresso, including the GUI and programmatic access by API and command line tools.
See also this news blog.