Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity

Copyright and License

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.

Supplemental Material

• Supplementary File S1[supplements/631539_file03.pdf]
• Supplementary Table 1[supplements/631539_file04.xlsx]
• Supplementary Table 1 Caption[supplements/631539_file05.pdf]
• Supplementary Table 2[supplements/631539_file06.csv]
• Supplementary Table 2 Caption[supplements/631539_file07.pdf]

Data Availability

• https://github.com/WormBase/curation-sentence-classification
• https://github.com/WormBase/huggingface-document-classifier
• https://github.com/alliance-genome/agr_sentence_classifier

Acknowledgement

We thank Chris Grove, Ranjana Kishore, and Pengyuan Li for critical feedback on this work. Their insightful comments and constructive suggestions greatly improved the quality and clarity of this publication.

Funding

The ACKnowledge project is funded by RO1 OD023041 from the National Library of Medicine. The Alliance of Genome Resources is funded by U24HG010859 from the National Human Genome Research Institute and the National Heart, Lung and Blood Institute. WormBase and FlyBase are funded by the National Human Genome Research Institute by U24HG002223 and U41HG000739, respectively. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Contributions

Daniela Raciti - Conceptualization, Data curation, Funding acquisition, Investigation, Validation, Writing – original draft, Writing – review & editing Kimberly Van Auken - Conceptualization, Data curation, Funding acquisition, Investigation, Validation, Writing – original draft, Writing – review & editing Valerio Arnaboldi - Conceptualization, Formal Analysis, Funding acquisition, Investigation, Methodology, Software, Writing – original draft, Writing – review & editing