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Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.
Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, Kim H, Moxon S, Reese JT, Haendel MA, Robinson PN, Mungall CJ. Caufield JH, et al. Among authors: kim h. Bioinformatics. 2024 Mar 4;40(3):btae104. doi: 10.1093/bioinformatics/btae104. Bioinformatics. 2024. PMID: 38383067 Free PMC article.
Gene Set Summarization Using Large Language Models.
Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Joachimiak MP, et al. Among authors: kim h. ArXiv [Preprint]. 2024 Jul 4:arXiv:2305.13338v3. ArXiv. 2024. PMID: 37292480 Free PMC article. Preprint.
A Simple Standard for Sharing Ontological Mappings (SSSOM).
Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde HB, Hoyt AL, Hoyt CT, Jiao D, Jiménez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ. Matentzoglu N, et al. Among authors: kim h. Database (Oxford). 2022 May 25;2022:baac035. doi: 10.1093/database/baac035. Database (Oxford). 2022. PMID: 35616100 Free PMC article.
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.
Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Matentzoglu N, et al. Among authors: kim h. Database (Oxford). 2022 Oct 8;2022:baac087. doi: 10.1093/database/baac087. Database (Oxford). 2022. PMID: 36208225 Free PMC article.
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