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Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation.
Effects of cromakalim and pinacidil on large epicardial and small coronary arteries in conscious dogs
J F Giudicelli, C D la Rochelle, and A Berdeaux · 1990
Earlier work this paper cites.
Units of measure in clinical information systems
G Schadow, C J McDonald, J G Suico, U Föhring, and T Tolxdorff · 1999
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The medical dictionary for regulatory activities (MedDRA)
Elliot G Brown, Louise Wood, and Sue Wood · 1999
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Risk of transient hyperammonemic encephalopathy in cancer patients who received continuous infusion of 5-fluorouracil with the complication of dehydration and infection
C C Liaw, H M Wang, C H Wang, T S Yang, J S Chen, H K Chang, Y C Lin, S J Liaw, and C T Yeh · 1999
Earlier work this paper cites.
Medical subject headings (MeSH)
C E Lipscomb · 2000
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Language models are Few-Shot learners
Tom B Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, Sandhini Agarwal, Ariel Herbert-Voss, Gretchen Krueger, Tom Henighan, Rewon Child, Aditya Ramesh, Daniel M Ziegler, Jeffrey Wu, Clemens Winter, Christopher Hesse, Mark Chen, Eric Sigler, Mateusz Litwin, Scott Gray, Benjamin Chess, Jack Clark, Christopher Berner, Sam McCandlish, Alec Radford, Ilya Sutskever, and Dario Amodei · 2005
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NCI thesaurus: a semantic model integrating cancer-related clinical and molecular information
Nicholas Sioutos, Sherri de Coronado, Margaret W Haber, Frank W Hartel, Wen-Ling Shaiu, and Lawrence W Wright · 2006
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DBpedia - a crystallization point for the web of data
Christian Bizer, Jens Lehmann, Georgi Kobilarov, Sören Auer, Christian Becker, Richard Cyganiak, and Sebastian Hellmann · 2009
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The open biomedical annotator
Clement Jonquet, Nigam H Shah, and Mark A Musen · 2009
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Long-term lithium therapy leading to hyperparathyroidism: a case report
Mian M Rizwan and Nancy D Perrier · 2009
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BioPortal: enhanced functionality via new web services from the national center for biomedical ontology to access and use ontologies in software applications
P L Whetzel, N F Noy, N H Shah, P R Alexander, C Nyulas, T Tudorache, and M A Musen · 2011
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Wikidata: A new platform for collaborative data collection
Denny Vrandečić · 2012
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Advancing ELK: Not only performance matters
Yevgeny Kazakov and Pavel Klinov · 2015
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UTH-CCB@BioCreative V CDR task: Identifying chemical-induced disease relations in biomedical text
Jun Xu, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Ruiling Liu, Qiang Wei, and Hua Xu · 2015
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The protégé project: A look back and a look forward
Mark A Musen and Protégé Team · 2015
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BioCreative V CDR task corpus: a resource for chemical disease relation extraction
Jiao Li, Yueping Sun, Robin J Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J Mattingly, Thomas C Wiegers, and Zhiyong Lu · 2016
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ChEBI in 2016: Improved services and an expanding collection of metabolites
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, and Christoph Steinbeck · 2016
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, Illia Polosukhin, Lukasz Kaiser, and Illia Polosukhin · 2017
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AgroPortal: A vocabulary and ontology repository for agronomy
Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A Musen, Valeria Pesce, and Pierre Larmande · 2017
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The monarch initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, and Melissa A Haendel · 2017
Earlier work this paper cites.
The reactome pathway knowledgebase
Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas Roca, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek Varusai, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, and Peter D’Eustachio · 2018
Cited alongside, same era.
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
Damion M Dooley, Emma J Griffiths, Gurinder S Gosal, Pier L Buttigieg, Robert Hoehndorf, Matthew C Lange, Lynn M Schriml, Fiona S L Brinkman, and William W L Hsiao · 2018
Cited alongside, same era.
DrugBank 5.0: a major update to the DrugBank database for 2018
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda, Nazanin Assempour, Ithayavani Iynkkaran, Yifeng Liu, Adam Maciejewski, Nicola Gale, Alex Wilson, Lucy Chin, Ryan Cummings, Diana Le, Allison Pon, Craig Knox, and Michael Wilson · 2018
Cited alongside, same era.
Generating ontologies from templates: A Rule-Based approach for capturing regularity
Christian Kindermann, Daniel P Lupp, Uli Sattler, and Evgenij Thorstensen · 2018
Cited alongside, same era.
A review of SHACL: From data validation to schema reasoning for RDF graphs
Paolo Pareti and George Konstantinidis · 2022
Later among the works it cites.
linkml/linkml-owl: v0.2.4
Chris Mungall, Sujay Patil, and Nomi Harris · 2022
Later among the works it cites.
Structured information extraction from complex scientific text with fine-tuned large language models
Alexander Dunn, John Dagdelen, Nicholas Walker, Sanghoon Lee, Andrew S Rosen, Gerbrand Ceder, Kristin Persson, and Anubhav Jain · 2022
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Is ChatGPT a biomedical expert? – exploring the Zero-Shot performance of current GPT models in biomedical tasks
Samy Ateia and Udo Kruschwitz · 2023
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Will generative artificial intelligence deliver on its promise in health care?
Robert M Wachter and Erik Brynjolfsson · 2023
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YAML ain’t markup language (YAML™) version 1.2.2
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The gene ontology resource: 20 years and still GOing strong
The Gene Ontology Consortium · 2019
Cited alongside, same era.
Adoption of BioPortal’s ontology registry software: The emerging OntoPortal community
John Graybeal, Clement Jonquet, Nicola Fiore, and Mark A Musen · 2019
Cited alongside, same era.
OGER : hybrid multi-type entity recognition
Lenz Furrer, Anna Jancso, Nicola Colic, and Fabio Rinaldi · 2019
Cited alongside, same era.
ROBOT: A tool for automating ontology workflows
Rebecca C Jackson, James P Balhoff, Eric Douglass, Nomi L Harris, Christopher J Mungall, and James A Overton · 2019
Cited alongside, same era.
Human disease ontology 2018 update: classification, content and workflow expansion
Lynn M Schriml, Elvira Mitraka, James Munro, Becky Tauber, Mike Schor, Lance Nickle, Victor Felix, Linda Jeng, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion, Brooke Hyman, David Kurland, Connor Patrick Oates, Siobhan Kibbey, Poorna Sreekumar, Chris Le, Michelle Giglio, and Carol Greene · 2019
Cited alongside, same era.
What BERT is not: Lessons from a new suite of psycholinguistic diagnostics for language models
Allyson Ettinger · 2020
Cited alongside, same era.
The 2019 n2c2/OHNLP track on clinical semantic textual similarity: Overview
Yanshan Wang, Sunyang Fu, Feichen Shen, Sam Henry, Ozlem Uzuner, and Hongfang Liu · 2020
Cited alongside, same era.
Quantification of BERT diagnosis generalizability across medical specialties using semantic dataset distance
Mihir P Khambete, William Su, Juan C Garcia, and Marcus A Badgeley · 2021
Cited alongside, same era.
Oren Ben-Kiki, Clark Evans, and Ingy Döt Net · 2023
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OpenAI API
OpenAI · 2023
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http://json-schema.org/ , 2022
JSON schema · 2023
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INCATools/ontology-access-kit: v0.2.1
Chris Mungall, Harshad, Patrick Kalita, Charles Tapley Hoyt, Sujay Patil, Marcin p Joachimiak, Joe Flack, David Linke, Deepak, Sierra Moxon, Nico Matentzoglu, Vinícius de Souza, Glass, Harry Caufield, Jules Jacobsen, Justin Reese, Nomi Harris, and Shawn Tan · 2023
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A new ontology lookup service at EMBL-EBI
Simon Jupp, Tony Burdett, James Malone, Catherine Leroy, Matt Pearce, Julie Mcmurry, and Helen Parkinson · 2023
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LLMs4OL: Large language models for ontology learning
Hamed Babaei Giglou, Jennifer D’Souza, and Sören Auer · 2023
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MapperGPT: Large language models for linking and mapping entities
Nicolas Matentzoglu, J Harry Caufield, Harshad B Hegde, Justin T Reese, Sierra Moxon, Hyeongsik Kim, Nomi L Harris, Melissa A Haendel, and Christopher J Mungall · 2023
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Agent-OM: Leveraging large language models for ontology matching
Zhangcheng Qiang, Weiqing Wang, and Kerry Taylor · 2023
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Llama: Open and efficient foundation language models
Hugo Touvron, Thibaut Lavril, Gautier Izacard, Xavier Martinet, Marie-Anne Lachaux, Timothée Lacroix, Baptiste Rozière, Naman Goyal, Eric Hambro, Faisal Azhar, Aurelien Rodriguez, Armand Joulin, Edouard Grave, and Guillaume Lample · 2023
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Llama-adapter: Efficient fine-tuning of language models with zero-init attention
Renrui Zhang, Jiaming Han, Aojun Zhou, Xiangfei Hu, Shilin Yan, Pan Lu, Hongsheng Li, Peng Gao, and Yu Qiao · 2023
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BioMedGPT: Open multimodal generative pre-trained transformer for BioMedicine
Yizhen Luo, Jiahuan Zhang, Siqi Fan, Kai Yang, Yushuai Wu, Mu Qiao, and Zaiqing Nie · 2023
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Radiology-Llama2: Best-in-Class large language model for radiology
Zhengliang Liu, Yiwei Li, Peng Shu, Aoxiao Zhong, Longtao Yang, Chao Ju, Zihao Wu, Chong Ma, Jie Luo, Cheng Chen, Sekeun Kim, Jiang Hu, Haixing Dai, Lin Zhao, Dajiang Zhu, Jun Liu, Wei Liu, Dinggang Shen, Tianming Liu, Quanzheng Li, and Xiang Li · 2023
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Dead simple OWL design patterns
David Osumi-Sutherland, Melanie Courtot, James P Balhoff, and Christopher Mungall · 2041
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Unifying the identification of biomedical entities with the bioregistry
Charles Tapley Hoyt, Meghan Balk, Tiffany J Callahan, Daniel Domingo-Fernández, Melissa A Haendel, Harshad B Hegde, Daniel S Himmelstein, Klas Karis, John Kunze, Tiago Lubiana, Nicolas Matentzoglu, Julie McMurry, Sierra Moxon, Christopher J Mungall, Adriano Rutz, Deepak R Unni, Egon Willighagen, Donald Winston, and Benjamin M Gyori · 2052
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