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Publication search results
found 34 matches
- 2024
- J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, Hyeongsik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinform. 40(3) (2024) - Anando Sen, Victoria Hedley, Eva Degraeuwe, Steven Hirschfeld, Ronald Cornet, Ramona Walls, John Owen, Peter N. Robinson, Edward G. Neilan, Thomas Liener, Giovanni Nisato, Neena Modi, Simon Woodworth, Avril Palmeri, Ricarda Gaentzsch, Melissa Walsh, Teresa Berkery, Joanne Lee, Laura Persijn, Kasey Baker, Kristina An Haack, Sonia Segovia Simon, Julius O. B. Jacobsen, Giorgio Reggiardo, Melissa A. Kirwin, Jessie Trueman, Claudia Pansieri, Donato Bonifazi, Sinéad Nally, Fedele Bonifazi, Rebecca Leary, Volker Straub:
Learning from conect4children: A Collaborative Approach towards Standardisation of Disease-Specific Paediatric Research Data. Data 9(4): 55 (2024) - Lauren E. Chan, Elena Casiraghi, Justin T. Reese, Quaker E. Harmon, Kevin Schaper, Harshad Hegde, Giorgio Valentini, Charles Schmitt, Alison A. Motsinger-Reif, Janet E. Hall, Christopher J. Mungall, Peter N. Robinson, Melissa A. Haendel:
Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. Int. J. Medical Informatics 187: 105461 (2024) - Gustavo M. C. Coelho, Eduardo Nascimento, Yenier Torres Izquierdo, Grettel M. García, Lucas Feijó, Melissa Lemos, Robinson Luiz Souza Garcia, Aiko R. de Oliveira, João Pinheiro, Marco A. Casanova:
Improving the Accuracy of Text-to-SQL Tools Based on Large Language Models for Real-World Relational Databases. DEXA (1) 2024: 93-107 - Eduardo Nascimento, Grettel M. García, Lucas Feijó, Wendy Victorio, Yenier Torres Izquierdo, Aiko R. de Oliveira, Gustavo M. C. Coelho, Melissa Lemos, Robinson Luiz Souza Garcia, Luiz André P. Paes Leme, Marco A. Casanova:
Text-to-SQL Meets the Real-World. ICEIS (1) 2024: 61-72 - Elvismary Molina de Armas, Geiza Maria Hamazaki da Silva, Yenier Torres Izquierdo, Melissa Lemos, Paulo Vinícius De Lima Britto, Eduardo Thadeu Corseuil, Robinson Luiz Souza Garcia:
A Proposal of a Knowledge Graph for Digital Engineering Systems Integration for Operation and Maintenance Activities in Industrial Plants. SBSI 2024: 67:1-67:10 - 2023
- Lauren E. Chan, Anne E. Thessen, William D. Duncan, Nicolas Matentzoglu, Charles Schmitt, Cynthia J. Grondin, Nicole A. Vasilevsky, Julie A. McMurry, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel:
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. J. Biomed. Semant. 14(1): 3 (2023) - Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner Jr., Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne Davies, James A. Feinstein, Asiyah Y. Lin, Blake Martin, Nicolas A. Matentzoglu, Daniella Meeker, Justin T. Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingmin Aaron Zhang, Joshua C. Denny, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Melissa A. Haendel, Peter N. Robinson, Lawrence E. Hunter, Michael G. Kahn:
Ontologizing health systems data at scale: making translational discovery a reality. npj Digit. Medicine 6 (2023) - Eduardo Nascimento, Grettel García, Wendy Victorio, Melissa Lemos, Yenier Izquierdo, Robinson Luiz Souza Garcia, Luiz André P. Paes Leme, Marco A. Casanova:
A family of natural language interfaces for databases based on ChatGPT and LangChain (short paper). ER (Companion) 2023 - Jia Lin Chua, Qin Xiao, Tong Li, Yajia Gu, Melissa L. Robinson, Kriscia Tapia, Sarah Lewis, Phuong Dung Trieu:
Diagnostic performance characteristics of Chinese radiologists in breast cancer detection with FFDM versus DBT images. Medical Imaging: Image Perception, Observer Performance, and Technology Assessment 2023 - J. Harry Caufield, Tim E. Putman, Kevin Schaper, Deepak R. Unni, Harshad Hegde, Tiffany J. Callahan, Luca Cappelletti, Sierra A. T. Moxon, Vida Ravanmehr, Seth Carbon, Lauren E. Chan, Katherina Cortes, Kent A. Shefchek, Glass Elsarboukh, James P. Balhoff, Tommaso Fontana, Nicolas Matentzoglu, Richard M. Bruskiewich, Anne E. Thessen, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall, Justin T. Reese:
KG-Hub - Building and Exchanging Biological Knowledge Graphs. CoRR abs/2302.10800 (2023) - J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, HyeongSik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. CoRR abs/2304.02711 (2023) - 2022
- Jason A. Thomas, Randi E. Foraker, Noa Zamstein, Jon D. Morrow, Philip R. O. Payne, Adam B. Wilcox, Melissa A. Haendel, Christopher G. Chute, Kenneth R. Gersing, Anita Walden, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Hongfang Liu, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Justin Starren, Christine Suver, Chunlei Wu, Davera Gabriel, Stephanie S. Hong, Kristin Kostka, Harold P. Lehmann, Richard A. Moffitt, Michele Morris, Matvey B. Palchuk, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Mark M. Bissell, Marshall Clark, Andrew T. Girvin, Adam M. Lee, Robert T. Miller, Kellie M. Walters, Yooree Chae, Connor Cook, Alexandra Dest, Racquel R. Dietz, Thomas Dillon, Patricia A. Francis, Rafael Fuentes, Alexis Graves, Andrew J. Neumann, Shawn T. O'Neil, Usman Sheikh, Andréa M. Volz, Elizabeth Zampino, Christopher P. Austin, Samuel Bozzette, Mariam Deacy, Nicole Garbarini, Michael G. Kurilla, Sam G. Michael, Joni L. Rutter, Meredith Temple-O'Connor, Katie Rebecca Bradwell, Amin Manna, Nabeel Qureshi, Mary Morrison Saltz, Julie A. McMurry, Carolyn T. Bramante, Jeremy Richard Harper, Wenndy Hernandez, Farrukh M. Koraishy, Federico Mariona, Saidulu Mattapally, Amit Saha, Satyanarayana Vedula, Yujuan Fu, Nisha Mathews, Ofer Mendelevitch:
Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 29(8): 1350-1365 (2022) - Elena Casiraghi, Rachel Wong, Margaret Hall, Ben D. Coleman, Marco Notaro, Michael D. Evans, Jena S. Tronieri, Hannah Blau, Bryan Laraway, Tiffany J. Callahan, Lauren E. Chan, Carolyn T. Bramante, John B. Buse, Richard A. Moffitt, Til Sturmer, Steven G. Johnson, Yu Raymond Shao, Justin T. Reese, Peter N. Robinson, Alberto Paccanaro, Giorgio Valentini, Jared D. Huling, Kenneth Wilkins:
Tell Bennet, Christopher Chute, Peter DeWitt, Kenneth Gersing, Andrew Girvin, Melissa Haendel, Jeremy Harper, Janos Hajagos, Stephanie Hong, Emily Pfaff, Jane Reusch, Corneliu Antoniescu, Kimberly Robaski: A Methodological Framework for the Comparative Evaluation of Multiple Imputation Methods: Multiple Imputation of Race, Ethnicity and Body Mass Index in the U.S. National COVID Cohort Collaborative. CoRR abs/2206.06444 (2022) - Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner Jr., Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne Davies, James A. Feinstein, Melissa A. Haendel, Asiyah Y. Lin, Blake Martin, Nicolas Matentzoglu, Daniella Meeker, Justin T. Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingman A. Zhang, Peter N. Robinson, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Lawrence E. Hunter, Michael G. Kahn:
Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality. CoRR abs/2209.04732 (2022) - 2021
- Melissa A. Haendel, Christopher G. Chute, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Philip R. O. Payne, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Christine Suver, John Wilbanks, Adam B. Wilcox, Andrew E. Williams, Chunlei Wu, Clair Blacketer, Robert L. Bradford, James J. Cimino, Marshall Clark, Evan W. Colmenares, Patricia A. Francis, Davera Gabriel, Alexis Graves, Raju Hemadri, Stephanie S. Hong, George Hripcsak, Dazhi Jiao, Jeffrey G. Klann, Kristin Kostka, Adam M. Lee, Harold P. Lehmann, Lora Lingrey, Robert T. Miller, Michele Morris, Shawn N. Murphy, Karthik Natarajan, Matvey B. Palchuk, Usman Sheikh, Harold Solbrig, Shyam Visweswaran, Anita Walden, Kellie M. Walters, Griffin M. Weber, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Andrew T. Girvin, Amin Manna, Nabeel Qureshi, Michael G. Kurilla, Sam G. Michael, Lili M. Portilla, Joni L. Rutter, Christopher P. Austin, Ken R. Gersing:
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J. Am. Medical Informatics Assoc. 28(3): 427-443 (2021) - Michael Ripperger, Sarah C. Lotspeich, Drew Wilimitis, Carrie E. Fry, Allison Roberts, Matthew C. Lenert, Charlotte Cherry, Sanura Latham, Katelyn Robinson, Qingxia Chen, Melissa McPheeters, Ben Tyndall, Colin G. Walsh:
Ensemble learning to predict opioid-related overdose using statewide prescription drug monitoring program and hospital discharge data in the state of Tennessee. J. Am. Medical Informatics Assoc. 29(1): 22-32 (2021) - Sebastian Köhler, Michael A. Gargano, Nicolas Matentzoglu, Leigh Carmody, David Lewis-Smith, Nicole A. Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M. Brower, Tiffany J. Callahan, Christopher G. Chute, Johanna L. Est, Peter D. Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L. Harris, Michael Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A. McMurry, Jillian A. Miller, Monica C. Munoz-Torres, Rebecca L. Peters, Christina K. Rapp, Ana Rath, Shahmir A. Rind, Avi Z. Rosenberg, Michael M. Segal, Markus G. Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A. Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
The Human Phenotype Ontology in 2021. Nucleic Acids Res. 49(Database-Issue): D1207-D1217 (2021) - Sung-Ho Lee, Margaret A. Broadwater, Woomi Ban, Tzu-Wen Winnie Wang, Hyeon-Joong Kim, Jaiden Seongmi Dumas, Ryan P. Vetreno, Melissa A. Herman, A. Leslie Morrow, Joyce Besheer, Thomas L. Kash, Charlotte A. Boettiger, Donita L. Robinson, Fulton Crews, Yen-Yu Ian Shih:
An isotropic EPI database and analytical pipelines for rat brain resting-state fMRI. NeuroImage 243: 118541 (2021) - Justin T. Reese, Deepak R. Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent A. Shefchek, Benjamin M. Good, James P. Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall:
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. Patterns 2(1): 100155 (2021) - 2020
- Kent A. Shefchek, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu, Deepak R. Unni, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland:
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 48(Database-Issue): D704-D715 (2020) - Nicole A. Vasilevsky, Shahim Essaid, Nicolas Matentzoglu, Nomi L. Harris, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper). ICBO/ODLS 2020: 1-2 - 2019
- Sebastian Köhler, Leigh Carmody, Nicole A. Vasilevsky, Julius O. B. Jacobsen, Daniel Danis, Jean-Philippe F. Gourdine, Michael A. Gargano, Nomi L. Harris, Nicolas Matentzoglu, Julie A. McMurry, David Osumi-Sutherland, Valentina Cipriani, James P. Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh J. S. Dawkins, Michael Segal, Anna C. Jansen, Ahmed Muaz, Willie H. Chang, Jenna Bergerson, Stanley J. F. Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F. Freeman, Panagiotis I. Sergouniotis, Daniel Durkin, Andrea L. Storm, Marc Hanauer, Michael Brudno, Susan M. Bello, Murat Sincan, Kayli Rageth, Matthew T. Wheeler, Renske Oegema, Halima Lourghi, Maria G. Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C. Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin Aaron Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia L. Smith, Joshua D. Milner, Dorothée Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa A. Haendel, Chris Mungall, Peter N. Robinson:
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 47(Database-Issue): D1018-D1027 (2019) - Xingmin Aaron Zhang, Amy Yates, Nicole A. Vasilevsky, Jean-Philippe F. Gourdine, Tiffany J. Callahan, Leigh C. Carmody, Daniel Danis, Marcin P. Joachimiak, Vida Ravanmehr, Emily R. Pfaff, James Champion, Kimberly Robasky, Hao Xu, Karamarie Fecho, Nephi A. Walton, Richard L. Zhu, Justin Ramsdill, Christopher J. Mungall, Sebastian Köhler, Melissa A. Haendel, Clement J. McDonald, Daniel J. Vreeman, David B. Peden, Tellen D. Bennett, James A. Feinstein, Blake Martin, Adrianne L. Stefanski, Lawrence E. Hunter, Christopher G. Chute, Peter N. Robinson:
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. npj Digit. Medicine 2 (2019) - Daniel S. Katz, Daina Bouquin, Neil P. Chue Hong, Jessica Hausman, Catherine Mary Jones, Daniel Chivvis, Tim Clark, Mercè Crosas, Stephan Druskat, Martin Fenner, Tom Gillespie, Alejandra N. González-Beltrán, Morane Gruenpeter, Ted Habermann, Robert Haines, Melissa Harrison, Edwin A. Henneken, Lorraine J. Hwang, Matthew B. Jones, Alastair A. Kelly, David N. Kennedy, Katrin Leinweber, Fernando Rios, Carly Robinson, Ilian T. Todorov, Mingfang Wu, Qian Zhang:
Software Citation Implementation Challenges. CoRR abs/1905.08674 (2019) - 2017
- Sebastian Köhler, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie A. McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske, Patrick F. Chinnery, Valentina Cipriani, Laureen E. Connell, Hugh J. S. Dawkins, Laura E. DeMare, Andrew Devereau, Bert B. A. de Vries, Helen V. Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna Jähn, Roger James, Roland Krause, Stanley J. F. Laulederkind, Hanns Lochmüller, Gholson J. Lyon, Soichi Ogishima, Annie Olry, Willem H. Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H. Scott, Michael Segal, Panagiotis I. Sergouniotis, Richard Sever, Cynthia L. Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W. M. Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O. B. Jacobsen, Tudor Groza, Damian Smedley, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
The Human Phenotype Ontology in 2017. Nucleic Acids Res. 45(Database-Issue): D865-D876 (2017) - Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles D. Borromeo, Matthew H. Brush, Seth Carbon, Tom Conlin, Nathan A. Dunn, Mark Engelstad, Erin Foster, Jean-Philippe F. Gourdine, Julius O. B. Jacobsen, Dan Keith, Bryan Laraway, Suzanna E. Lewis, Jeremy NguyenXuan, Kent A. Shefchek, Nicole A. Vasilevsky, Zhou Yuan, Nicole L. Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Melissa A. Haendel:
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 45(Database-Issue): D712-D722 (2017) - Nicole A. Vasilevsky, James P. Balhoff, Christopher J. Mungall, David Osumi-Sutherland, Sebastian Köhler, Susan M. Bello, Cynthia L. Smith, Peter N. Robinson, Melissa A. Haendel:
Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns. ICBO 2017 - 2016
- Rebecca Lake, Ling Li, Melissa T. Baysari, Mary Byrne, M. Robinson, Johanna I. Westbrook:
Capturing Accurate and Useful Information on Medication-Related Telenursing Triage Calls. HIC 2016: 74-79 - Robin E. Mays, Melissa O. Braxton, Andrew B. L. Berry, John Robinson:
Considering Practitioner-Driven Innovations: Accommodating Information Systems Within Successful Humanitarian Work. ICE/ITMC 2016: 1-9
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