Melissa A. Haendel

According to our database, Melissa A. Haendel authored at least 92 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

An evaluation of GPT models for phenotype concept recognition.

Tudor Groza, J. Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall, Justin T. Reese

BMC Medical Informatics Decis. Mak., December, 2024

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).

Sabrina Toro, Anna V. Anagnostopoulos, Susan M. Bello, Kai Blumberg, Rhiannon Cameron, Leigh Carmody, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Petra Fey, Pascale Gaudet, Nomi L. Harris, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig-Barbe, Justin T. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall

J. Biomed. Semant., December, 2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

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

Bioinform., March, 2024

Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests.

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

Int. J. Medical Informatics, 2024

The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization.

Kathleen R. Mullen, Imke Tammen, Nicolas A. Matentzoglu, Marius Mather, Christopher J. Mungall, Melissa A. Haendel, Frank W. Nicholas, Sabrina Toro, the Vertebrate Breed Ontology Consortium

CoRR, 2024

2023

The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond.

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

J. Biomed. Semant., December, 2023

An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C).

Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu

J. Am. Medical Informatics Assoc., November, 2023

De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the <i>All of Us</i> data repository.

Emily R. Pfaff, Andrew T. Girvin, Miles Crosskey, Srushti Gangireddy, Hiral Master, Wei-Qi Wei, Vern Eric Kerchberger, Mark G. Weiner, Paul A. Harris, Melissa A. Basford, Christopher Lunt, Christopher G. Chute, Richard A. Moffitt, Melissa A. Haendel

J. Am. Medical Informatics Assoc., June, 2023

Biomonitoring and precision health in deep space supported by artificial intelligence.

Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-Min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart J. Chalk, Guillermo M. Delgado-Aparicio, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Héctor García Martín, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes

Nat. Mac. Intell., March, 2023

Biological research and self-driving labs in deep space supported by artificial intelligence.

Lauren M. Sanders, Ryan T. Scott, Jason H. Yang, Amina Ann Qutub, Héctor García Martín, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart J. Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Seung-Min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes

Nat. Mac. Intell., March, 2023

Ontologizing health systems data at scale: making translational discovery a reality.

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

npj Digit. Medicine, 2023

Clinical encounter heterogeneity and methods for resolving in networked EHR data: a study from N3C and RECOVER programs.

Peter Leese, Adit Anand, Andrew T. Girvin, Amin Manna, Saaya Patel, Yun Jae Yoo, Rachel Wong, Melissa A. Haendel, Christopher G. Chute, Tellen D. Bennett, Janos G. Hajagos, Emily R. Pfaff, Richard A. Moffitt

J. Am. Medical Informatics Assoc., 2023

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).

Sabrina Toro, Anna V. Anagnostopoulos, Sue Bello, Kai Blumberg, Rhiannon Cameron, Leigh Carmody, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Petra Fey, Pascale Gaudet, Nomi L. Harris, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig, Justin P. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall

CoRR, 2023

MapperGPT: Large Language Models for Linking and Mapping Entities.

Nicolas Matentzoglu, J. Harry Caufield, Harshad B. Hegde, Justin T. Reese, Sierra A. T. Moxon, Hyeongsik Kim, Nomi L. Harris, Melissa A. Haendel, Christopher J. Mungall

CoRR, 2023

KG-Hub - Building and Exchanging Biological Knowledge Graphs.

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

CoRR, 2023

2022

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).

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

J. Am. Medical Informatics Assoc., 2022

Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative.

Emily R. Pfaff, Andrew T. Girvin, Davera Gabriel, Kristin Kostka, Michele Morris, Matvey B. Palchuk, Harold P. Lehmann, Benjamin R. C. Amor, Mark Bissell, Katie R. Bradwell, Sigfried Gold, Stephanie S. Hong, Johanna Loomba, Amin Manna, Julie A. McMurry, Emily Niehaus, Nabeel Qureshi, Anita Walden, Xiaohan Tanner Zhang, Richard L. Zhu, Richard A. Moffitt, Christopher G. Chute, William G. Adams, Shaymaa Al-Shukri, Alfred Anzalone, Ahmad Baghal, Tellen D. Bennett, Elmer V. Bernstam, Mark M. Bissell, Brian Bush, Thomas R. Campion Jr., Victor Castro, Jack Chang, Deepa D. Chaudhari, Wenjin Chen, San Chu, James J. Cimino, Keith A. Crandall, Mark Crooks, Sara J. Deakyne Davies, John Dipalazzo, David A. Dorr, Dan Eckrich, Sarah E. Eltinge, Daniel G. Fort, George Golovko, Snehil Gupta, Melissa A. Haendel, Janos G. Hajagos, David A. Hanauer, Brett M. Harnett, Ronald Horswell, Nancy Huang, Steven G. Johnson, Michael Kahn, Kamil Khanipov, Curtis Kieler, Katherine Ruiz De Luzuriaga, Sarah E. Maidlow, Ashley Martinez, Jomol Mathew, James C. McClay, Gabriel McMahan, Brian Melancon, Stéphane M. Meystre, Lucio Miele, Hiroki Morizono, Ray Pablo, Lav P. Patel, Jimmy Phuong, Daniel J. Popham, Claudia P. Pulgarin, Carlos Santos, Indra Neil Sarkar, Nancy Sazo, Soko Setoguchi, Selvin Soby, Sirisha Surampalli, Christine Suver, Uma Maheswara Reddy Vangala, Shyam Visweswaran, James von Oehsen, Kellie M. Walters, Laura K. Wiley, David A. Williams, Adrian H. Zai

J. Am. Medical Informatics Assoc., 2022

Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset.

Katie R. Bradwell, Jacob T. Wooldridge, Benjamin R. C. Amor, Tellen D. Bennett, Adit Anand, Carolyn Bremer, Yun Jae Yoo, Zhenglong Qian, Steven G. Johnson, Emily R. Pfaff, Andrew T. Girvin, Amin Manna, Emily Niehaus, Stephanie S. Hong, Xiaohan Tanner Zhang, Richard L. Zhu, Mark Bissell, Nabeel Qureshi, Joel H. Saltz, Melissa A. Haendel, Christopher G. Chute, Harold P. Lehmann, Richard A. Moffitt

J. Am. Medical Informatics Assoc., 2022

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality.

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

CoRR, 2022

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies.

Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland

CoRR, 2022

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science.

Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew H. Brush, Richard M. Bruskiewich, Paul A. Clemons, Vlado Dancík, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim E. Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall

CoRR, 2022

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.

Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland

Database J. Biol. Databases Curation, 2022

A Simple Standard for Sharing Ontological Mappings (SSSOM).

Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall

Database J. Biol. Databases Curation, 2022

Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO).

Sabrina Toro, Nicolas Matentzoglu, Kathleen R. Mullen, Nicole A. Vasilevsky, Halie Rando, Melissa A. Haendel, Christopher J. Mungall, Zhi-Liang Hu, Gregoire Leroy, Imke Tammen, Frank W. Nicholas

Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022

From Survey to Ontology, the Challenges and Opportunities in Ontologizing Questions and Answers.

Lauren E. Chan, Jimmy Phuong, Anne E. Thessen, Stephanie S. Hong, Shahim Essaid, Melissa A. Haendel

Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022

Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid.

Saurav Sengupta, Johanna Loomba, Suchetha Sharma, Donald E. Brown, Lorna E. Thorpe, Melissa A. Haendel, Christopher G. Chute, Stephanie S. Hong

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.

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

Patterns, 2021

The Human Phenotype Ontology in 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

Nucleic Acids Res., 2021

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

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

J. Am. Medical Informatics Assoc., 2021

Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs.

Lauren M. Sanders, Jason H. Yang, Ryan T. Scott, Amina Ann Qutub, Héctor García Martín, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart J. Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Seung-Min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes

CoRR, 2021

Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health.

Ryan T. Scott, Erik L. Antonsen, Lauren M. Sanders, Jaden J. A. Hastings, Seung-Min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart J. Chalk, Guillermo M. Delgado-Aparicio, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Héctor García Martín, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes

CoRR, 2021

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C).

Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu

CoRR, 2021

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Mélanie Courtot, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters

Database J. Biol. Databases Curation, 2021

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research.

Lauren E. Chan, Nicole A. Vasilevsky, Anne E. Thessen, Julie A. McMurry, Melissa A. Haendel

Database J. Biol. Databases Curation, 2021

Reclassification of Infectious Disease in the Mondo Disease Ontology.

Nicole A. Vasilevsky, Sabrina Toro, Nicolas Matentzoglu, Dazhi Jiao, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall

Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021

The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics.

Sierra A. T. Moxon, Harold Solbrig, Deepak R. Unni, Dazhi Jiao, Richard M. Bruskiewich, James P. Balhoff, Gaurav Vaidya, William D. Duncan, Harshad Hegde, Mark Miller, Matthew H. Brush, Nomi L. Harris, Melissa A. Haendel, Christopher J. Mungall

Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021

A Semantic Model Leveraging Pattern-based Ontology Terms to Bridge Environmental Exposures and Health Outcomes.

Lauren E. Chan, Nicole A. Vasilevsky, Anne E. Thessen, Nicolas Matentzoglu, William D. Duncan, Christopher J. Mungall, Melissa A. Haendel

Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021

2020

Transforming the study of organisms: Phenomic data models and knowledge bases.

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel

PLoS Comput. Biol., 2020

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

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

Nucleic Acids Res., 2020

Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology.

William D. Duncan, Thankam Thyvalikakath, Melissa A. Haendel, Carlo Torniai, Pedro Hernández, Mei Song, Amit Acharya, Daniel J. Caplan, Titus Schleyer, Alan Ruttenberg

J. Biomed. Semant., 2020

Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper).

Nicole A. Vasilevsky, Shahim Essaid, Nicolas Matentzoglu, Nomi L. Harris, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall

Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020

Global research consortia and data harmonization projects drive the clinical interpretation of cancers.

Justin Guinney, Subha Madhavan, Melissa A. Haendel, Alex H. Wagner, Ratna R. Thangudu

Proceedings of the AMIA 2020, 2020

2019

Ten quick tips for biocuration.

Y. Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C. Munoz-Torres, Drashtti Vasant, Eleanor Williams, Melissa A. Haendel

PLoS Comput. Biol., 2019

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery.

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

npj Digit. Medicine, 2019

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

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

Nucleic Acids Res., 2019

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery.

Jean-Philippe F. Gourdine, Matthew H. Brush, Nicole A. Vasilevsky, Kent A. Shefchek, Sebastian Köhler, Nicolas Matentzoglu, Monica C. Munoz-Torres, Julie A. McMurry, Xingmin Aaron Zhang, Peter N. Robinson, Melissa A. Haendel

Database J. Biol. Databases Curation, 2019

Architecting Attribution: expanding the scope of academic credit.

Kristi L. Holmes, Nicole A. Vasilevsky, Marijane White, Matthew H. Brush, Lisa O'Keefe, Karen Gutzman, Melissa A. Haendel

Proceedings of Workshop on Research Objects (RO2019), 2019

2018

Making it count: a computational approach to attribution.

Kristi L. Holmes, Karen Gutzman, Patricia Smith, David Eichmann, Melissa A. Haendel

Proceedings of Workshop on Research Objects (RO2018), 2018

Expanding the Molecular Glycophenotype Ontology to include model organisms and acquired diseases.

Jean-Philippe F. Gourdine, Nicole A. Vasilevsky, Lilly Winfree, Matthew H. Brush, Melissa A. Haendel

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

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 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

Nucleic Acids Res., 2017

The Human Phenotype Ontology in 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

Nucleic Acids Res., 2017

OpenVIVO: Transparency in Scholarship.

Violeta Ilik, Michael Conlon, Graham Triggs, Marijane White, Muhammad Javed, Matthew H. Brush, Karen Gutzman, Shahim Essaid, Paul Friedman, Simon Porter, Martin Szomszor, Melissa Anne Haendel, David Eichmann, Kristi L. Holmes

Frontiers Res. Metrics Anal., 2017

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus.

Michael Bada, Nicole A. Vasilevsky, William A. Baumgartner Jr., Melissa A. Haendel, Lawrence E. Hunter

Database J. Biol. Databases Curation, 2017

Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns.

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

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

Tailoring the NCI Thesaurus for Use in The OBO Library.

James P. Balhoff, Matthew H. Brush, Laura Christopherson, Sherri de Coronado, Gilberto Fragoso, Melissa A. Haendel, Christopher J. Mungall, Kimberly Robasky, Nicole A. Vasilevsky, Lawrence W. Wright

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

2016

The Resource Identification Initiative: A Cultural Shift in Publishing.

Anita E. Bandrowski, Matthew H. Brush, Jeffrey S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean L. Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena S. Tan, Nicole L. Washington, Elena V. Zudilova-Seinstra, Nicole A. Vasilevsky

Neuroinformatics, 2016

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall

J. Biomed. Semant., 2016

Session Introduction.

Melissa A. Haendel, Maricel G. Kann, Nicole L. Washington

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Enhancing SciENcv through Semantic Research Profile Integration with the VIVO-ISF Ontology.

Marijane White, Matthew H. Brush, Shahim Essaid, Robin Champieux, Adrienne Zell, Melissa A. Haendel, Colin Grove, Syeda Momina Tabish, David Eichmann

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Enhancing the Human Phenotype Ontology for Use by the Layperson.

Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Chris Mungall, Peter N. Robinson, Sebastian Köhler, Melissa A. Haendel

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases.

Jean-Philippe F. Gourdine, Thomas O. Metz, David Koeller, Matthew H. Brush, Melissa A. Haendel

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

SEPIO: A Semantic Model for the Integration and Analysis of Scientific Evidence.

Matthew H. Brush, Kent A. Shefchek, Melissa A. Haendel

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions.

Michael Bada, Nicole A. Vasilevsky, Melissa A. Haendel, Lawrence Hunter

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015

Achieving human and machine accessibility of cited data in scholarly publications.

Joan Starr, Eleni Castro, Mercè Crosas, Michel Dumontier, Robert R. Downs, Ruth E. Duerr, Laurel L. Haak, Melissa A. Haendel, Iván Herman, Simon Hodson, Joe Hourclé, John Ernest Kratz, Jennifer Lin, Lars Holm Nielsen, Amy Nurnberger, Stefan Pröll, Andreas Rauber, Simone Sacchi, Arthur P. Smith, Michael Taylor, Tim Clark

PeerJ Prepr., 2015

Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.

Christopher Ochs, Yehoshua Perl, James Geller, Melissa A. Haendel, Matthew H. Brush, Sivaram Arabandi, Samson W. Tu

J. Biomed. Informatics, 2015

2014

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Sebastian Köhler, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig, Andrew P. Jackson, Kathleen Freson, Marta Gîrdea, Ingo Helbig, Jane A. Hurst, Johanna Jähn, Laird G. Jackson, Anne M. Kelly, David H. Ledbetter, Sahar Mansour, Christa L. Martin, Celia Moss, Andrew D. Mumford, Willem H. Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H. Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J. Wapner, Andrew O. M. Wilkie, Caroline F. Wright, Anneke T. Vulto-van Silfhout, Nicole de Leeuw, Bert B. A. de Vries, Nicole L. Washington, Cynthia L. Smith, Monte Westerfield, Paul N. Schofield, Barbara J. Ruef, Georgios V. Gkoutos, Melissa A. Haendel, Damian Smedley, Suzanna E. Lewis, Peter N. Robinson

Nucleic Acids Res., 2014

A sea of standards for omics data: sink or swim?

Jessica D. Tenenbaum, Susanna-Assunta Sansone, Melissa A. Haendel

J. Am. Medical Informatics Assoc., 2014

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.

Robert W. Thacker, Maria Díaz, Adeline Kerner, Régine Vignes-Lebbe, Erik Segerdell, Melissa A. Haendel, Christopher J. Mungall

J. Biomed. Semant., 2014

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.

Ceri E. Van Slyke, Yvonne M. Bradford, Monte Westerfield, Melissa A. Haendel

J. Biomed. Semant., 2014

CLO: The cell line ontology.

Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He

J. Biomed. Semant., 2014

The influence of disease categories on gene candidate predictions from model organism phenotypes.

Anika Oellrich, Sebastian Köhler, Nicole L. Washington, Chris Mungall, Suzanna Lewis, Melissa A. Haendel, Peter N. Robinson, Damian Smedley

J. Biomed. Semant., 2014

Thematic series on biomedical ontologies in JBMS: challenges and new directions.

Robert Hoehndorf, Dietrich Rebholz-Schuhmann, Melissa A. Haendel, Robert Stevens

J. Biomed. Semant., 2014

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Melissa A. Haendel, James P. Balhoff, Frederic B. Bastian, David C. Blackburn, Judith A. Blake, Yvonne M. Bradford, Aurélie Comte, Wasila M. Dahdul, Thomas Dececchi, Robert E. Druzinsky, Terry F. Hayamizu, Nizar Ibrahim, Suzanna E. Lewis, Paula M. Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C. Sereno, Christopher J. Mungall

J. Biomed. Semant., 2014

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.

Wasila M. Dahdul, Hong Cui, Paula M. Mabee, Christopher J. Mungall, David Osumi-Sutherland, Ramona L. Walls, Melissa A. Haendel

J. Biomed. Semant., 2014

2013

Ontology based molecular signatures for immune cell types via gene expression analysis.

Terrence F. Meehan, Nicole A. Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl

BMC Bioinform., 2013

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu

Database J. Biol. Databases Curation, 2013

Finding common ground: integrating the eagle-i and VIVO ontologies.

Carlo Torniai, Shahim Essaid, Brian Lowe, Jon Corson-Rikert, Melissa A. Haendel

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

eagle-i: ontology-driven federated search and data entry tools for discovering biomedical research resources.

Melissa A. Haendel, Carlo Torniai, Nicole A. Vasilevsky, Scott Hoffmann, Daniela Bourges-Waldegg

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Enabling semantic search in a bio-specimen repository.

Shahim Essaid, Carlo Torniai, Melissa A. Haendel

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights.

Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data.

Matthew H. Brush, Chris Mungall, Nicole L. Washington, Melissa A. Haendel

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

2012

Research resources: curating the new eagle-i discovery system.

Nicole A. Vasilevsky, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew H. Brush, Erik Segerdell, Melanie Wilson, Chris Shaffer, David Robinson, Melissa A. Haendel

Database J. Biol. Databases Curation, 2012

2011

Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned.

Carlo Torniai, Matthew H. Brush, Nicole A. Vasilevsky, Erik Segerdell, Melanie Wilson, Tenille Johnson, Karen Corday, Chris Shaffer, Melissa A. Haendel

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Modularization for the Cell Ontology.

Christopher J. Mungall, Melissa A. Haendel, Amelia Ireland, Shahid Manzoor, Terry Meehan, David Osumi-Sutherland, Carlo Torniai, Alexander D. Diehl

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases.

Chris Mungall, David Anderson, Anita E. Bandrowski, Brian A. Canada, Andrew Chatr-aryamontri, Keith C. Cheng, P. Michael Conn, Kara Dolinski, Mark H. Ellisman, Janan T. Eppig, Jeffrey S. Grethe, Joseph W. Kemnitz, Shawn Iadonato, Stephen D. Larson, Charles Magness, Maryann E. Martone, Mike Tyers, Carlo Torniai, Olga G. Troyanskaya, Judith Turner, Monte Westerfield, Melissa A. Haendel

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Aligning Research Resource and Researcher Representation: The eagle-i and VIVO Use Case.

Stella Mitchell, Carlo Torniai, Brian Lowe, Jon Corson-Rikert, Melanie Wilson, Mansoor Ahmed, Shanshan Chen, Ying Ding, Nicholas Rejack, Melissa A. Haendel

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Developing a Reagent Application Ontology within the OBO Foundry Framework.

Matthew H. Brush, Nicole A. Vasilevsky, Carlo Torniai, Tenille Johnson, Chris Shaffer, Melissa A. Haendel

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2008

CARO - The Common Anatomy Reference Ontology.

Melissa A. Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr., Chris Mungall, Barry Smith

Proceedings of the Anatomy Ontologies for Bioinformatics, Principles and Practice, 2008

The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.

Judy Sprague, Leyla Bayraktaroglu, Yvonne M. Bradford, Tom Conlin, Nathan A. Dunn, David Fashena, Ken Frazer, Melissa A. Haendel, Douglas G. Howe, Jonathan Knight, Prita Mani, Sierra A. T. Moxon, Christian Pich, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Xiang Shao, Amy Singer, Peiran Song, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield

Nucleic Acids Res., 2008

NLP and Phenotypes: using Ontologies to link Human Diseases to Animal Models.

Nicole L. Washington, M. Gibson, Chris Mungall, Michael Ashburner, Georgios V. Gkoutos, Monte Westerfield, Melissa A. Haendel, Suzanna E. Lewis

Proceedings of the Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03., 2008

2007

OBO-Edit - an ontology editor for biologists.

John Day-Richter, Midori A. Harris, Melissa A. Haendel, Suzanna Lewis

Bioinform., 2007

2006

The Zebrafish Information Network: the zebrafish model organism database.

Judy Sprague, Leyla Bayraktaroglu, Dave Clements, Tom Conlin, David Fashena, Ken Frazer, Melissa A. Haendel, Douglas G. Howe, Prita Mani, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, Sierra Taylor, Ceri E. Van Slyke, Monte Westerfield

Nucleic Acids Res., 2006