Jeffrey S. Grethe

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 22

Top Topics

Natural Language Processing

Question Answering

Biomedical Data

Top Venues

Neuroinformatics

Frontiers Neuroinformatics

Database J. Biol. Databases Curation

Publications

Nazek Queder, Vivian B. Tien, Sanu Ann Abraham, Sebastian Georg Wenzel Urchs, Karl G. Helmer, Derek Chaplin, Theo G. M. van Erp, David N. Kennedy, Jean-Baptiste Poline, Jeffrey S. Grethe, Satrajit S. Ghosh, David B. Keator
NIDM-Terms: community-based terminology management for improved neuroimaging dataset descriptions and query. Frontiers Neuroinformatics 17 (2023)
Anita E. Bandrowski, Mason Pairish, Peter Eckmann, Jeffrey S. Grethe, Maryann E. Martone
The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res. 51 (D1) (2023)
Ashmita Kumar, Albert Crowley, Nazek Queder, Jean-Baptiste Poline, Satrajit S. Ghosh, David N. Kennedy, Jeffrey S. Grethe, Karl G. Helmer, David B. Keator
The Neuroimaging Data Model Linear Regression Tool (nidm_linreg): PyNIDM Project. F1000Research 11 (2022)
Monique Surles-Zeigler, Troy Sincomb, Thomas H. Gillespie, Bernard de Bono, Jacqueline Bresnahan, Gary M. Mawe, Jeffrey S. Grethe, Susan J. Tappan, Maci L. Heal, Maryann E. Martone
Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. Frontiers Neuroinformatics 16 (2022)
Jean-Baptiste Poline, David N. Kennedy, Friedrich T. Sommer, Giorgio A. Ascoli, David C. Van Essen, Adam R. Ferguson, Jeffrey S. Grethe, Michael Hawrylycz, Paul M. Thompson, Russell A. Poldrack, Satrajit S. Ghosh, David B. Keator, Thomas L. Athey, Joshua T. Vogelstein, Helen S. Mayberg, Maryann E. Martone
Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data. Neuroinformatics 20 (2) (2022)
Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek James Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone
A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinformatics 20 (1) (2022)
Abel Torres-Espin, Carlos A. Almeida, Austin Chou, J. Russell Huie, Michael Chiu, Romana Vavrek, Jeff Sacramento, Michael B. Orr, John C. Gensel, Jeffrey S. Grethe, Maryann E. Martone, Karim Fouad, Adam R. Ferguson, Warren Alilain, Mark Bacon, Nicholas Batty, Michael Beattie, Jacqueline Bresnahan, Emily Burnside, Sarah Busch, Randall Carpenter, Isaac Francos Quijorna, Xiaohui Guo, Agnes Haggerty, Sarah Haroon, Jack Harris, Lyn Jakeman, Linda Jones, Naomi Kleitman, Timothy Kopper, Michael Lane, Francisco Magana, David Magnuson, Ines Maldonado, Verena May, Katelyn McFarlane, Kazuhito Morioka, Martin Oudega, Philip Leo Pascual, Jean-Baptiste Poline, Ephron S. Rosenzweig, Emma Schmidt, Wolfram Tetzlaff, Lana Zholudeva
Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons for Spinal Cord Injury (odc-sci.org). Neuroinformatics 20 (1) (2022)
Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek James Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone
Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinformatics 20 (1) (2022)
Chun-Nan Hsu, Chia-Hui Chang, Thamolwan Poopradubsil, Amanda Lo, Karen A. William, Ko-Wei Lin, Anita E. Bandrowski, Ibrahim Burak Özyurt, Jeffrey S. Grethe, Maryann E. Martone
Antibody Watch: Text mining antibody specificity from the literature. PLoS Comput. Biol. 17 (5) (2021)
Ibrahim Burak Özyurt, Anita E. Bandrowski, Jeffrey S. Grethe
Bio-AnswerFinder: a system to find answers to questions from biomedical texts. Database J. Biol. Databases Curation 2020 (2020)
Chun-Nan Hsu, Anita E. Bandrowski, Tom Gillespie, Jon Udell, Ko-Wei Lin, Ibrahim Burak Özyurt, Jeffrey S. Grethe, Maryann E. Martone
Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software, and Other Digital Artifacts. Comput. Sci. Eng. 22 (2) (2020)
Chun-Nan Hsu, Chia-Hui Chang, Thamolwan Poopradubsil, Amanda Lo, Karen A. William, Ko-Wei Lin, Anita E. Bandrowski, Ibrahim Burak Özyurt, Jeffrey S. Grethe, Maryann E. Martone
Antibody Watch: Text Mining Antibody Specificity from the Literature. CoRR (2020)
David N. Kennedy, Sanu A. Abraham, Julianna F. Bates, Albert Crowley, Satrajit S. Ghosh, Tom Gillespie, Mathias Goncalves, Jeffrey S. Grethe, Yaroslav O. Halchenko, Michael Hanke, Christian Haselgrove, Steven M. Hodge, Dorota Jarecka, Jakub Kaczmarzyk, David B. Keator, Kyle Meyer, Maryann E. Martone, Smruti Padhy, Jean-Baptiste Poline, Nina Preuss, Troy Sincomb, Matt Travers
Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. Frontiers Neuroinformatics 13 (2019)
John D. Van Horn, Sumiko Abe, José Luis Ambite, Teresa K. Attwood, Niall Beard, Louisa Bellis, Avnish Bhattrai, Alex A. T. Bui, Gully Burns, Lily Fierro, Jonathan Gordon, Jeffrey S. Grethe, Jeana Kamdar, Xiaoyu Lei, Kristina Lerman, Annette McGrath, Nicola J. Mulder, Caroline O'Driscoll, Crystal Stewart, Sonika Tyagi
Advancing the international data science workforce through shared training and education. F1000Research 8 (2019)
Ibrahim Burak Özyurt, Jeffrey S. Grethe
Iterative Document Retrieval via Deep Learning Approaches for Biomedical Question Answering. eScience (2019)
Ibrahim Burak Özyurt, Jeffrey S. Grethe
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. Database J. Biol. Databases Curation 2018 (2018)
Xiaoling Chen, Anupama E. Gururaj, Ibrahim Burak Özyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra N. González-Beltrán, Claudiu Farcas, Todd Johnson, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Ian Fore, Lucila Ohno-Machado, Jeffrey S. Grethe, Hua Xu
DataMed - an open source discovery index for finding biomedical datasets. J. Am. Medical Informatics Assoc. 25 (3) (2018)
Chun-Nan Hsu, Anita E. Bandrowski, Jeffrey S. Grethe, Maryann E. Martone
Assessing value of biomedical digital repositories. PeerJ Prepr. 5 (2017)
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
The Resource Identification Initiative: A Cultural Shift in Publishing. Neuroinformatics 14 (2) (2016)
Friedrich T. Sommer, Thomas Wachtler, Jeffrey L. Teeters, Jan Benda, Andrew P. Davison, Stephen J. Eglen, Richard C. Gerkin, Jeffrey S. Grethe, Jan Grewe, Kenneth D. Harris, Christian Johannes Kellner, Yann Le Franc, Roman Moucek, Dimiter Prodanov, Robert Pröpper, Hyrum L. Sessions, Leslie Smith, Andrey Sobolev, Adrian Stoewer, Barry Wark
Requirements for storing electrophysiology data. CoRR (2016)
Hua Xu, Jeffrey S. Grethe, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Yueling Li, Ibrahim Burak Özyurt, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado
Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Groundwork for Biomedical Data Discovery. AMIA (2016)
Jeffrey S. Grethe, Ibrahim Burak Özyurt, Hua Xu, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado
A Scalable Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System. AMIA (2016)
Luis N. Marenco, Rixin Wang, Anita E. Bandrowski, Jeffrey S. Grethe, Gordon M. Shepherd, Perry L. Miller
Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources. Frontiers Neuroinformatics 8 (2014)
Amarnath Gupta, Anita E. Bandrowski, Christopher Condit, Xufei Qian, Jeffrey S. Grethe, Maryann E. Martone
Semantic query reformulation: the NIF experience. SSDBM (2013)
Fahim T. Imam, Stephen D. Larson, Anita E. Bandrowski, Jeffrey S. Grethe, Amarnath Gupta, Maryann E. Martone
Maturation of Neuroscience Information Framework: An Ontology Driven Information System for Neuroscience. FOIS (2012)
Anita E. Bandrowski, Jonathan Cachat, Yuling Li, Hans-Michael Müller, Paul W. Sternberg, Paolo Ciccarese, Tim Clark, Luis N. Marenco, Rixin Wang, Vadim Astakhov, Jeffrey S. Grethe, Maryann E. Martone
A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database J. Biol. Databases Curation 2012 (2012)
Vadim Astakhov, Anita E. Bandrowski, Amarnath Gupta, A. W. Kulungowski, Jeffrey S. Grethe, James Bouwer, T. Molin, V. Rowley, S. Penticoff, Masako Terada, W. Wong, Hiroyuki Hakozaki, O. Kwon, Maryann E. Martone, Mark H. Ellisman
Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics. ICCS (2012)
Syam Gadde, Nicole Aucoin, Jeffrey S. Grethe, David B. Keator, Daniel S. Marcus, Steve Pieper
XCEDE: An Extensible Schema for Biomedical Data. Neuroinformatics 10 (1) (2012)
Shulei Sun, Jing Chen, Weizhong Li, Ilkay Altintas, Abel W. Lin, Steven Peltier, Karen I. Stocks, Eric E. Allen, Mark H. Ellisman, Jeffrey S. Grethe, John C. Wooley
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39 (Database-Issue) (2011)
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
An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. ICBO (2011)
Fahim T. Imam, Stephen D. Larson, Jeffrey S. Grethe, Amarnath Gupta, Anita E. Bandrowski, Maryann E. Martone
NIFSTD and NeuroLex: Comprehensive Neuroscience Ontology Development Based on Multiple Biomedical Ontologies and Community Involvement. ICBO (2011)
Ilkay Altintas, Abel W. Lin, Jing Chen, Chris Churas, Madhusudan Gujral, Shulei Sun, Weizhong Li, Ramil Manansala, Mayya Sedova, Jeffrey S. Grethe, Mark H. Ellisman
CAMERA 2.0: A Data-centric Metagenomics Community Infrastructure Driven by Scientific Workflows. SERVICES (2010)
I. Burak Özyurt, David B. Keator, Dingying Wei, Christine Fennema-Notestine, Karen R. Pease, Henry Jeremy Bockholt, Jeffrey S. Grethe
Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database. Neuroinformatics 8 (4) (2010)
David N. Kennedy, Christian Haselgrove, Robert Buccigrossi, Jeffrey S. Grethe
Software Development for Neuroimaging: Promoting Community Access And Best Practices Through NITRC. ISBI (2009)
Lynn Young, Samson W. Tu, Lakshika Tennakoon, David Vismer, Vadim Astakhov, Amarnath Gupta, Jeffrey S. Grethe, Maryann E. Martone, Amar K. Das, Matthew J. McAuliffe
Ontology driven data integration for autism research. CBMS (2009)
David B. Keator, Dingying Wei, Syam Gadde, Henry Jeremy Bockholt, Jeffrey S. Grethe, Daniel S. Marcus, Nicole Aucoin, Ibrahim Burak Özyurt
Derived data storage and exchange workflow for large-scale neuroimaging analyses on the BIRN grid. Frontiers Neuroinformatics 3 (2009)
David B. Keator, Jeffrey S. Grethe, Daniel S. Marcus, I. Burak Özyurt, Syam Gadde, Shawn N. Murphy, Steve Pieper, Douglas N. Greve, R. Notestine, Henry Jeremy Bockholt, Philip M. Papadopoulos
A National Human Neuroimaging Collaboratory Enabled by the Biomedical Informatics Research Network (BIRN). IEEE Trans. Inf. Technol. Biomed. 12 (2) (2008)
William J. Bug, Giorgio A. Ascoli, Jeffrey S. Grethe, Amarnath Gupta, Christine Fennema-Notestine, Angela R. Laird, Stephen D. Larson, Daniel L. Rubin, Gordon M. Shepherd, Jessica A. Turner, Maryann E. Martone
The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience. Neuroinformatics 6 (3) (2008)
Amarnath Gupta, William J. Bug, Luis N. Marenco, Xufei Qian, Christopher Condit, Arun Rangarajan, Hans-Michael Müller, Perry L. Miller, Brian Sanders, Jeffrey S. Grethe, Vadim Astakhov, Gordon M. Shepherd, Paul W. Sternberg, Maryann E. Martone
Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF). Neuroinformatics 6 (3) (2008)
Daniel Gardner, Huda Akil, Giorgio A. Ascoli, Douglas M. Bowden, William J. Bug, Duncan E. Donohue, David H. Goldberg, Bernice Grafstein, Jeffrey S. Grethe, Amarnath Gupta, Maryam Halavi, David N. Kennedy, Luis N. Marenco, Maryann E. Martone, Perry L. Miller, Hans-Michael Müller, Adrian Robert, Gordon M. Shepherd, Paul W. Sternberg, David C. Van Essen, Robert W. Williams
The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. Neuroinformatics 6 (3) (2008)
Shawn N. Murphy, Michael Mendis, Jeffrey S. Grethe, Randy L. Gollub, David N. Kennedy, Bruce R. Rosen
A Web Portal that Enables Collaborative Use of Advanced Medical Image Processing and Informatics Tools through the Biomedical Informatics Research Network (BIRN). AMIA (2006)
Ron Kikinis, Tina Kapur, Martha Elizabeth Shenton, Jeffrey S. Grethe, Mark H. Ellisman
"Big Science" and Schizophrenia. ISBI (2006)
Vadim Astakhov, Amarnath Gupta, Jeffrey S. Grethe, Edward Ross, David Little, Aylin Yilmaz, Xufei Qian, Simone Santini, Maryann E. Martone, Mark H. Ellisman
Semantically Based Data Integration Environment for Biomedical Research. CBMS (2006)
David B. Keator, Syam Gadde, Jeffrey S. Grethe, Derek V. Taylor, Steven G. Potkin, First Birn
A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics 4 (2) (2006)
Vadim Astakhov, Amarnath Gupta, Simone Santini, Jeffrey S. Grethe
Data Integration in the Biomedical Informatics Research Network (BIRN). DILS (2005)
Jeffrey S. Grethe, Chaitan Baru, Amarnath Gupta, Mark James, Bertram Ludäscher, Maryann E. Martone, Philip M. Papadopoulos, Steven Peltier, Arcot Rajasekar, Simone Santini, Ilya Zaslavsky, Mark H. Ellisman
Biomedical Informatics Research Network: Building a National Collaboratory to Hasten the Derivation of New Understanding and Treatment of Disease. HealthGrid (2005)
Amarnath Gupta, Bertram Ludäscher, Jeffrey S. Grethe, Maryann E. Martone
Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Networks 16 (9) (2003)