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ORCIDSierra A. T. Moxon
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- affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Journal Articles
- 2024
[j10]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)- 2022
- [j9]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 B. 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:
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022(2022) (2022) - 2021
- [j8]Douglas G. Howe, Sridhar Ramachandran, Yvonne M. Bradford, David Fashena, Sabrina Toro, Anne E. Eagle, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock, Christian Pich, Leyla Ruzicka, Kevin Schaper, Xiang Shao, Amy Singer, Ceri E. Van Slyke, Monte Westerfield:
The Zebrafish Information Network: major gene page and home page updates. Nucleic Acids Res. 49(Database-Issue): D1058-D1064 (2021) - 2020
- [j7]Julie Agapite, Laurent-Philippe Albou, Suzi A. Aleksander, Joanna Argasinska, Valerio Arnaboldi, Helen Attrill, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jae-Hyoung Cho, Karen R. Christie, Madeline A. Crosby, Jeff de Pons, Mary E. Dolan, Gilberto dos Santos, Barbara Dunn, Nathan A. Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Ken Frazer, Sibyl Gao, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Todd W. Harris, Marie-Claire Harrison, Douglas G. Howe, Kevin L. Howe, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Stanley J. F. Laulederkind, Raymond Y. N. Lee, Kevin A. MacPherson, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Stuart R. Miyasato, Sierra A. T. Moxon, Hans-Michael Müller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S. Nash, Patrick Ng, Michael Paulini, Norbert Perrimon, Christian Pich, Daniela Raciti, Joel E. Richardson, Matthew Russell, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Mary Shimoyama, Matt Simison, Cynthia L. Smith, David R. Shaw, Ajay Shrivatsav, Marek S. Skrzypek, Jennifer R. Smith, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Shur-Jen Wang, Shuai Weng, Monte Westerfield, Gary Williams, Edith D. Wong, Adam Wright, Karen Yook:
Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 48(Database-Issue): D650-D658 (2020) - 2019
- [j6]Leyla Ruzicka, Douglas G. Howe, Sridhar Ramachandran, Sabrina Toro, Ceri E. Van Slyke, Yvonne M. Bradford, Anne E. Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock, Christian Pich, Kevin Schaper, Xiang Shao, Amy Singer, Monte Westerfield:
The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources. Nucleic Acids Res. 47(Database-Issue): D867-D873 (2019) - 2017
- [j5]Douglas G. Howe, Yvonne M. Bradford, Anne E. Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran, Leyla Ruzicka, Kevin Schaper, Xiang Shao, Amy Singer, Sabrina Toro, Ceri E. Van Slyke, Monte Westerfield:
The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic Acids Res. 45(Database-Issue): D758-D768 (2017) - 2013
- [j4]Douglas G. Howe, Yvonne M. Bradford, Tom Conlin, Anne E. Eagle, David Fashena, Ken Frazer, Jonathan Knight, Prita Mani, Ryan Martin, Sierra A. T. Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran, Barbara J. Ruef, Leyla Ruzicka, Kevin Schaper, Xiang Shao, Amy Singer, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield:
ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res. 41(Database-Issue): 854-860 (2013) - 2011
- [j3]Yvonne M. Bradford, Tom Conlin, Nathan A. Dunn, David Fashena, Ken Frazer, Douglas G. Howe, Jonathan Knight, Prita Mani, Ryan Martin, Sierra A. T. Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran, Barbara J. Ruef, Leyla Ruzicka, Holle Bauer Schaper, Kevin Schaper, Xiang Shao, Amy Singer, Judy Sprague, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield:
ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic Acids Res. 39(Database-Issue): 822-829 (2011) - 2008
- [j2]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:
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 36(Database-Issue): 768-772 (2008) - 2006
- [j1]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:
The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 34(Database-Issue): 581-585 (2006)
Conference and Workshop Papers
- 2021
- [c1]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:
The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics. ICBO 2021: 148-151
Informal and Other Publications
- 2023
- [i5]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) - [i4]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) - [i3]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:
MapperGPT: Large Language Models for Linking and Mapping Entities. CoRR abs/2310.03666 (2023) - 2022
- [i2]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:
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. CoRR abs/2203.13906 (2022) - 2021
- [i1]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 B. 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:
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR abs/2112.07051 (2021)
Coauthor Index
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