Tanya Z. Berardini - researchr alias

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Viewing Publication 1 - 21 from 21

2023

Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata ConsortiumJennifer L. Clarke, Laurel D. Cooper, Monica F. Poelchau, Tanya Z. Berardini, Justin Elser, Andrew D. Farmer, Stephen P. Ficklin, Sunita Kumari, Marie-Angélique Laporte, Rex T. Nelson, Rie Sadohara, Peter Selby, Anne E. Thessen, Brandon Whitehead, Taner Z. Sen. biodb, 2023, 2023. [doi]

2021

The Gene Ontology resource: enriching a GOld mineSeth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James Munro, Rebecca Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser. nar, 49(Database-Issue), 2021. [doi]

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)Jolene Ramsey, Brenley K. McIntosh, Daniel P. Renfro, Suzanne A. Aleksander, Sandra A. LaBonte, Curtis Ross, Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades, Tanya Z. Berardini, Jennifer A. Bennett, Siobhan M. Brady, Robert Britton, Seth Carbon, Steven M. Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L. Doyle, Iddo Friedberg, Susan M. R. Gurney, Lee Hughes, Allison Johnson, Jason M. Kowalski, Donghui Li, Ruth C. Lovering, Tamara L. Mans, Fiona McCarthy, Sean D. Moore, Rebecca Murphy, Timothy D. Paustian, Sarah Perdue, Celeste N. Peterson, Birgit M. Prüß, Margaret S. Saha, Robert R. Sheehy, John T. Tansey, Louise Temple, Alexander William Thorman, Saul Trevino, Amy Cheng Vollmer, Virginia Walbot, Joanne Willey, Deborah A. Siegele, James C. Hu. ploscb, 17(10), 2021. [doi]

2019

2018

'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of LifeIan Braun, James P. Balhoff, Tanya Z. Berardini, Laurel Cooper, Georgios V. Gkoutos, Lisa C. Harper, Eva Huala, Pankaj Jaiswal, Toni Kazic, Hilmar Lapp, James A. Macklin, Chelsea D. Specht, Todd J. Vision, Ramona L. Walls, Carolyn J. Lawrence-Dill. In Anne E. Thessen, editor, Application of Semantic Technology in Biodiversity Science. Volume 33 of Studies on the Semantic Web, pages 187-205, IOS Press, 2018. [doi]

AgBioData consortium recommendations for sustainable genomics and genetics databases for agricultureLisa C. Harper, Jacqueline Campbell, Ethalinda K. S. Cannon, Sook Jung, Monica Poelchau, Ramona L. Walls, Carson M. Andorf, Elizabeth Arnaud, Tanya Z. Berardini, Clayton Birkett, Steve Cannon, James Carson, Bradford Condon, Laurel Cooper, Nathan A. Dunn, Christine G. Elsik, Andrew Farmer, Stephen P. Ficklin, David Grant, Emily Grau, Nic Herndon, Zhi-Liang Hu, Jodi Humann, Pankaj Jaiswal, Clément Jonquet, Marie-Angélique Laporte, Pierre Larmande, Gerard Lazo, Fiona McCarthy, Naama Menda, Christopher J. Mungall, Monica C. Munoz-Torres, Sushma Naithani, Rex T. Nelson, Daureen Nesdill, Carissa A. Park, James M. Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak R. Unni, Liya Wang, Doreen Ware, Jill L. Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main. biodb, 2018, 2018. [doi]

2016

2014

TermGenie - A web application for pattern-based ontology class generationHeiko Dietze, Tanya Z. Berardini, Rebecca E. Foulger, David P. Hill, Jane Lomax, David Osumi-Sutherland, Paola Roncaglia, Christopher J. Mungall. biomedsem, 5:48, 2014. [doi]

2013

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developmentsPaola Roncaglia, Maryann E. Martone, David P. Hill, Tanya Z. Berardini, Rebecca E. Foulger, Fahim T. Imam, Harold J. Drabkin, Christopher J. Mungall, Jane Lomax. biomedsem, 4:20, 2013. [doi]

2012

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIRKimberly Van Auken, Petra Fey, Tanya Z. Berardini, Robert Dodson, Laurel Cooper, Donghui Li, Juancarlos Chan, Yuling Li, Siddhartha Basu, Hans-Michael Müller, Rex L. Chisholm, Eva Huala, Paul W. Sternberg. biodb, 2012, 2012. [doi]

Assessment of community-submitted ontology annotations from a novel database-journal partnershipTanya Z. Berardini, Donghui Li, Robert Muller, Raymond Chetty, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala. biodb, 2012, 2012. [doi]

Biocurators and Biocuration: surveying the 21st century challengesSarah W. Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, J. Michael Cherry, Claire O'Donovan, Ioannis Xenarios, Pascale Gaudet. biodb, 2012, 2012. [doi]

Arabidopsis literature corpusDonghui Li, Tanya Z. Berardini, Robert J. Muller, Eva Huala. biodb, 2012, 2012. [doi]

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstractsChih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu. biodb, 2012, 2012. [doi]

2011

Cross-product extensions of the Gene OntologyChristopher J. Mungall, Michael Bada, Tanya Z. Berardini, Jennifer I. Deegan, Amelia Ireland, Midori A. Harris, David P. Hill, Jane Lomax. jbi, 44(1):80-86, 2011. [doi]

2008

The Arabidopsis Information Resource (TAIR): gene structure and function annotationDavid Swarbreck, Christopher Wilks, Philippe Lamesch, Tanya Z. Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang, Eva Huala. nar, 36(Database-Issue):1009-1014, 2008. [doi]

2005

PatMatch: a program for finding patterns in peptide and nucleotide sequencesThomas Yan, Danny Yoo, Tanya Z. Berardini, Lukas A. Mueller, Dan C. Weems, Shuai Weng, J. Michael Cherry, Seung Yon Rhee. nar, 33(Web-Server-Issue):262-266, 2005. [doi]

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