Mary Shimoyama

According to our database, Mary Shimoyama authored at least 37 papers between 2002 and 2020.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2020

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.

Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Stanley J. F. Laulederkind, Matthew J. Hoffman, Mary L. Kaldunski, Monika Tutaj, Jyothi Thota, Harika S. Nalabolu, Santoshi L. R. Ellanki, Marek Tutaj, Jeffrey DePons, Anne E. Kwitek, Melinda R. Dwinell, Mary Shimoyama

Nucleic Acids Res., 2020

Alliance of Genome Resources Portal: unified model organism research platform.

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

Nucleic Acids Res., 2020

Automated generation of gene summaries at the Alliance of Genome Resources.

Ranjana Kishore, Valerio Arnaboldi, Ceri E. Van Slyke, Juancarlos Chan, Robert S. Nash, Jose-Maria Urbano, Mary E. Dolan, Stacia R. Engel, Mary Shimoyama, Paul W. Sternberg, The Alliance of Genome Resources

Database J. Biol. Databases Curation, 2020

2019

Predicting instances of pathway ontology classes for pathway integration.

Lucy Lu Wang, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary Shimoyama, John H. Gennari

J. Biomed. Semant., 2019

Quantitative phenotype analysis to identify, validate and compare rat disease models.

Yiqing Zhao, Jennifer R. Smith, Shur-Jen Wang, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2019

Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.

Shur-Jen Wang, Stanley J. F. Laulederkind, Yiqing Zhao, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Jyothi Thota, Marek Tutaj, Matthew J. Hoffman, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2019

PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks.

Cagatay Dursun, Naoki Shimoyama, Mary Shimoyama, Michael Schläppi, Serdar Bozdag

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

Adapting Disease Vocabularies for Curation at the Rat Genome Database.

Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Elizabeth R. Bolton, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Mary Shimoyama, Melinda R. Dwinell

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

2017

Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database.

Omid Ghiasvand, Mary Shimoyama

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

The Chinchilla Research Resource Database: resource for an otolaryngology disease model.

Mary Shimoyama, Jennifer R. Smith, Jeff de Pons, Marek Tutaj, Pawjai Khampang, Wenzhou Hong, Christy B. Erbe, Garth D. Ehrlich, Lauren O. Bakaletz, Joseph E. Kerschner

Database J. Biol. Databases Curation, 2016

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

G. Thomas Hayman, Stanley J. F. Laulederkind, Jennifer R. Smith, Shur-Jen Wang, Victoria Petri, Rajni Nigam, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2016

Introducing a Text Annotation Tool (OntoMate), Assisting Curation at Rat Genome Database.

Omid Ghiasvand, Mary Shimoyama

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

Disease Connections at RGD.

Mary Shimoyama, Stanley J. F. Laulederkind, Jeff de Pons, Marek Tutaj, Victoria Petri, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jyothi Thota, Omid Ghiasvand, Melinda R. Dwinell

Proceedings of the AMIA 2016, 2016

2015

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.

Mary Shimoyama, Jeff de Pons, G. Thomas Hayman, Stanley J. F. Laulederkind, Weisong Liu, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Shur-Jen Wang, Elizabeth A. Worthey, Melinda R. Dwinell, Howard J. Jacob

Nucleic Acids Res., 2015

PhenoMiner: a quantitative phenotype database for the laboratory rat, <i>Rattus norvegicus</i>. Application in hypertension and renal disease.

Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Weisong Liu, Jennifer R. Smith, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2015

OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

Weisong Liu, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2015

2014

The pathway ontology - updates and applications.

Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G. Thomas Hayman, Jennifer R. Smith, Jeff de Pons, Stanley J. F. Laulederkind, Timothy Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R. Dwinell, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob

J. Biomed. Semant., 2014

2013

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Jennifer R. Smith, Carissa A. Park, Rajni Nigam, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Timothy Lowry, Victoria Petri, Jeff de Pons, Marek Tutaj, Weisong Liu, Elizabeth A. Worthey, Mary Shimoyama, Melinda R. Dwinell

J. Biomed. Semant., 2013

The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species.

Carissa A. Park, Susan M. Bello, Cynthia L. Smith, Zhi-Liang Hu, Diane H. Munzenmaier, Rajni Nigam, Jennifer R. Smith, Mary Shimoyama, Janan T. Eppig, James M. Reecy

J. Biomed. Semant., 2013

Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.

Rajni Nigam, Diane H. Munzenmaier, Elizabeth A. Worthey, Melinda R. Dwinell, Mary Shimoyama, Howard J. Jacob

J. Biomed. Semant., 2013

Analysis of disease-associated objects at the Rat Genome Database.

Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Jennifer R. Smith, Victoria Petri, Timothy Lowry, Rajni Nigam, Melinda R. Dwinell, Elizabeth A. Worthey, Diane H. Munzenmaier, Mary Shimoyama, Howard J. Jacob

Database J. Biol. Databases Curation, 2013

PhenoMiner: quantitative phenotype curation at the rat genome database.

Stanley J. F. Laulederkind, Weisong Liu, Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Victoria Petri, Timothy Lowry, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2013

The Rat Genome Database 2013 - data, tools and users.

Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Jennifer R. Smith, Timothy Lowry, Rajni Nigam, Victoria Petri, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob

Briefings Bioinform., 2013

Next generation ontology browser.

Tomasz Adamusiak, Naoki Shimoyama, Marek Tutaj, Mary Shimoyama

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

Innovative Use of Ontologies: Association of Physiological Pathways to Corresponding Computational Models and Disparate Data Types.

Nazanin Tabesh-Saleki, Brian E. Carlson, Christopher T. Thompson, Maxwell Lewis Neal, Daniel L. Cook, Mary Shimoyama

Proceedings of the AMIA 2013, 2013

Inadvertent Disclosure of Protected Health Information (PHI) in Randomly Shifted Date Elements for De-identification.

Tomasz Adamusiak, Mary Shimoyama

Proceedings of the AMIA 2013, 2013

2012

Ontology searching and browsing at the Rat Genome Database.

Stanley J. F. Laulederkind, Marek Tutaj, Mary Shimoyama, G. Thomas Hayman, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, Melinda R. Dwinell, Howard J. Jacob

Database J. Biol. Databases Curation, 2012

Ontologies Put More Meaning into Meaningful Use.

Tomasz Adamusiak, Naoki Shimoyama, Alexandra Fuiks, Mary Shimoyama

Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Making Computational Models Accessible through Ontologies and Visualization Tools.

Nazanin Tabesh-Saleki, Mary Shimoyama, Brian E. Carlson, Christopher T. Thompson, Daniel Beard

Proceedings of the AMIA 2012, 2012

Gene Annotator Tool.

Mary Shimoyama

Proceedings of the AMIA 2012, 2012

2011

The Rat Genome Database Pathway Portal.

Victoria Petri, Mary Shimoyama, G. Thomas Hayman, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Diane H. Munzenmaier, Simon N. Twigger, Howard J. Jacob

Database J. Biol. Databases Curation, 2011

The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data.

Stanley J. F. Laulederkind, Mary Shimoyama, G. Thomas Hayman, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, George Kowalski, Weisong Liu, Wes Rood, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob

Database J. Biol. Databases Curation, 2011

2009

The Rat Genome Database Curators: Who, What, Where, Why.

Mary Shimoyama, G. Thomas Hayman, Stanley J. F. Laulederkind, Rajni Nigam, Timothy Lowry, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob

PLoS Comput. Biol., 2009

The Rat Genome Database 2009: variation, ontologies and pathways.

Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-Gungor, Jeffrey DePons, Stanley J. F. Laulederkind, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Alexander Stoddard, Simon N. Twigger, Howard J. Jacob

Nucleic Acids Res., 2009

2007

The Rat Genome Database, update 2007 - Easing the path from disease to data and back again.

Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob

Nucleic Acids Res., 2007

2005

The Rat Genome Database (RGD): developments towards a phenome database.

Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon N. Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R. Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne E. Kwitek, Peter J. Tonellato, Howard J. Jacob

Nucleic Acids Res., 2005

2002

Rat Genome Database (RGD): mapping disease onto the genome.

Simon N. Twigger, Jian Lu, Mary Shimoyama, Dan Chen, Dean Pasko, Hanping Long, Jessica Ginster, Chin-Fu Chen, Rajni Nigam, Anne E. Kwitek, Janan T. Eppig, Lois Maltais, Donna R. Maglott, Gregory D. Schuler, Howard J. Jacob, Peter J. Tonellato

Nucleic Acids Res., 2002