Data Management for Genomic Mapping Applications: A Case Study. - Victor M. Markowitz; Suzanna Lewis; John L. McCarthy; Frank Olken; Manfred Zorn (SSDBM, 1992)

An Evaluation of Ontology Exchange Languages for Bioinformatics. - Robin McEntire; Peter D. Karp; Neil F. Abernethy; David Benton; Gregg Helt; Matt DeJongh; Robert Kent; Anthony Kosky; Suzanna Lewis; Dan Hodnett; Eric P. Neumann; Frank Olken; et al. (ISMB, 2000)

A short study on the success of the Gene Ontology. - Michael Bada; Robert Stevens 001; Carole A. Goble; Yolanda Gil; Michael Ashburner; Judith A. Blake; J. Michael Cherry; Midori A. Harris; Suzanna Lewis (J. Web Semant., 2004)

Reactome: a knowledgebase of biological pathways. - G. Joshi-Tope; Marc Gillespie; Imre Vastrik; Peter D'Eustachio; Esther Schmidt; Bernard de Bono; Bijay Jassal; Gopal R. Gopinath; G. R. Wu; Lisa Matthews; Suzanna Lewis; Ewan Birney; et al. (Nucleic Acids Res., 2005)

Reactome - A Knowledgebase of Biological Pathways. - Esther Schmidt; Ewan Birney; David Croft 001; Bernard de Bono; Peter D'Eustachio; Marc Gillespie; Gopal Gopinath; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Lincoln Stein; Imre Vastrik; et al. (OTM Workshops (1), 2006)

Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes. - Mark Yandell; Chris Mungall; Chris Smith; Simon Prochnik; Joshua S. Kaminker; George Hartzell; Suzanna Lewis; Gerald M. Rubin (PLoS Comput. Biol., 2006)

OBO-Edit - an ontology editor for biologists. - John Day-Richter; Midori A. Harris; Melissa A. Haendel; Suzanna Lewis (Bioinform., 2007)

Reactome: An integrated expert model of human molecular processes and access toolkit. - Bernard de Bono; Imre Vastrik; Peter D'Eustachio; Esther Schmidt; Gopal Gopinath; David Croft 001; Marc Gillespie; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Guanming Wu; Ewan Birney; et al. (J. Integr. Bioinform., 2007)

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 (Ontologies and Text Mining for Life Sciences, 2008)

AmiGO: online access to ontology and annotation data. - Seth Carbon; Amelia Ireland; Christopher J. Mungall; Shengqiang Shu; Brad Marshall; Suzanna Lewis (Bioinform., 2009)

Apollo: a community resource for genome annotation editing. - Ed Lee; Nomi L. Harris; Mark Gibson; Raymond Chetty; Suzanna Lewis (Bioinform., 2009)

Survey-based naming conventions for use in OBO Foundry ontology development. - Daniel Schober; Barry Smith 001; Suzanna E. Lewis; Waclaw Kusnierczyk; Jane Lomax; Chris Mungall; Chris F. Taylor; Philippe Rocca-Serra; Susanna-Assunta Sansone (BMC Bioinform., 2009)

Reactome knowledgebase of human biological pathways and processes. - Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft 001; Bernard de Bono; Phani V. Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alexander Kanapin; Suzanna Lewis; et al. (Nucleic Acids Res., 2009)

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. - Huaiyu Mi; Qing Dong; Anushya Muruganujan; Pascale Gaudet; Suzanna Lewis; Paul D. Thomas (Nucleic Acids Res., 2010)

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. - Pascale Gaudet; Michael S. Livstone; Suzanna E. Lewis; Paul D. Thomas (Briefings Bioinform., 2011)

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. - Nicole L. Washington; E. O. Stinson; Marc D. Perry; Peter Ruzanov; Sergio Contrino; Richard N. Smith; Zheng Zha; Rachel Lyne; Adrian Carr; Paul Lloyd; Ellen T. Kephart; Sheldon J. McKay; et al. (Database J. Biol. Databases Curation, 2011)

Towards BioDBcore: a community-defined information specification for biological databases. - Pascale Gaudet; Amos Bairoch; Dawn Field; Susanna-Assunta Sansone; Chris F. Taylor; Teresa K. Attwood; Alex Bateman; Judith A. Blake; Carol J. Bult; J. Michael Cherry; Rex L. Chisholm; Guy Cochrane; et al. (Nucleic Acids Res., 2011)

modMine: flexible access to modENCODE data. - Sergio Contrino; Richard N. Smith; Daniela Butano; Adrian Carr; Fengyuan Hu; Rachel Lyne; Kim Rutherford; Alex Kalderimis; Julie M. Sullivan; Seth Carbon; Ellen T. Kephart; Paul Lloyd; et al. (Nucleic Acids Res., 2012)

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. - Paul D. Thomas; Valerie Wood; Christopher J. Mungall; Suzanna E. Lewis; Judith A. Blake (PLoS Comput. Biol., 2012)

PhenoDigm: analyzing curated annotations to associate animal models with human diseases. - Damian Smedley; Anika Oellrich; Sebastian Köhler 001; Barbara J. Ruef; Monte Westerfield; Peter N. Robinson; Suzanna Lewis; Christopher J. Mungall (Database J. Biol. Databases Curation, 2013)

The environment ontology: contextualising biological and biomedical entities. - Pier Luigi Buttigieg; Norman Morrison; Barry Smith 001; Christopher J. Mungall; Suzanna E. Lewis (J. Biomed. Semant., 2013)

A knowledge based approach to matching human neurodegenerative disease and animal models. - Sarah Maynard; Christopher J. Mungall; Suzanna E. Lewis; Fahim T. Imam; Maryann E. Martone (Frontiers Neuroinformatics, 2013)

Standardized description of scientific evidence using the Evidence Ontology (ECO). - Marcus C. Chibucos; Christopher J. Mungall; Rama Balakrishnan; Karen R. Christie; Rachael P. Huntley; Owen White; Judith A. Blake; Suzanna E. Lewis; Michelle G. Giglio (Database J. Biol. Databases Curation, 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; et al. (J. Biomed. Semant., 2014)

The influence of disease categories on gene candidate predictions from model organism phenotypes. - Anika Oellrich; Sebastian Köhler 001; Nicole L. Washington; Chris Mungall; Suzanna Lewis; Melissa A. Haendel; Peter N. Robinson; Damian Smedley (J. Biomed. Semant., 2014)

BioJS: an open source standard for biological visualisation - its status in 2014. - Manuel Corpas; Rafael C. Jiménez; Seth Carbon; Alexander García Castro; Leyla Jael Castro; Tatyana Goldberg; John Gómez; Alex Kalderimis; Suzanna E. Lewis; Ian Mulvany; Aleksandra Pawlik; Francis Rowland; et al. (F1000Research, 2014)

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. - Sebastian Köhler 001; Sandra C. Doelken; Christopher J. Mungall; Sebastian Bauer 002; Helen V. Firth; Isabelle Bailleul-Forestier; Graeme C. M. Black; Danielle L. Brown; Michael Brudno; Jennifer Campbell; David R. FitzPatrick; Janan T. Eppig; et al. (Nucleic Acids Res., 2014)

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. - Frederic B. Bastian; Marcus C. Chibucos; Pascale Gaudet; Michelle G. Giglio; Gemma L. Holliday; Hong Huang; Suzanna E. Lewis; Anne Niknejad; Sandra E. Orchard; Sylvain Poux; Nives Skunca; Marc Robinson-Rechavi (Database J. Biol. Databases Curation, 2015)

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. - Marc Feuermann; Pascale Gaudet; Huaiyu Mi; Suzanna E. Lewis; Paul D. Thomas (Database J. Biol. Databases Curation, 2016)

MSAViewer: interactive JavaScript visualization of multiple sequence alignments. - Guy Yachdav; Sebastian Wilzbach; Benedikt Rauscher; Robert Sheridan; Ian Sillitoe; James B. Procter; Suzanna E. Lewis; Burkhard Rost; Tatyana Goldberg (Bioinform., 2016)

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. - Pier Luigi Buttigieg; Evangelos Pafilis; Suzanna E. Lewis; Mark P. Schildhauer; Ramona L. Walls; Christopher J. Mungall (J. Biomed. Semant., 2016)

Best practice data life cycle approaches for the life sciences. - Philippa C. Griffin; Jyoti Khadake; Kate S. LeMay; Suzanna E. Lewis; Sandra E. Orchard; Andrew Pask; Bernard J. Pope; Ute Roessner; Keith Russell; Torsten Seemann; Andrew E. Treloar; Sonika Tyagi; et al. (F1000Research, 2017)

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. - Christopher J. Mungall; Julie A. McMurry; Sebastian Köhler 001; James P. Balhoff; Charles D. Borromeo; Matthew H. Brush; Seth Carbon; Tom Conlin; Nathan A. Dunn; Mark Engelstad; Erin Foster; Jean-Philippe F. Gourdine; et al. (Nucleic Acids Res., 2017)

Gearing up to handle the mosaic nature of life in the quest for orthologs. - Kristoffer Forslund; Cécile Pereira; Salvador Capella-Gutiérrez; Alan W. Sousa da Silva; Adrian M. Altenhoff; Jaime Huerta-Cepas; Matthieu Muffato; Mateus Patricio; Klaas Vandepoele; Ingo Ebersberger; Judith A. Blake; Jesualdo Tomás Fernández-Breis; et al. (Bioinform., 2018)

Apollo: Democratizing genome annotation. - Nathan A. Dunn; Deepak R. Unni; Colin M. Diesh; Monica C. Munoz-Torres; Nomi L. Harris; Eric Yao; Helena Rasche; Ian H. Holmes; Christine G. Elsik; Suzanna E. Lewis (PLoS Comput. Biol., 2019)

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; et al. (Nucleic Acids Res., 2020)

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; et al. (Database J. Biol. Databases Curation, 2021)