Suzanna Lewis Explained

Suzanna Lewis
Workplaces:Lawrence Berkeley National Laboratory
Known For:Biomedical Ontologies
Awards:Fellow of the AAAS

Suzanna (Suzi) E. Lewis was a scientist and Principal investigator at the Berkeley Bioinformatics Open-source Project based at Lawrence Berkeley National Laboratory until her retirement in 2019. Lewis led the development of open standards and software for genome annotation and ontologies.[1] [2] [3]

Education

Lewis has Master of Science degrees in Biology and Computer science.[4]

Research

She led the team responsible for the systematic annotation[5] of the Drosophila melanogaster genome, which included development of the Gadfly[6] annotation pipeline and database framework, and the annotation curation tool Apollo.[7] Lewis' work in genome annotation also includes playing instrumental roles in the GASP[8] community assessment exercises to evaluate the state of the art in genome annotation, development of the Gbrowse[9] genome browser, and the data coordination center for the modENCODE project.[10] In addition to her work in genome annotation, Lewis has been a leader in the development of Open Biomedical Ontologies (OBO),[11] National Center for Biomedical Ontology (NCBO),[12] [13] contributing to the Gene Ontology[14] Sequence Ontology,[15] Uberon anatomy ontologies,[16] and developing open software for editing and navigating ontologies such as AmiGO,[17] OBO-Edit[18] and Phenote.

Awards and honors

In 2005 Lewis was elected a fellow of the American Association for the Advancement of Science in recognition of her contributions to science in the fields of Information, Computing, and Communication.[19]

Notes and References

  1. Web site: Nominations for the Benjamin Franklin Award for Open Access in the Life Sciences 2012. 2013-01-12. https://web.archive.org/web/20130112225523/http://caseybergman.wordpress.com/2012/02/18/nominations-for-the-benjamin-franklin-award-for-open-access-in-the-life-sciences/. dead.
  2. Web site: Suzi Lewis - BioPerl . 2012-02-05 . https://web.archive.org/web/20120205063954/http://www.bioperl.org/wiki/Suzi_Lewis . dead .
  3. Web site: Berkeley Drosophila Genome Project BDGP: Contact Info. 2012-03-16. https://web.archive.org/web/20120316221953/http://www.fruitfly.org/about/contacts.html. dead.
  4. Web site: https://web.archive.org/web/20121023110705/http://www.berkeleybop.org/person/suzanna-lewis. 2012-10-23. Suzanna Lewis: Berkeley Bioinformatics Open-source Projects (BBOP).
  5. 10.1186/gb-2002-3-12-research0083 . Misra . S. . Crosby . M. . Mungall . C. . Matthews . B. . Campbell . K. . Hradecky . P. . Huang . Y. . Kaminker . J. . Millburn . G. . Prochnik . S. E. . Smith . C. D. . Tupy . J. L. . Whitfied . E. J. . Bayraktaroglu . L. . Berman . B. P. . Bettencourt . B. R. . Celniker . S. E. . De Grey . A. D. . Drysdale . R. A. . Harris . N. L. . Richter . J. . Russo . S. . Schroeder . A. J. . Shu . S. Q. . Stapleton . M. . Yamada . C. . Ashburner . M. . Gelbart . W. M. . Rubin . G. M. . Lewis . S. E. . Annotation of the Drosophila melanogaster euchromatic genome: A systematic review . Genome Biology . 3 . 12 . research0083.research0081–83.research0081 . 2002 . 12537572 . 151185. free .
  6. 10.1186/gb-2002-3-12-research0081 . Mungall . C. J. . Misra . S. . Berman . B. P. . Carlson . J. . Frise . E. . Harris . N. . Marshall . B. . Shu . S. . Kaminker . J. S. . Prochnik . S. E. . Smith . C. D. . Smith . E. . Tupy . J. L. . Wiel . C. . Rubin . G. M. . Lewis . S. E. . An integrated computational pipeline and database to support whole-genome sequence annotation . Genome Biology . 3 . 12 . research0081.research0081–81.research0081 . 2002 . 12537570 . 151183. free .
  7. 10.1186/gb-2002-3-12-research0082 . Lewis . S. E. . Suzanna Lewis. Searle . S. M. . Harris . N. . Gibson . M. . Lyer . V. . Richter . J. . Wiel . C. . Bayraktaroglir . L. . Birney . E. . Ewan Birney . Crosby . M. A. . Kaminker . J. S. . Matthews . B. B. . Prochnik . S. E. . Smithy . C. D. . Tupy . J. L. . Rubin . G. M. . Misra . S. . Mungall . C. J. . Clamp . M. E.. Apollo: A sequence annotation editor . Genome Biology . 3 . 12 . research0082.research0081–82.research0081 . 2002 . 12537571 . 151184. free .
  8. Reese . M. G. . Hartzell . G. . Harris . N. L. . Ohler . U. . Abril . J. F. . Lewis . S. E. . Suzanna Lewis. Genome annotation assessment in Drosophila melanogaster . Genome Research . 10 . 4 . 483–501 . 2000 . 10779488 . 310877 . 10.1101/gr.10.4.483.
  9. Stein . L. D. . Lincoln Stein. Mungall . C. . Shu . S. . Caudy . M. . Mangone . M. . Day . A. . Nickerson . E. . Stajich . J. E. . Harris . T. W. . Arva . A. . Lewis . S. . The Generic Genome Browser: A Building Block for a Model Organism System Database . 10.1101/gr.403602 . Genome Research . 12 . 10 . 1599–1610 . 2002 . 12368253 . 187535 .
  10. Washington . N. L. . Stinson . E. O. . Perry . M. D. . Ruzanov . P. . Contrino . S. . Smith . R. . Zha . Z. . Lyne . R. . Carr . A. . Lloyd . P. . Kephart . E. . McKay . S. J. . Micklem . G. . Stein . L. D. . Lewis . S. E. . The modENCODE Data Coordination Center: Lessons in harvesting comprehensive experimental details . 10.1093/database/bar023 . Database . 2011 . bar023 . 2011 . 21856757 . 3170170 .
  11. Smith . B. . Barry Smith (ontologist). Ashburner . M. . Michael Ashburner. Rosse . C. . Bard . J. . Bug . W. . Ceusters . W. . Goldberg . L. J. . Eilbeck . K. . Ireland . A. . Mungall . 10.1038/nbt1346 . C. J. . Leontis . N. . Rocca-Serra . P. . Ruttenberg . A. . Sansone . S. A. . Scheuermann . R. H. . Shah . N. . Whetzel . P. L. . Lewis . S. . Suzanna Lewis. The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration . . 25 . 11 . 1251–1255 . 2007 . 17989687 . 2814061 .
  12. Musen . M. A. . Noy . N. F. . Shah . N. H. . Whetzel . P. L. . Chute . C. G. . Story . M. -A. . Smith . B. . And The Ncbo . T. . The National Center for Biomedical Ontology . 10.1136/amiajnl-2011-000523 . Journal of the American Medical Informatics Association . 19 . 2 . 190–195 . 2011 . 22081220 . 3277625 .
  13. Rubin . D. L. . Lewis . S. E. . Suzanna Lewis. Mungall . C. J. . Misra . S. . Westerfield . M. . Ashburner . M. . Michael Ashburner. Sim . I. . Chute . C. G. . Storey . M. A. . 10.1089/omi.2006.10.185 . Smith . B. . Day-Richter . J. . Noy . N. F. . Musen . M. A. . Musen . M. A. . National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge . OMICS: A Journal of Integrative Biology . 10 . 2 . 185–198 . 2006 . 16901225 . 14097452 .
  14. Botstein . D. . David Botstein. Cherry . J. M. . Ashburner . M. . Michael Ashburner. Ball . C. A. . Blake . J. A. . Butler . H. . Davis . A. P. . Dolinski . K. . Dwight . S. S. . Eppig . J. T. . Harris . M. A. . Hill . D. P. . Issel-Tarver . L. . Kasarskis . A. . Lewis . S. . Suzanna Lewis. Matese . J. C. . Richardson . J. E. . Ringwald . M. . Rubin . G. M. . Gerald M. Rubin. Sherlock . G. . Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium . . 25 . 1 . 25–29 . 10.1038/75556 . 2000 . 10802651 . 3037419 .
  15. Eilbeck . K. . Lewis . S. E. . Suzanna Lewis. Mungall . C. J. . Yandell . M. . Stein . L. . Lincoln Stein. Durbin . R. . Richard M. Durbin. Ashburner . M. . Michael Ashburner. The Sequence Ontology: A tool for the unification of genome annotations . Genome Biology . 6 . 5 . R44 . 2005 . 10.1186/gb-2005-6-5-r44 . 15892872 . 1175956 . free .
  16. Mungall . C. J. . Torniai . C. . Gkoutos . G. V. . Lewis . S. E. . Suzanna Lewis. Haendel . M. A. . Uberon, an integrative multi-species anatomy ontology . 10.1186/gb-2012-13-1-r5 . Genome Biology . 13 . 1 . R5 . 2012 . 22293552 . 3334586. free .
  17. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S; AmiGO Hub; Web Presence Working Group. 10.1093/bioinformatics/btn615 . AmiGO: Online access to ontology and annotation data . Bioinformatics . 25 . 2 . 288–289 . 2008 . 19033274 . 2639003 .
  18. Day-Richter . J. . Harris . M. A. . Haendel . M. . Lewis . S. . Suzanna Lewis. 10.1093/bioinformatics/btm112 . OBO-Edit an ontology editor for biologists . Bioinformatics . 23 . 16 . 2198–2200 . 2007 . 17545183 .
  19. Web site: AAAS News & Notes. https://web.archive.org/web/20130318015754/http://www.aaas.org/news/newsandnotes/inside125.shtml. 2013-03-18. 16 June 2012. dead.

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