Suzanna Lewis

Suzanna Lewis
Known forBiomedical Ontologies
AwardsFellow of the AAAS[1]
Scientific career
InstitutionsLawrence Berkeley National Laboratory
Websiteberkeleybop.github.io/people/suzanna-lewis/

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.[2][3][4]

Education

Lewis has Master of Science degrees in Biology and Computer science.[5]

Research

She led the team responsible for the systematic annotation[6] of the Drosophila melanogaster genome, which included development of the Gadfly[7] annotation pipeline and database framework, and the annotation curation tool Apollo.[8] Lewis' work in genome annotation also includes playing instrumental roles in the GASP[9] community assessment exercises to evaluate the state of the art in genome annotation, development of the Gbrowse[10] genome browser, and the data coordination center for the modENCODE project.[11] In addition to her work in genome annotation, Lewis has been a leader in the development of Open Biomedical Ontologies (OBO),[12] National Center for Biomedical Ontology (NCBO),[13][14] contributing to the Gene Ontology[15] Sequence Ontology,[16] Uberon anatomy ontologies,[17] and developing open software for editing and navigating ontologies such as AmiGO,[18] OBO-Edit[19] 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.[1]

References

  1. ^ a b "AAAS News & Notes". Archived from the original on 2013-03-18. Retrieved 16 June 2012.
  2. ^ "Nominations for the Benjamin Franklin Award for Open Access in the Life Sciences 2012". Archived from the original on 2013-01-12.
  3. ^ "Suzi Lewis - BioPerl". Archived from the original on 2012-02-05.
  4. ^ "Berkeley Drosophila Genome Project BDGP: Contact Info". Archived from the original on 2012-03-16.
  5. ^ "Suzanna Lewis: Berkeley Bioinformatics Open-source Projects (BBOP)". Archived from the original on 2012-10-23.
  6. ^ 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. (2002). "Annotation of the Drosophila melanogaster euchromatic genome: A systematic review". Genome Biology. 3 (12): research0083.research0081–83.research0081. doi:10.1186/gb-2002-3-12-research0083. PMC 151185. PMID 12537572.
  7. ^ 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. (2002). "An integrated computational pipeline and database to support whole-genome sequence annotation". Genome Biology. 3 (12): research0081.research0081–81.research0081. doi:10.1186/gb-2002-3-12-research0081. PMC 151183. PMID 12537570.
  8. ^ Lewis, S. E.; Searle, S. M.; Harris, N.; Gibson, M.; Lyer, V.; Richter, J.; Wiel, C.; Bayraktaroglir, L.; Birney, E.; 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. (2002). "Apollo: A sequence annotation editor". Genome Biology. 3 (12): research0082.research0081–82.research0081. doi:10.1186/gb-2002-3-12-research0082. PMC 151184. PMID 12537571.
  9. ^ Reese, M. G.; Hartzell, G.; Harris, N. L.; Ohler, U.; Abril, J. F.; Lewis, S. E. (2000). "Genome annotation assessment in Drosophila melanogaster". Genome Research. 10 (4): 483–501. doi:10.1101/gr.10.4.483. PMC 310877. PMID 10779488.
  10. ^ Stein, L. D.; Mungall, C.; Shu, S.; Caudy, M.; Mangone, M.; Day, A.; Nickerson, E.; Stajich, J. E.; Harris, T. W.; Arva, A.; Lewis, S. (2002). "The Generic Genome Browser: A Building Block for a Model Organism System Database". Genome Research. 12 (10): 1599–1610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253.
  11. ^ 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. (2011). "The modENCODE Data Coordination Center: Lessons in harvesting comprehensive experimental details". Database. 2011: bar023. doi:10.1093/database/bar023. PMC 3170170. PMID 21856757.
  12. ^ Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; Goldberg, L. J.; Eilbeck, K.; Ireland, A.; Mungall, C. J.; Leontis, N.; Rocca-Serra, P.; Ruttenberg, A.; Sansone, S. A.; Scheuermann, R. H.; Shah, N.; Whetzel, P. L.; Lewis, S. (2007). "The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–1255. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687. Open access icon
  13. ^ Musen, M. A.; Noy, N. F.; Shah, N. H.; Whetzel, P. L.; Chute, C. G.; Story, M. -A.; Smith, B.; And The Ncbo, T. (2011). "The National Center for Biomedical Ontology". Journal of the American Medical Informatics Association. 19 (2): 190–195. doi:10.1136/amiajnl-2011-000523. PMC 3277625. PMID 22081220.
  14. ^ Rubin, D. L.; Lewis, S. E.; Mungall, C. J.; Misra, S.; Westerfield, M.; Ashburner, M.; Sim, I.; Chute, C. G.; Storey, M. A.; Smith, B.; Day-Richter, J.; Noy, N. F.; Musen, M. A.; Musen, M. A. (2006). "National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge" (PDF). OMICS: A Journal of Integrative Biology. 10 (2): 185–198. doi:10.1089/omi.2006.10.185. PMID 16901225. S2CID 14097452.
  15. ^ Botstein, D.; Cherry, J. M.; Ashburner, M.; 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.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. (2000). "Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics. 25 (1): 25–29. doi:10.1038/75556. PMC 3037419. PMID 10802651. Open access icon
  16. ^ Eilbeck, K.; Lewis, S. E.; Mungall, C. J.; Yandell, M.; Stein, L.; Durbin, R.; Ashburner, M. (2005). "The Sequence Ontology: A tool for the unification of genome annotations". Genome Biology. 6 (5): R44. doi:10.1186/gb-2005-6-5-r44. PMC 1175956. PMID 15892872.
  17. ^ Mungall, C. J.; Torniai, C.; Gkoutos, G. V.; Lewis, S. E.; Haendel, M. A. (2012). "Uberon, an integrative multi-species anatomy ontology". Genome Biology. 13 (1): R5. doi:10.1186/gb-2012-13-1-r5. PMC 3334586. PMID 22293552.
  18. ^ Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S; AmiGO Hub; Web Presence Working Group (2008). "AmiGO: Online access to ontology and annotation data". Bioinformatics. 25 (2): 288–289. doi:10.1093/bioinformatics/btn615. PMC 2639003. PMID 19033274.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  19. ^ Day-Richter, J.; Harris, M. A.; Haendel, M.; Lewis, S. (2007). "OBO-Edit an ontology editor for biologists". Bioinformatics. 23 (16): 2198–2200. doi:10.1093/bioinformatics/btm112. PMID 17545183.