Suzanna Lewis

Last updated
Suzanna Lewis
Known for Biomedical Ontologies
Awards Fellow of the AAAS [1]
Scientific career
Institutions Lawrence Berkeley National Laboratory
Website berkeleybop.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]

Contents

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]

Related Research Articles

The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.

<span class="mw-page-title-main">Michael Ashburner</span>

Michael Ashburner is a biologist and Emeritus Professor in the Department of Genetics at University of Cambridge. He is also the former joint-head and co-founder of the European Bioinformatics Institute (EBI) of the European Molecular Biology Laboratory (EMBL) and a Fellow of Churchill College, Cambridge.

The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases

The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.

<span class="mw-page-title-main">Generic Model Organism Database</span>

The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.

<span class="mw-page-title-main">Robert Stevens (scientist)</span>

Robert David Stevens is a professor of bio-health informatics. and former Head of Department of Computer Science at The University of Manchester

Gerald Mayer Rubin is an American biologist, notable for pioneering the use of transposable P elements in genetics, and for leading the public project to sequence the Drosophila melanogaster genome. Related to his genomics work, Rubin's lab is notable for development of genetic and genomics tools and studies of signal transduction and gene regulation. Rubin also serves as a vice president of the Howard Hughes Medical Institute and executive director of the Janelia Research Campus.

SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.

<span class="mw-page-title-main">Richard M. Durbin</span> British computational biologist

Richard Michael Durbin is a British computational biologist and Al-Kindi Professor of Genetics at the University of Cambridge. He also serves as an associate faculty member at the Wellcome Sanger Institute where he was previously a senior group leader.

DNA annotation or genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. An annotation is a note added by way of explanation or commentary. Once a genome is sequenced, it needs to be annotated to make sense of it. Genes in a eukaryotic genome can be annotated using various annotation tools such as FINDER. A modern annotation pipeline can support a user-friendly web interface and software containerization such as MOSGA. Modern annotation pipelines for prokaryotic genomes are Bakta, Prokka and PGAP.

<span class="mw-page-title-main">Lincoln Stein</span>

Lincoln David Stein is a scientist and Professor in bioinformatics and computational biology at the Ontario Institute for Cancer Research.

The Sequence Ontology (SO) is an ontology suitable for describing biological sequences. It is designed to make the naming of DNA sequence features and variants consistent and therefore machine-readable and searchable.

The Uber-anatomy ontology (Uberon) is a comparative anatomy ontology representing a variety of structures found in animals, such as lungs, muscles, bones, feathers and fins. These structures are connected to other structures via relationships such as part-of and develops-from. One of the uses of this ontology is to integrate data from different biological databases, and other species-specific ontologies such as the Foundational Model of Anatomy.

<span class="mw-page-title-main">Julian Parkhill</span>

Julian Parkhill is the Marks & Spencer Professor of Farm Animal Health, Food Science and Safety in the Department of Veterinary Medicine at the University of Cambridge. He previously served as head of pathogen genomics at the Wellcome Sanger Institute.

PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and annotated features, together with a wide range of manually curated functional gene-specific data. The PomBase website was redeveloped in 2016 to provide users with a more fully integrated, better-performing service.

Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.

Judith Anne Blake is a computational biologist at the Jackson Laboratory and Professor of Mammalian Genetics.

<span class="mw-page-title-main">Biocuration</span>

Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.

Cytochrome P450, family 305, also known as CYP305, is an animal cytochrome P450 family found in insect genome. The first gene identified in this family is the CYP305A1 from the Drosophila melanogaster.

References

  1. 1 2 "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 logo PLoS transparent.svg
  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 logo PLoS transparent.svg
  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.
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