Lewis Lab
Research Interest
The Berkeley Bioinformatics Open-source Projects (BBOP) is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems.
Our group is focused on the development, use, and integration of ontolgies into biological data analysis. We are interested in the management of large-scale biological data: describing it rigorously using ontologies; designing databases that are flexible enough to be easily maintained; quickly searching and accurately retrieving data; and presenting it effectively to researchers and biologists. We believe that the only way to develop effective software is through user-centered design. In broad terms, user-centered design (UCD) is a design philosophy and a process in which the needs, wants, and limitations of the end user of an interface or document are given extensive attention at each stage of the design process. We have biologists on our development team so that the software designers get to know their needs.
Members of the group contribute to a number of projects, including the Gene Ontology, the National Center for Biomedical Ontology, modENCODE, and the Generic Model Organism Database Project.
Selected Publications
Haendel, M.A., F. Neuhaus, D.S. Osumi-Sutherland, P.M. Mabee, J.L.V. Mejino, C.J. Mungall and B. Smith. (2008) CARO - The Common Anatomy Reference Ontology. Chapter 16. In: Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. 2007. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 25(11):1251-5.
Smith CD, Shu S, Mungall CJ, Karpen GH. 2007. The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science 316(5831):1586-9.
Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. 2007. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. 22(7):345-50.
Day-Richter J, Harris MA, Haendel M; Gene Ontology OBO-Edit Working Group, Lewis S. 2007. OBO-Edit--an ontology editor for biologists. Bioinformatics. 23(16):2198-200.
Thomas PD, Mi H, Lewis S. 2007. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol.i> 11(1):4-11
Mungall CJ, D.B. Emmert, S. Cain, SQ Shu, P. Zhang, P. Zhou, W.M. Gelbart, G.M. Rubin, L. Stein, S.E. Lewis. 2007. A Case Study from Chado: An Ontology-based Modular Schema for Representing our Knowledge of Organisms. Bioinformatics 23(13): i337-46.
Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA. (2006) National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge. OMICS. 10(2): 185-98.
Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. 2005. Relations in biomedical ontologies. Genome Biol. 6(5):R46.
Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 6(5):R44.
Lewis SE. (2005) Gene Ontology: looking backwards and forwards. Genome Biol. 6(1):103.
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32(Database issue):D258-61.
Mungall, CJ. Obol: integrating language and meaning in bio-ontologies. (2004) Compar Func Genomics5(6-7).
Ashburner M, Mungall CJ, Lewis SE. (2003) Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb Symp Quant Biol. 68:227-35.
Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME. (2002) Apollo: a sequence annotation editor. Genome Biology 3(12):RESEARCH0082.
