Publications

Selected Publications

E. Lee, G. A. Helt, J. T. Reese, M. C. Munoz-Torres, C. P. Childers, R. M. Buels, L. Stein, I. H. Holmes, C. G. Elsik, S. E. Lewis (2013) Web Apollo: a web-based genomic annotation editing platform. Genome Biol 14:R93.

E. Lee, N. Harris, M. Gibson, R. Chetty, and S. Lewis (2009). Apollo: a community resource for genome annotation editing. Bioinformatics, 25(14): 1836-1837.

Seth Carbon, Amelia Ireland, Christopher J. Mungall, ShengQiang Shu, Brad Marshall, Suzanna Lewis, the AmiGO Hub, the Web Presence Working Group (2008). AmiGO: online access to ontology and annotation data Bioinformatics, 25 (2): 288-289.

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. [Abstract] [PDF]

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 [Abstract] [PDF]

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 [Abstract] [PDF]

Thomas PD, Mi H, Lewis S. 2007. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 11(1):4-11 [Abstract] [PDF]

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. [Abstract] [PDF]

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. [Abstract] [PDF]

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 [Abstract] [PDF]

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. [Abstract] [PDF]

Lewis SE. (2005) Gene Ontology: looking backwards and forwards. Genome Biol. 6(1):103. [Abstract] [PDF]

S Misra and N Harris (2005) Using Apollo to Browse and Edit Genome Annotations. Current Protocols in Bioinformatics, Unit 9.5, published by John Wiley & Sons, Inc.

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. [Abstract] [PDF]

Mungall, CJ (2004). Obol: integrating language and meaning in bio-ontologies. Compar Func Genomics5(6-7). [Abstract] [PDF]

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. [link]

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. [Abstract] [PDF]