Apollo: An Extensible Genome Annotation Editor

Suzanna E Lewis, Research Associate
Genome & Computational Biologyuniversity Of Calif-lawrenc Berkeley Lab

Grant 5R01GM080203-02 from National Institute Of General Medical Sciences, IRG: ZRG1

Abstract: Annotation of DMA sequences is an essential prerequisite for understanding the biology of genes and gene products in any organism. An annotation is any feature that can be tied to genomic sequence, such as an exon, transcript, promoter, or transposable element. The highest-quality annotation is obtained by combining automated sequence analysis results with the expert knowledge of biologists. Apollo is a cross-platform annotation editing tool that streamlines this process by providing an interactive graphical display that allows biologists to view many different computational analyses of a genomic region and use them, together with their knowledge of direct experimental results, to create and refine detailed annotations. Apollo is an Open Source Java application that is easy to install and run on any platform. Since its initial release in 2002, Apollo has become one of the most widely used annotation editors. Factors contributing to its success include its intuitive, interactive user interface; configurability; simple installation process; extensive documentation; highly responsive mailing list; extensibility; and an Open Source code-base. It has been downloaded thousands of times, and a wide variety of both academic and commercial research groups have modified or extended it to suit their individual needs (see Appendix 1), thereby saving countless hours of development time We are requesting funding for continued support and improvement of this valuable software resource Our goals include making Apollo fully aware of the Sequence Ontology, to better support community-wide annotation of diverse organisms; designing new configuration interfaces to simplify the process of loading data from different sources and setting display preferences; and adding two new specialized editors a multiple alignment transcript viewer and editor, to allow gene models to be modified in direct reference to alignment data; and a repetitive element editor. We also plan to offer more support and outreach, including workshops and on-site visits to train biologists to use Apollo and show software developers how to integrate their existing tools into Apollo´s extensible framework. The work in this proposal will be performed as a collaboration between Lawrence Berkeley National Laboratory (LBNL) and The Arabidopsis Information Resource (TAIR) at the Carnegie Institution, with LBNL supplying the bulk of the software development and Carnegie providing targeted software development resources and annotation expertise

Keywords: gene, genome Arabidopsis, base, biology, community, computer program /software, computer system design /evaluation, element, gait, model, motivation, nucleic acid sequence, organism, preference, success, training, transposon /insertion element, vocabulary, workshop

Project start date: 2007-08-01

Project end date: 2009-07-31

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Apollo: An Extensible Genome Annotation Editor

Suzanna E Lewis, Research Associate
Genome & Computational Biologyuniversity Of Calif-lawrenc Berkeley Lab

Grant 5R01GM080203-02 from National Institute Of General Medical Sciences, IRG: ZRG1

Abstract: Annotation of DMA sequences is an essential prerequisite for understanding the biology of genes and gene products in any organism. An annotation is any feature that can be tied to genomic sequence, such as an exon, transcript, promoter, or transposable element. The highest-quality annotation is obtained by combining automated sequence analysis results with the expert knowledge of biologists. Apollo is a cross-platform annotation editing tool that streamlines this process by providing an interactive graphical display that allows biologists to view many different computational analyses of a genomic region and use them, together with their knowledge of direct experimental results, to create and refine detailed annotations. Apollo is an Open Source Java application that is easy to install and run on any platform. Since its initial release in 2002, Apollo has become one of the most widely used annotation editors. Factors contributing to its success include its intuitive, interactive user interface; configurability; simple installation process; extensive documentation; highly responsive mailing list; extensibility; and an Open Source code-base. It has been downloaded thousands of times, and a wide variety of both academic and commercial research groups have modified or extended it to suit their individual needs (see Appendix 1), thereby saving countless hours of development time We are requesting funding for continued support and improvement of this valuable software resource Our goals include making Apollo fully aware of the Sequence Ontology, to better support community-wide annotation of diverse organisms; designing new configuration interfaces to simplify the process of loading data from different sources and setting display preferences; and adding two new specialized editors a multiple alignment transcript viewer and editor, to allow gene models to be modified in direct reference to alignment data; and a repetitive element editor. We also plan to offer more support and outreach, including workshops and on-site visits to train biologists to use Apollo and show software developers how to integrate their existing tools into Apollo´s extensible framework. The work in this proposal will be performed as a collaboration between Lawrence Berkeley National Laboratory (LBNL) and The Arabidopsis Information Resource (TAIR) at the Carnegie Institution, with LBNL supplying the bulk of the software development and Carnegie providing targeted software development resources and annotation expertise

Keywords: gene, genome Arabidopsis, base, biology, community, computer program /software, computer system design /evaluation, element, gait, model, motivation, nucleic acid sequence, organism, preference, success, training, transposon /insertion element, vocabulary, workshop

Project start date: 2007-08-01

Project end date: 2009-07-31

1R01GM080203-01 (2007): $383483

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008 Aug; 26( 8): 889-96. No abstract available. PMID: 18688244

Eilbeck K, Lewis SE.

Sequence ontology annotation guide. Comp Funct Genomics. 2004; 5( 8): 642-7. PMID: 18629179

Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.

The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008 May; 26( 5): 541-7. PMID: 18464787

Swedlow JR, Lewis SE, Goldberg IG.

Modelling data across labs, genomes, space and time. Nat Cell Biol. 2006 Nov; 8( 11): 1190-4. Review. PMID: 17060903

Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.

EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 2006; 7 Suppl 1: S2.1-31. Epub 2006 Aug 7. Review. PMID: 16925836

Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA.

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS. 2006 Summer; 10( 2): 185-98. Review. PMID: 16901225

Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E.

The RNA Ontology Consortium: an open invitation to the RNA community. RNA. 2006 Apr; 12( 4): 533-41. Epub 2006 Feb 16. PMID: 16484377

Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M.

The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005; 6( 5): R44. Epub 2005 Apr 29. PMID: 15892872

Lewis SE.

Gene Ontology: looking backwards and forwards. Genome Biol. 2005; 6( 1): 103. Epub 2004 Dec 15. PMID: 15642104

Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM.

Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002; 3( 12): RESEARCH0088. Epub 2002 Dec 23. PMID: 12537577

Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE.

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2002; 3( 12): RESEARCH0084. Epub 2002 Dec 23. PMID: 12537573

Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE.

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002; 3( 12): RESEARCH0083. Epub 2002 Dec 31. Review. PMID: 12537572

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