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How to Build a MOD

How to Build a MOD. Lincoln Stein Cold Spring Harbor Laboratory. What’s a MOD?. Model Organism Database Repository for reagents Stocks, vectors, clones Genetic & physical maps Large-scale data sets Genome EST sets, microarray results, 2-cell hybrid interactions Literature

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How to Build a MOD

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  1. How to Build a MOD Lincoln Stein Cold Spring Harbor Laboratory

  2. What’s a MOD? • Model Organism Database • Repository for reagents • Stocks, vectors, clones • Genetic & physical maps • Large-scale data sets • Genome • EST sets, microarray results, 2-cell hybrid interactions • Literature • Ontologies & Nomenclature • Meetings, announcements

  3. WormBase Web Site

  4. WormBase Tour: Looking for MAP Kinase Kinase

  5. mek-2 RNAi Studies Found a Genetic Locus: mek-2 mek-2 Phenotype & Expr Pattern

  6. mek-2 RNAi Phenotype

  7. mek-2 Sequence View

  8. mek-2 Genome View

  9. Elegans/Briggsae Synteny

  10. mek-2 PCR Assays

  11. mek-2 Bibliography

  12. mek-2 Citation

  13. VBx Neuroanatomy

  14. How WormBase Works Web server Images, Movies Perl scripts You Database access library Genomic Data ACeDB MySQL

  15. .ace .ace .ace .ace .ace WormBase Information Workflow CalTech Sanger WashU NCBI CGC Sanger CalTech Caltech.wormbase.org CSHL www.wormbase.org

  16. Curating a Paper Clipping Service Domain Expert Gene Record Database Entry Cell Record Mutant Record CalTechAce .ACE Files .ACE File

  17. Can You Reuse WormBase Software for your Favorite Organism? No!

  18. Sorry Charlie • Wormbase website difficult to install • Data model nematode-centric • Curators tools very process-specific • Customization difficult • Software documentation uneven • Standard operating procedure documentation uneven

  19. MOD Redux • SGD, MGD, FlyBase, TAIR… • The same basic idea as WormBase • Implementation entirely different • Wheel reinvented many times • Little software sharing • This madness must stop!

  20. The GMOD Project • Portable, open source software to support model organism databases • Multiple MODs involved • Worm, fly, yeast, mouse, arabidopsis, rat, monocot, [fugu], [E. coli] • Funded by NIH as of June 2002 • Programmers, coordinator, quarterly meetings http://www.gmod.org

  21. GMOD Home Page

  22. Modular Applications The GMOD Pyramid Modular Schema Open Source DBMS & Middleware

  23. genetic maps liter- ature genome A MOD Construction Set map browser map editor Appplication Layer annotation pipeline genome browser genome editor citation browser citation editor Bioperl BioJava BioPython Middleware Layer genomes maps citations Database Layer

  24. Current GMOD Packages • Chado modular schema • Apollo genome annotation editor • Gbrowse generic genome browser • PubSearch literature curation editor • CMAP comparative map browser • LabDoc standard operating procedure editor

  25. Chado – Modular Schema • Immediate goal: common schema for use by FlyBase and WormBase • Ontology Driven • Small number of generic tables e.g. “feature” • Controlled vocabulary names subtypes & describes relationships among them • e.g. “transcript fg83.2 encodesprotein fp1803” • Detail tables provide further information on subtypes

  26. Apollo – BDGP & Sanger Center

  27. Apollo Data adapters • Parser -> data models -> display • Existing data adapters • GAME XML • GFF • Ensembl CGI server • DAS • Write your own data adapter! • Extend AbstractDataAdapter class • Display options defined in config file

  28. Who is Using Apollo? • BDGP • Reannotated Drosophila genome • Bristol-Myers Squibb • Launching Apollo from web browser via mime types • GNF • JDBC adapter layer over BioSQL • Biogen • View human genome alignment between public and Biogen internal database • Connected BLAT pipeline to Apollo • HGMP-RC Fugu Genomics group • Displaying annotations on fugu scaffolds

  29. PubSearch – TAIR & RatDB

  30. PubSearch – Gene Association

  31. CMap – Gramene

  32. Cmap – Detailed View

  33. GBrowse – WormBase

  34. GBrowse – Zoomed in

  35. GBrowse – Zoomed Way In

  36. GBrowse – Zoomed Way Way In

  37. GBrowse – Keyword Search

  38. GBrowse – Third Party Annotations

  39. Sequence dumps & other reports

  40. Extensively Customizable • End-user • Turn tracks on and off, change order, change packing & labeling attributes (stored in cookie) • Data provider • Change fonts, colors, text. • Change overview – genetic map, contigs, coverage, karyotype. • Define new tracks using simple config file. • Tinker with track appearance to hearts content.

  41. Adding a New Track (a) Create a GFF file named “deletions.gff” Chr1 targeted deletion 1293224 1294901 . . . Deletion d101k2 Chr1 targeted deletion 8239811 8241116 . . . Deletion d680k2 Chr2 targeted deletion 5866382 5866500 . . . Deletion d007k2 (b) Run the load_gff.pl script > load_gff.pl –d example_database deletions.gff Loading features… Done. 3 features loaded. (c) Add a new track “stanza” to the gbrowse configuration file [Knockout] feature= deletion glyph= span fgcolor= red key = Knockouts link = http://example.org/cgi-bin/knockout_details?$name citation= These are deletion knockouts produced by the example knockout consortium (http://example.org/knockouts.html)

  42. Extensively Extensible Plugins gbrowse CGI script Apache Web Server Glyphs Bio::Graphics library Oracle adaptor BioPerl library Flat File adaptor Bio::DB::GFF adaptor Chado adaptor Oracle MySQL/Postgres Flat Files

  43. GenBank Proxy Adaptor Bio::DB::GFF adaptor GenBank MySQL GBrowse on GenBank? GBrowse on GenBank! Plugins gbrowse CGI script Apache Web Server Glyphs Bio::Graphics library BioPerl library

  44. B. burgdorferi via GenBank proxy

  45. Who is Using GBrowse? • GMOD Members • WormBase, FlyBase, RatDB • HGMP-RC Fugu genomics group • KEGG (multiple microorganisms) • Ingenium AG (mouse) • Bristoll-Myers Squibb (drosophila) • Texas A&M University (salmonella) • Institute of Systems Biology (human)

  46. Coming Soon to www.gmod.org • Biopipe – genome annotation pipeline • Insertional mutagenesis analysis pipeline • Tree browser • Pathway browsers • Generic MOD web site framework

  47. Joining GMOD • Go to www.gmod.org • Examine software matrix • Find a project or suggest new one • Contact Scott Cain: cain@cshl.org • Or mail gmod-dev@lists.sourceforge.net

  48. Credits CSHL Adrian Arva Shuly Avraham Scott Cain Ken Clark Allen Day BDGP Nomi Harris Suzanna Lewis Chris Mungall John Richter ShengQiang Shu Colin Weil EBI Michele Clamp Stephen Searle Carnegie Institute Sue Rhee Danny Yoo Harvard David Emmert Stan Letovsky http://www.gmod.org

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