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TableEdit

TableEdit. A Mediawiki Extension. overview. Goals Merge free-form wiki's with tabular biological data Make tables useful in MediaWiki Make it easy to add data (for the uninitiated) Get data in/out en masse Some examples: Gene Ontology terms & community annotation

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TableEdit

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  1. TableEdit A Mediawiki Extension

  2. overview • Goals • Merge free-form wiki's with tabular biological data • Make tables useful in MediaWiki • Make it easy to add data (for the uninitiated) • Get data in/out en masse • Some examples: • Gene Ontology terms & community annotation • A list of participants at a GMOD 2010 meeting • Protein interaction data

  3. example

  4. example

  5. example

  6. creating tables

  7. creating tables

  8. creating tables • template based system • transclusion allows for abstraction

  9. creating (templated) tables <newTableEdit> Template:Gene_Nomenclature_table </newTableEdit>

  10. test the demo gods

  11. the good stuff • really big tables & jQuery / DataTables • conflict detector • help links - 100% user editable • the loader - for mass imports / edits • documentation / specs (in progress) • modules/plug-ins • "foreign tables" & mirroring

  12. jQuery / DataTables

  13. summary tables

  14. summary tables

  15. driving images thanks to Mary Dolan @ MGI

  16. driving images thanks to Mary Dolan @ MGI

  17. conflict detector

  18. help links

  19. the loader // Instantiate the object $loader = new TableEdit_Loader;  // set some options $loader->setVerbose(true); $loader->setUser("WikiBot"); $loader->blah("foo");   // load pretty much anything into tables from either an *.ifalt file. $loader->loadFromFile( $your_data );

  20. ifalt • page title lacZ:Gene • page template Gene • table template Gene_nomenclature • row data field1 || field2 || field3 • metadata metadata-for-the-row • update type append • misc key=value&arr[]=foo+bar

  21. …as related to GMOD • Gbrowse roundtrip • requires SeqFeature::Store • requires valid GFF3 • requires 'prokaryotic' genbank2gff3 • User defined gene-models • CHADO frontend • User defined everything • Bio::Chado::Schema / DBIx::Class

  22. thanks • Jim Hu, the rest of the Hu Lab • EcoliHub(.org) & NIH • GMOD • Mediawiki Developers Mailing List Daniel Renfro bluecurio@gmail.comhttp://gmod.org/TableEdit

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