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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
TableEdit

A Mediawiki Extension

overview
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
creating tables2
creating tables
  • template based system
    • transclusion allows for abstraction
creating templated tables
creating (templated) tables

<newTableEdit>

Template:Gene_Nomenclature_table

</newTableEdit>

the good stuff
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
driving images
driving images

thanks to Mary Dolan @ MGI

driving images1
driving images

thanks to Mary Dolan @ MGI

the loader
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 );

ifalt
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
as related to gmod
…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
thanks
thanks
  • Jim Hu, the rest of the Hu Lab
  • EcoliHub(.org) & NIH
  • GMOD
  • Mediawiki Developers Mailing List

Daniel Renfro [email protected]://gmod.org/TableEdit