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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