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TableEditA Mediawiki Extension

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overview

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• 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

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example

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QuickTime™ and a decompressor

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example

QuickTime™ and a decompressor

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QuickTime™ and a decompressor

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example

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QuickTime™ and a decompressor

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creating tables

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QuickTime™ and a decompressor

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creating tables

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QuickTime™ and a decompressor

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creating tables

• template based system– transclusion allows for abstraction

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QuickTime™ and a decompressor

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creating (templated) tables

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<newTableEdit>

Template:Gene_Nomenclature_table

</newTableEdit>

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test the demo gods

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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

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jQuery / DataTables

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summary tables

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summary tables

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driving images

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thanks to Mary Dolan @ MGI

QuickTime™ and a decompressor

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driving images

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QuickTime™ and a decompressor

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conflict detector

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help links

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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 );

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ifalt1. page title lacZ:Gene

2. page template Gene

3. table template Gene_nomenclature

4. row data field1 || field2 || field3

5. metadata metadata-for-the-row

6. update type append

7. misc key=value&arr[]=foo+bar

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…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

QuickTime™ and a decompressor

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thanks

• Jim Hu, the rest of the Hu Lab• EcoliHub(.org) & NIH• GMOD• Mediawiki Developers Mailing List

Daniel Renfro bluecurio@gmail.com

http://gmod.org/TableEdit