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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.

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Presentation on theme: "TableEdit A Mediawiki Extension. overview Goals –Merge free-form wiki's with tabular biological data –Make tables useful in MediaWiki –Make it easy to."— Presentation transcript:

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

5

6 creating tables

7

8 template based system –transclusion allows for abstraction

9 creating (templated) tables Template:Gene_Nomenclature_table

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

15 driving images thanks to Mary MGI

16 driving images

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 1.page titlelacZ:Gene 2.page template Gene 3.table templateGene_nomenclature 4.row datafield1 || field2 || field3 5.metadatametadata-for-the-row 6.update typeappend 7.misckey=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


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