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TableEdit

TableEdit. A Mediawiki Extension. some background. wiki’s are innately free-form biological data is innately tabular how do you incorporate the two? you sneak structure into the mix…. overall goals. make it easy for (all) users to edit tables / tabular data lower the unit of submission

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TableEdit

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  1. TableEdit A Mediawiki Extension

  2. some background • wiki’s are innately free-form • biological data is innately tabular • how do you incorporate the two? • you sneak structure into the mix…

  3. overall goals • make it easy for (all) users to edit tables / tabular data • lower the unit of submission • make it easy to mine data / text from the wiki • contribute to the Mediawiki community

  4. example

  5. example

  6. example

  7. example

  8. example

  9. creating tables

  10. creating tables

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

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

  13. creating (templated) tables • select • checkbox • text • lookup • calc • lookupcalc • timestamp • foreign table properties column rules • <headings> • <heading_style> • <type> • <box_style> • <style> • <help[1-4]> • <above> • <below>

  14. column rules <headings> Qualifier||qualifier|select| |NOT|Contributes to|Colocalizes with|Obsolete … GO ID||go_id|text GO term name||go_term|lookupcalc|SELECT page_title FROM GO_archive.term WHERE go_id = '{{{go_id}}}' ORDER BY term_update DESC LIMIT 1|page_title|split|_!_|1 Reference(s)||refs Evidence Code||evidence|select| |IC: Inferred by Curator|IDA: Inferred from Direct Assay|IEA: Inferred from Electronic Annotation|IEP: Inferred from Expression|IGC: Inferred from Genomic Context|IGI: Inferred from Genetic Interaction|IMP: Inferred from Mutant Phenotype|IPI: Inferred from Physical Interaction|ISS: Inferred from Sequence or Structural Similarity … with/from||with|text Aspect||aspect|lookup|SELECT namespace from GO_archive.term WHERE go_id = '{{{go_id}}}' ORDER BY term_update DESC LIMIT 1|namespace Notes||Notes Status||status|calc|reqcomplete|go_id|refs|go_term|evidence </headings> <heading_style>{{table_heading_style}}</heading_style> [[Category:Table templates|GO table product]]

  15. the cool stuff • really big tables • conflict detector - keeps things correct • help links - 100% user editable • the loader - for mass imports / edits • documentation / specs - always good • modules - extensions of extensions • " foreign tables " & mirroring

  16. applications 12 x >67

  17. applications

  18. applications

  19. applications thanks to Mary Dolan @ MGI

  20. applications thanks to Mary Dolan @ MGI

  21. conflict detector

  22. help links

  23. the loader // Instantiate the object $loader = new TableEdit_Loader;  // set some options $loader->setVerbose(); $loader->setUser(); $loader->printInfo();   // load pretty much anything into tables from either an *.ifalt file. $loader->loadFromFile(array_pop($argv));

  24. 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

  25. 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 ifalt vs. XML 


  26. merging • A = B rows are exactly the same • A ⊆ B A is a subset of B • A ∩ B ≠ Ø mutually exclusive • A ∩ B = Ø disjoint

  27. docs • PHPdoc (like Javadoc) • wiki pages as HTML / PDFs

  28. modules • TableEdit_links • MirrorAnnotations

  29. foreign tables • how to mirror data from one table to another? • keeping data fresh… relations table

  30. database layout

  31. v2.0 • AJAX • constrain searching tables / subset of tables • better object/relational mapping • Chado roundtrip • constructive user feedback…

  32. get it • http://www.mediawiki.org/wiki/Extension:TableEdit • http://ecoliwiki.[net|org|com] • http://gowiki.tamu.edu • username: demo • Password: pag

  33. thanks • Jim Hu • Brenley McIntosh • the rest of the Hu Lab • EcoliHub(.org) & NIH • GMOD guys • Mediawiki Developers Mailing List • O'Reilly

  34. demo pcnB on dev

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