1 / 34

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

teddy
Download Presentation

TableEdit

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related