Help:State of the Wiki

Done

Operating system

• The Debian operating system has been installed on hardware good enough for group testing and initial deployment.
• All dependencies necessary for the wiki software have been installed and configured (e.g. Apache HTTP server, MySQL database software, PHP scripting language, etc.).

Wiki software

• The MediaWiki free open source wiki software, the same software behind Wikipedia, has been installed and configured.
• Several important extensions to the base MediaWiki software have been installed and configured to enable greater functionality for wiki users.

  WikiEditor

  This extension improves the user experience by adding a toolbar to help in editing wiki markup or wikitext.

  Cite

  This extension allows users to cite references and create a list of references.

  PubMed

  This extension pulls in literature data from scientific articles stored in PubMed

  Semantic MediaWiki (SMW)

  This extension lets you store and query structured data, not just free text, within the pages of the wiki making the wiki a "collaborative database" in addition to a "collaborative book".

  Semantic Forms

  This extension allows you to have forms for adding, editing and querying data on your wiki, without any programming.

Seeding data

• Scripts have been written in the Python programming language for initially seeding data into the wiki in three steps:
  1. Relevant data from Chado XML for the current release is converted to a Python data structure and stored for later use.
  2. This Chado XML data is combined with the precomputed gene summaries for the current release and written to wikitext files for each page in the wiki.
  3. Each wikitext file is then uploaded by a bot, which is a program that automatically retrieves or updates wiki pages, overwriting any pages that exist.
• A 15 gene wiki page sample set has been seeded.
  • Dmel\Adh
  • Dmel\Antp
  • Dmel\CG5071
  • Dmel\cnn
  • Dmel\Dl
  • Dmel\dpp
  • Dmel\if
  • Dmel\Khc
  • Dmel\oc
  • Dmel\rhea
  • Dmel\vn
  • Dmel\w
  • Dmel\W
  • Dmel\αTub67C
  • Dmel\γTub23C
• 3,737 allele wiki pages associated to the gene sample set have been seeded.
• 8,742 reference wiki pages associated to the gene sample set have been seeded.

Gene wiki page

• An initial layout of gene wiki pages has been made.

  Stub

  A stub is an article deemed too short and each initially seeded gene page has been tagged as one and an explanatory banner added to the top of the page.

  Lead

  The lead section of a Wikipedia article is the section before the table of contents and the first heading and where the automated gene summary has been placed on each page.

  Infobox

  An infobox is a fixed-format table in the top right-hand corner of articles and where some identifying information for each gene has been placed.

  TOC

  The tabel of contents is auto-generated and ...

  Publications

  Alleles

• The overall idea being:

  p

Edit gene wiki page with form

• Summary tab

In progress

Gene wiki page

• Infobox

Edit gene wiki page with form

• Alleles Tab

• References Tab

Documentaion

• Tour/walkthrough

To-dos

Access control

• Currently doing work as 'FlyBase Bot' and 'FlyBase Administrator'.
• Readers
• writers
• editors
• administrators