Help:State of the Wiki

Done

Overall idea

The overall idea is to have a wiki that is centered on gene summarization. Wrapped around the core gene organizing concept are related data as necessary. It is to have one wiki page per Drosophila melanogaster gene that is seeded with the current automated summary as free text and an invitation to replace with human written free text using regular wiki technology. It is to take most or all of the data that is contained in the automated summary and put it into tables of structured data to the right of and below the user contributed gene summary to retain for reference purposes for writers and to enable the making of new connections between the gene and other FB datatypes using semantic wiki technology.

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

  A table of contents (TOC) is automatically generated and shows any section headings that follow.

  Publications

  Tables of recent reviews and papers that have data on each gene have been automatically generated in place using semantic wiki technology for use as reference while writing a summary and while citing assertions. See also ...

  Alleles

  A table of alleles of each gene has been automatically generated in place using semantic wiki technology for use as reference writing a summary. See also ...

Edit with form

• An edit with form tab has been enabled using semantic wiki technology hiding the complexity of editing raw wikitext.
• Summary tab of gene form separates the place where the automated gene summary is to be deleted and replaced with user contributed summary using WikiEditor toolbar for guidance.

In progress

Gene wiki page

• Infobox

Edit with form

• References Tab. Very obvious reviews on recently linked to genes. Very obvious missing PMIDs. Making text inviting users to use forms to fill these gaps in our data.

• Alleles Tab. Kathy's good idea. Making text inviting users to contribute data do not or can not curate easily but that is highly valuable to working geneticists in our community.

Documentaion

• Example page for a user edited gene summary.

• Visual tour / walkthrough showing how to accomplish certain tasks.

To-dos

• reciprocal links with FB for gene pages

Access control

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

Ontologies

• Human disease
• FB cv
• GO

Logo

• Chop fly off as an iconic rep of FB and write FlyBase Wiki underneath.