Help:State of the Wiki

Working towards... The goal has been to have a wiki that is centered/focused on gene summarization but capable of more and is 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 to give users a starting point 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. A description of the current state of the wiki and progress towards this goal is given below.

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 to function have been installed and configured.

Wiki software

• The MediaWiki free and 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 in the wiki:

  WikiEditor

  This extension improves the user experience by adding a toolbar to help in editing wiki markup (wikitext) in free text.

  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 allows for the storage and querying of structured data within the pages of the wiki, thus allowing it to be a "collaborative database" in addition to a "collaborative book".

  Semantic Forms

  This extension allows for the building of forms for adding, editing and querying data on the wiki, without any programming.

Seeding data

• Scripts have been written for initially seeding data into the wiki in three steps:
  1. Relevant data from Chado XML for the current release is converted to a data structure and stored for later use.
  2. This 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 already 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 for the above gene wiki pages has been made with these features:

  Stub

  A stub is an article deemed too short.

  Each seeded gene page has been tagged as a stub and had 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.

  This is where the automated gene summary has been placed on each page with the expectation it will be replaced.

  Infobox

  An infobox is a fixed-format table in the top right-hand corner of articles.

  This is where some identifying information for each gene has been placed.

  TOC

  The table of contents 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 made in the free text.

  Alleles

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

Edit with form

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

In progress

Gene wiki page

• More identifiying data is being added to the infobox on gene pages.
• Links to references tab of gene form requesting the addition of missing recent reviews and missing PMIDs are being addeed to the gene pages.
• Link to alleles tab of gene form requesting help identifying e.g. "best null" is being added to the gene pages.

Allele wiki page

• Just enough information is being added to be useful on gene summary page and its form.

Reference wiki page

• Just enough information is being added to be useful on gene summary page and its form.

Edit with form

• References tab

  Functionality is being added to enable wiki users to add more recent reviews for a gene and any missing PMIDs.

• Alleles tab

  Functionality is being added to enable wiki users to contribute data we do not curate that is highly valuable to our community, e.g. "best null".

Documentation

• An example page for what a finished human-edited gene summary should look like is being written.

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

Documentation

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

Logo

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