Help:State of the Wiki

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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 data 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 fifteen gene wiki page sample set has been seeded for:
  • 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.
  • Doing work as 'FlyBase Bot' and 'FlyBase Administrator'.

Gene Summary Free Text

In progress

Alleles

References

Human disease

To-dos

Look and feel

Access control

  • Readers
  • writers
  • editors
  • administrators

Ontologies

Sync with FB after seeding / data flow

SPAM

Open ID

Legal