Difference between revisions of "Help:State of the Wiki"
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=== Seeding data === | === Seeding data === | ||
| − | * | + | * Scripts have been written in the Python programming language for initially seeding data into the wiki in three steps: |
| − | * | + | *# Relevant data from Chado XML for the current release is converted to a Python data structure and stored for later use. |
| − | * | + | *# 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. |
| − | * FlyBase Bot | + | *# 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 [[Category:Genes|gene]] wiki page sample set has been seeded for: | |
| − | + | ** [[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 [[Category:Alleles|allele]] wiki pages associated to the gene sample set have been seeded. | ||
| + | * 8,742 [[Category:References|reference]] wiki pages associated to the gene sample set have been seeded. | ||
| + | * Doing work as 'FlyBase Bot' and 'FlyBase Administrator'. | ||
=== Gene Summary Free Text === | === Gene Summary Free Text === | ||
Revision as of 22:06, 10 August 2012
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:
- Relevant data from Chado XML for the current release is converted to a Python data structure and stored for later use.
- 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.
- 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 wiki page sample set has been seeded for:
- 3,737 wiki pages associated to the gene sample set have been seeded.
- 8,742 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