Difference between revisions of "Help:State of the Wiki"
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*: This extension pulls in literature data from scientific articles stored in PubMed | *: This extension pulls in literature data from scientific articles stored in PubMed | ||
*; Semantic MediaWiki (SMW) | *; 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". | + | *: 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 | *; Semantic Forms | ||
*: This extension allows you to have forms for adding, editing and querying data on your wiki, without any programming. | *: This extension allows you to have forms for adding, editing and querying data on your wiki, without any programming. | ||
| Line 27: | Line 27: | ||
*# 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. | *# 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. | *# 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 | + | * A 15 [[:Category:Genes|gene]] wiki page sample set has been seeded. |
** [[Dmel\Adh]] | ** [[Dmel\Adh]] | ||
** [[Dmel\Antp]] | ** [[Dmel\Antp]] | ||
| Line 45: | Line 45: | ||
* 3,737 [[:Category:Alleles|allele]] wiki pages associated to the gene sample set have been seeded. | * 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. | * 8,742 [[:Category:References|reference]] wiki pages associated to the gene sample set have been seeded. | ||
| − | |||
| − | === Gene | + | === 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>p</p> | ||
| + | |||
| + | === Edit gene wiki page with form === | ||
| + | |||
| + | * Summary tab | ||
== In progress == | == In progress == | ||
| − | === | + | === Gene wiki page === |
| + | |||
| + | * Infobox | ||
| − | === | + | === Edit gene wiki page with form === |
| − | + | * Alleles Tab | |
| + | |||
| + | * References Tab | ||
| + | === Documentaion === | ||
| + | * Tour/walkthrough | ||
== To-dos == | == To-dos == | ||
| + | |||
| + | === Human disease === | ||
=== Look and feel === | === Look and feel === | ||
| Line 66: | Line 91: | ||
=== Access control === | === Access control === | ||
| + | * Currently doing work as 'FlyBase Bot' and 'FlyBase Administrator'. | ||
* Readers | * Readers | ||
* writers | * writers | ||
Revision as of 18:05, 11 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 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:
- 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 15 gene wiki page sample set has been seeded.
- 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
Human disease
Look and feel
Access control
- Currently doing work as 'FlyBase Bot' and 'FlyBase Administrator'.
- Readers
- writers
- editors
- administrators