PDBWiki Help
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[edit] What is a Wiki?
From http://biowiki.net/:
- Wiki is a web technology designed to allow multiple authors to freely add and edit website contents. Wiki is thus well suited for developing collaborative online knowledge bases, whose best known example is Wikipedia (http://wikipedia.org).
PDBWiki uses the same underlying software as Wikipedia, which is called MediaWiki. This is why the screen layout and user functionality looks similar to Wikipedia. However, PDBWiki is not part of Wikipedia and not affiliated with Wikipedia in any way except for the facts that both projects aim to freely create and share information. For more information on the aims of PDBWiki see About PDBWiki.
[edit] Editing pages
Anyone can edit pages in PDBWiki. This approach enables an 'open peer review' of the contents on this site. On any page, there is an 'Edit' button at the top which shows an editable version of the 'page source'. The page source is basically the text content of the page plus some 'markup' to format the text. In general, no knowledge of the markup is required to add content to a page. Simply follow the style of the existing text. You can preview your changes by using the 'Show preview' button at the bottom of the page. If the results are not satisfying you can revoke the changes by clicking 'Cancel'. To keep the changes, click 'Save page'. This will show the new page, including the new contents. Any change to a page can be reverted and older states are kept in the page history.
For more detailed information about MediaWiki markup see here.
[edit] Submitting user comments
One of the main features of PDBWiki is to provide user submitted annotations of PDB structures. To submit a comment on an individual PDB entry (e.g. 1tdr), the 'User comments' section on the entry page contains a link 'Add comment'. This link will open a simple web form where the comment text can be entered without the need to know specific MediaWiki markup syntax. See example annotations to get an idea of what kind of comments are typically submitted and how they should look like to be helpful for other users.
[edit] Embedding images
It is possible to embed images in pages or user comments. To embed an image:
- Upload the image file using the 'Upload file' function in the toolbox on the left
- Embed the file in your text using the following syntax: [[File:myimage.jpg]].
Allowed file types are: gif, png, jpg.
For example, adding the text [[File:Apple-blue.02.png]] to a page gives:
[edit] Embedding PDB files
It is also possible to embed PDB files with coordinates. The procedure is the same as the one described for images above. In this case the embedding produces a link to download the file.
Example: File:1tdr.pdb
[edit] Adding citations
User comments should include relevant citations of scientific articles whenever possible. PDBWiki provides an easy way of adding citations if the cited article is listed in the Pubmed database. The following syntax using the Pubmed ID of the article:
<pubmed>14634627</pubmed>
automatically extracts the required information from Pubmed and produces the following output:
Helen Berman, Kim Henrick, Haruki Nakamura
Announcing the worldwide Protein Data Bank.
Nat. Struct. Biol.: 2003, 10(12);980
[PubMed:14634627]
[DOI]
(P p)
This syntax can be used in any wiki page or in user comments.
[edit] Categories
PDBWiki uses a category system to allow easier and more powerful searching and navigation of the contents. Entries are classified according to two types of categories:
- Categories based on details about the structure, such as protein type, source organism or enzyme classification. These are derived from the original PDB data.
- Categories based on the type of user annotation, such as error report, references to related work or quartenary structure discussion.
When adding annotations, categories are automatically assigned based on the user's selection from a drop down list of available categories. If none of the categories are suitable, 'General comment' should be selected. Currently it is not possible to create new categories without knowledge of the MediaWiki category system and syntax. If you would like to suggest a new category please send an email to info@pdbwiki.org.
The categories that a page is assigned to appear in a navigation bar at the bottom of the page. Clicking on one of the categories will open a page with pages in the same category. For examples of how to use categories for finding specfific entries, see here.
[edit] Categories for developers
The following information is mainly useful for developers and users wanting to create new pages.
Every page in PDBWiki belongs to a category (see here for more information about MediaWiki categories). All categories are organized into the following category tree. The individual category pages contain more information about how they are to be used.
Browse the PDBWiki category tree:
Or, click to see an overview diagram:
[edit] Structure report templates
We have created some templates to easily create structure reports based on membership to a category or links from a page. See Structure reports to learn how to use them to create your own report pages.
[edit] Custom reports
More complex custom reports can be created using the Dynamic Page List syntax. See the source of the pages below for examples:
