How to annotate structures
From PDBWiki
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[edit] Basic idea
One of the main ideas of PDBWiki is to bring together users of PDB structures and allow them to provide additional annotation. This may include things like comments on the quality of the model, errors in the PDB annotation, additional information about the function of the protein or pointers to external references. Every structure entry in this Wiki contains some basic information derived from the PDB and an editable section for user annotations. The next paragraph gives step-by-step instructions for how to add such annotations.
[edit] Instructions
- Find the structure you want to annotate (e.g. 1pdb) by
- searching for the PDB code using the search box on the left, or
- browsing structures by categories (e.g. by release year, source organism, EC number, etc.)
- Click on add comment in section User comments and follow the instructions for adding user annotation
- The new annotation will appear on the page '1pdb'.
[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] Examples
- 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.
- Click here to see a complete list of all annotated entries
