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Genboree lets you describe custom links for integrating your annotations with other web-sites, databases, and services. This is done through HTTP "GET"-style URLs containing substitution tags which Genboree will automatically fill in.
The general process is:
To manage your custom links, Genboree provides the following functions:
6.2. Creating Custom Links:
To generate a custom link, you need to:
6.2.1. Constructing URL patterns
To generate a URL Pattern, you can usually:
Thus, seeing a specific URL such as:
We would probably create a URL pattern like this:
In this example, the Annotation's entry point (eg. chromosome name), start, and end fields are used to construct the value for the "position" parameter. This will provide a link from the annotation in Genboree to the equivalent region in the UCSC browser.
6.2.2. Example URL patterns
Static link (same URL for all annotations):
Simple link (annotation name determines an HTML page name):
Standard link (annotation data used for various parameters):
6.2.3. Simple tags
The following tags are simply replaced by the corresponding data from the annotation. The names correspond very closely to the LFF columns:
6.2.4. Regular expression tags
Regular expression tags are used for extracting a specific piece of information from a selected field. The format of a regular expression tag is:
NOTE: The text matched by the sub-group will be used for tag substitution.
For example, the following URL Pattern has a regular expression tag that extracts everything before a version number from the name field for use in the URL:
The following two examples are essentially identical and use custom attributes associated with the annotations to link to a matching region within Genboree itself. Both are placing the annotation's value for that attribute into the link:
NOTE: These are just examples from specific user databases and will almost certainly not as-is for your data.
NOTE: If you are trying to make custom links that point within Genboree itself—even to another one of your databases—you will need a specific "refSeqId" parameter as suggested by the examples above. This arbitrary value indicates the target database for the link.
6.2.5. Special Tags
Special tags cause the annotation data to first be processed in some way before being used in the URL. Currently there is a single such tag:
6.2.6. Genboree-Specific Tags
These tags can be used for links to Genboree pages requiring special parameters. Currently there is a single such tag:
6.3. Assigning Links to Tracks:
Each track can be assigned one or more links. These links will show up when the user clicks an annotation in the track (depicted above), and the link URL will be filled in with any annotation data you specified when creating the link.
This also means that a link you create can be used in multiple tracks.
To assign links to a track:
NOTE: The link list on the right is a standard multiple-selection list widget. On MS Windows, Ctrl-Click can be used to make multiple selections. Other operating systems may use another button combination, such as Open Apple-Click.