Genboree

HELP TOPIC: "6. Custom Links"




 
6.1. Overview:

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:

  1. Log into Genboree.
  2. Navigate via the menu to My Databases / Manage Tracks / Link Setup.
  3. Select the appropriate Group and Database in the droplists.
  4. Create the custom link.
  5. Assign the link to one or more tracks.
  6. NOTE: to manage custom links, you must have at least the Author role in the Group.

Once you have done this, the custom link(s) will be listed in the annotation's pop-up dialog and any substitution tags will be replaced with the appropriate annotation-specific data:  

To manage your custom links, Genboree provides the following functions:

  • Create
    - Describe the custom link's URL pattern. (details below)

  • Edit
    - Edit the link definition.

  • Delete
    - Delete links (entirely).

  • Assign
    - Assign links to tracks. (details below)


 
6.2. Creating Custom Links:

To generate a custom link, you need to:

  1. Decide on a Name for the link. This is what users will see in the pop-up.
  2. Construct a URL Pattern. This will be a dynamically-generated URL.

 

6.2.1. Constructing URL patterns

To generate a URL Pattern, you can usually:

  • - start with a specific URL that works in your browser
  • - identify the parameters the URL needs
  • - then replace any parameter values with substitution tags where annotation-specific data will be placed.

Thus, seeing a specific URL such as:

http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6:2891241-2892562&org=Mouse

We would probably create a URL pattern like this:

http://genome.ucsc.edu/cgi-bin/hgTracks?position=$entrypoint:$start-$stop&org=Mouse
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):

http://genetics.sefu.edu/~debruin/index.html

Simple link (annotation name determines an HTML page name):

http://genetics.sefu.edu/~debruin/geneAnalysis/$name.html

Standard link (annotation data used for various parameters):

http://msinfor.imgen.bcm.tmc.edu/hmprocess/showwin.cgi?begin=$start&end=$stop&chr=$entrypoint
 
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:

  • ${<fieldName>:<regexp>}
  • ${<"attributeName">:<regexp>}

  • - <fieldName> is one of the fields listed under "6.2.2 Simple tags" above
  • - <attributeName> is quoted and refers to a custom attribute in your annotations.
  • - <regexp> is a Perl5-syntax regular expression with exactly one (1) sub-group.

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:

http://www.hapmap.org/cgi/gbrowse/hapmap?name=${name:([^.]+)}

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:

http://www.genboree.org/java-bin/gbrowser.jsp?entryPointId=${"matePairChr"=(.+)}&from=${"matePairStart"=(.+)}&to=${"matePairStop"=(.+)}&refSeqId=$genboreeRefSeqId

http://www.genboree.org/java-bin/gbrowser.jsp?entryPointId=${"matePairChr"}&from=${"matePairStart"}&to=${"matePairStop"}&refSeqId=778

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.

 
If the link it to a Genboree view within the same database, simply use $genboreeRefSeqId. If the link is to a view in another of your databases, you will need its id value. The easiest way to get this value for your database is to use the "Full URL" menu item in the graphical Browser; that will also show the general form of a Genboree link. Examples of both of these cases are shown above.

 
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:

  • $stripName
    • - Removes any characters after, and including, the last "." from the annotation's name.
    • - Useful for removing version numbers or unique suffices.
    • - Equivalent to this regular expression tag: ${name:(.+?)(?:\.[^\.]*)?$}

 
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:

  • $genboreeRefSeqId
    • - The current database's id number. This value is most often used for the refSeqId parameter.
    • - Useful for Genboree Browser links to other locations within the same database.

 
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:

  1. Log into Genboree.
  2. Navigate via the menu to My Databases / Manage Tracks / Link Setup / Assign.
  3. Select the appropriate Group and Database in the droplists.
  4. Select a track from the list on the left.
  5. After a brief pause, any links assigned to the track will be highlighted on the right.
  6. You can change the selections to add or remove assigned links for this track.
  7. When finished with the selections for the track, click Assign.
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.

 

 

 


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