xQTL GBrowse integration

In the future (when gBrowse supports bigbed) it is that if a user want to view data on a gBrowse the following happens

• Produce a BigBed? (for annotations such as Marker) / BigWig? files (for decimal data such as QTL). This may take some time on first call, or if the files needs refreshing on change
• Include in MOLGENIS suitable links towards the gBrowse instance that include loading of that custom track
• Include in these files hyperlinks back to the molgenis instance

See ​http://bioinformatics.oxfordjournals.org/content/26/17/2204.full.pdf

How to add GBrowse linkouts to MOLGENIS databases

Add a query option to the 'rubberband' menu where you can drag to select a genomic region

Open your GBrowse *.conf file. The rubberband menu has HTML elements and looks like this:

[DETAIL SELECT MENU]
width = 250
html  = <table style="width:100%">
         <tr>
           <th style="background:lightgrey;cell-padding:5">
             SELECTION
             <span style="right:0px;position:absolute;color:blue;cursor:pointer"
                   onclick="SelectArea.prototype.cancelRubber()">
               [X]
             </span>
           </th>
         </tr>

We add a table row with the linkout to a URL like this:

<tr>
  <td onmouseup="SelectArea.prototype.cancelRubber()">
    <a href="http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=SELECTION" target="_BLANK">
    molgenis region query
    </a>
  </td>
</tr>

The value of SELECTION is a GBrowse notation, so the accepting service must be compatible with these requests. An example of a resulting request:

.../api/find/org.molgenis.xgap.Marker?name=chr1:3790000..4759999

At the moment there is no MolgenisService? to facility this, but it the principles are trivial. ​A first step was done to enhance the existing filters for this purpose, but this is not GBrowse syntax yet. The multifilters ​are used like this.

Add a popup balloon to an annotation track

Open your GBrowse *.conf file. In the track, which e.g. looks like this:

[hxb-sdp]
feature       = experimental_feature:hxb_sdp
database      = variations

We add a balloon property, with a hyperlink, like this:

balloon click = <h2>Marker $name</h2>
       <a href='http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=$id'>Marker info from molgenis</a><br>

When clicking this link, it will request a marker by ID. The correct mapping for the $-variable to MOLGENIS entity attribute should be investigated on a per-database basis.

.../api/find/org.molgenis.xgap.Marker?name=1

Online GBrowse at GWAS Central (HGV-Base)

​http://www.gwascentral.org/browser/genome?r=HGVRS1375,HGVRS1374,HGVRS1373&t=

Online GBrowse at WormBase

​http://www.wormbase.org/db/gb2/gbrowse/c_elegans/?name=I:10747696..10779324