Changes between Initial Version and Version 1 of GBrowse

Timestamp:

2011-11-25T10:33:01+01:00 (13 years ago)

Author:

jvelde

Comment:

--

GBrowse

@@ +1 @@
+= xQTL GBrowse integration =
+
+== 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.
+
+=== 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