Home spacer gif
spacer gif
Overview spacer gif
Technical spacer gif
XSPAN spacer gif
COBrA spacer gif
SAEL spacer gif
Cell Ontology spacer gif
Publications spacer gif
People spacer gif
Collaborators spacer gif
Contact Us
 
 
 
 
 

XSPAN Interfaces

XSPAN provides two methods of accessing the database.

The XSPAN GUI (Graphical User Interfaces) is now publically available, running as an applet.

To access the Help Pages for the Applets click on the following links:

XSPAN Applet Help

Click on the User Interface link in the menu to see further details including a screenshot of the GUI.

The XSPAN GUI is at the centre of the services provided by the XSPAN Project. The WebService used by the GUI to access the databse is also made available for use by third parties. Details of the WebService and a full list of the ontologies displayed are available on the web site.

 


The WSDL for the XSPAN service is available:

XSPAN SOAP

An example client (for the AXIS toolkit) is available by clicking here. It was tested on an Apple Mac running OS X (version 10.3), Java (version 1.4.2_05-141.3) and Axis (version 1.1) and has not been tested with any other platform or Java version.

For setup help please consult appropriate software provider.

 

 

XSPAN Applet Help

These pages apply to the XSPAN applet.


Click here to go to the XSPAN Home Page.

This Help page is to introduce you to the functionality of the XSPAN applet.

The larger screenshots on this page have been scaled down. To view the full-size image, click on the image.

The XSPAN applet takes about 20 seconds to load. To open the Graphical User Interface (GUI) that allows browsing of the ontologies, use the "Click to Launch the XSPAN Applet" button. The GUI opens in a new frame (window).

 

You are presented with a warning that there will be some delay in opening the GUI.

 

The GUI displays two ontologies side by side, and allows mappings between tissues to be identified. An initial ontology is selected from the top drop-down menu "Select Initial Ontology". "Abstract Human" is the default initial species.

 

A tissue is then selected from the initial ontology by clicking on the tree, and the selected tissue is highlighted in red ("Ectoderm" in the example). A target ontology is then selected from the second drop-down menu "Select Target Ontology ". This species ontology then appears as the Target Ontology tree ("Abstract Mouse" in the example). "All" is the default target species.

 

Next select the type of mapping desired. The XSPAN applet has "All" (default) , "Expert" and "Curated" as a mapping types. Expert mapping types are one-to-one mappings made individually by an expert, whereas Curated mappings are derived from the links made by experts from tissues to the Cell Type Ontology.

 

Click the "Search" button and a list of the mappings from the selected intial tissue to the target ontology appears in the table below the trees.

Clicking on a row in the table (one for each target species) opens a new frame which displays details of the mappings, and it also highlights the target tissue/s in the target tree in blue and expands the tree to show these (may need to scroll down).

 

The GUI can be reset to the default settings with the "Reset" button, or another target species selected and the search repeated.

Placing the mouse cursor over a tissue in any tree will reveal the unique accession number of that tissue in the tool-tip.

 

The initial organism and selected initial tissue can be used as a basis of a search for literature in PubMed by clicking on the "PubMed" button.

 

The PubMed search results are displayed in a new browser window/tab. From here the search results can be refined as usual.

 

 

Made on a Mac logo
 
Copyright 2011 http://www.xspan.org/.