XSPAN provides two methods of accessing the database.
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:
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.
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
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.