The Control Panel is the only way to customize the iHOPerator tag cloud.
This panel allows, among other things, the ability to toggle the visibility of the tag cloud, increase or decrease the tag clouds' font size, and choose custom tag cloud link actions. It is through this control that you will be able to toggle between viewing MeSH terms or viewing other genes that are known to interact with your search gene. The control panel will offer you the ability to retrieve relevant PubMed abstracts, to run a custom Taverna workflow or to browse available BioMOBY services using the gBrowse_moby web application.
View Controls are controls that control the visualization aspect of the iHOPerator application. As a user, you can choose what type of cloud to view, decide whether or not you would like to view the cloud at all, modify the font settings and re-sort a cloud that is no longer alphabetical.
Show
Choosing a value here will allow you to view either MeSH terms for the gene of interest or other genes that interact with your gene. These terms are obtained from the iHOP website and then transformed into your tag cloud.
Interacting Genes
When viewing iHOP pages for genes that are displaying interaction information, a tag cloud that conveys the same data is available for your visualization. When visualizing this type of cloud, you can easily see what genes are found to interact with your search gene by looking for the gene names with the largest text. In addition, iHOPerator allows you to invoke either a custom workflow (currently by calling a series of BioMOBY web services, but in the future using Taverna) that transforms a gene to a KEGG pathway diagram, or a session of gBrowse_moby using the gene as an inital program seed.
MeSH Terms
When you select this choice, you will view a cloud of MeSH terms associated with your gene of interest.
Show Tag Cloud
Here you can toggle the visibility of the iHOPerator tag cloud.
This setting only applies to the current page. However, you can save this setting by clicking on 'Save Settings'.
Tag Font Size
If the cloud appears too small or too large, you can modify the font size by simply choosing among the different size choices.
This setting only applies to the current page. However, you can save this setting by clicking on 'Save Settings'.
Re-Sort Cloud
This option allows you to re-sort the tag cloud alphabetically. This only needs to be done when you have manipulated the cloud using the 'Modify Tag Cloud Threshold' slider.
Modifying The Tag Threshold
This option allows users to modify the minimum frequency that a Term must have to show up in the tag cloud.
Initially, this value 0, so all terms that appear more than zero times are shown. Manipulating the slider so that the threshold is one, would cause all tags with a frequency of greater than one to appear.
Action Controls are controls that control the behaviour of tags in the iHOPerator application. As a user, you can choose to view PubMed abstracts, initialize a session of gBrowse_moby or run a custom workflow.
Tag Cloud Link Actions
Tag cloud link actions are actions that are initiated by clicking on the tags in the cloud.
These actions do a wide variety of things, such as querying PubMed to running pre-canned workflows.
Retrieve KEGG Pathways Diagram
The workflow, that in the future will be invoked using Taverna but currently makes a series of calls to the bioMOBY API, takes as input a gene name. In the case of iHOPerator, the gene is a tag that has been clicked on.
The gene is then passed to a BioMOBY service called getUniprotIdentifierByKeyword. This service returns an identifier that is valid under the UniProt namespace (if an identifier indeed exists).From a UniProt identifier, we obtain a KEGG id using the BioMOBY service convertIdentifier2KeggID.
Once a KEGG id is found, we obtain all of the KEGG pathways that the identifier is found to be associated with and we use this information to obtain diagrams of the pathways.
iHOPerator currently only displays one pathway diagram if some diagrams are found to exist using this workflow.
Use BioMOBY Services
If you choose not to run the workflow, you can choose to invoke a session of gBrowse_moby initialized with the selected gene. From there, you can choose to run a multitude of BioMOBY services discovered by the web application.Retrieve PubMed Abstracts
This is the only action available to iHOPerator users visualizing MeSH terms associated with your gene of interest.
When a user clicks on a tag, PubMed is queried for abstracts that contain the selected MeSH term and that is related to the gene of interest.
Open Links In New/Preview Window
This setting allows users of iHOPerator to open tag links in either a new window or to open links in a small 'preview' window.
If you choose to open links in the 'preview' window, the window will appear just below the tag cloud.
This setting only applies to the current page. However, you can save this setting by clicking on 'Save Settings'.
Remove Preview Window
This setting allows users to toggle the visibility of the 'preview' window.
To use this option, your browser must support and have cookies enabled.
The options currently saved are:
