Dec 21 2011

Concept Nodes

Published by at 11:09 am
Under Bioinformatics | Editing | Generative Medicine | Quodlibet

This entry is about an editing function in QUODLIBET. QUODLIBET is a computer program that creates, edits and queries biomedical networks. In addition to providing information about genetic-protein-phenotype interactions QUODLIBET also allows for additional information to be harvested, including data on the effects of natural products on gene-protein expression.  We are always looking for volunteers who are interested in helping out. Volunteers need not have any medical or super computer skills, just a passion for exactitude and a desire learn more about the genetics and biology.

Here is some documentation to get you going:

There is also a Forum for new users and potential editors.

Most of the nodes in a QUODLIBET network might be called ‘working nodes.’ Working nodes are, to say the least, nodes that do some sort of work: they might carry information about a gene, a naturopathic agent associated with that gene or even contain other constituent genes. These types of nodes are also involved in the calculations that drive the network Analytics. But most QUODLIBET canvases are not made up solely from working nodes. For example, a pathway may terminate in a node that describes a process of some sort, such as ‘Increased insulin resistance’ or ‘Acyl-CoA.’ We might consider these Concept Type Nodes: Nodes that identify and teach about the context by which the network functions and has meaning.

Unlike basic working nodes, where you are free (or even impelled) to ‘roll your own,’ concept nodes are chosen and inserted from a toolkit of currently available items. This is done to maintain conformity and continuity: The concept node ‘Acyl-CoA’ will hyperlink to the same description popup in the map are editing as it will in any other map it appears in. Thus we only have to produce on very good entry on Acyl-CoA versus create one anew for every different map that needs one.

A concept node in a network.

Inserting a concept node into a map is easy: try adding one into the Sandbox map. From the pull-down, select one of the available concept nodes and press Submit. The Concept node will appear as a white box with a grey border. From there you can link concept nodes with edges just link any other node. Here we’ve inserted the concept node Acyl-CoA and linked it to the Vancouver node.

Now when a user clicks on the concept node Acyl-CoA they will be treated to the following information pop-up:

Concept node user information popup

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