THE ADHERENCE TO GROWTH HORMONE THERAPY IN CHILDREN WITH GROWTH HORMONE DEFICIENCY

WOS: 000412595403207

SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

BACKGROUND:Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases. RESULTS:Towards this goal, we developed a web based viewer named SBGNViz for process description maps in SBGN (SBGN-PD). SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis. CONCLUSION:SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms

Sample layout.

<p>(A) A sample process description map laid out randomly. (B) The same map laid out using our specialized layout algorithm.</p

Ignoring a node group.

<p>(A) Selected nodes (in orange) are to be hidden from the drawing. (B) First, selected nodes are expanded. (C) Then, the remaining nodes (in orange) are expanded. (D) Only those nodes in the expanded group calculated in C are those nodes to be displayed.</p

Sample screenshot from SBNViz JS edition on a smart phone.

<p>Sample screenshot from SBNViz JS edition on a smart phone.</p

Sample screenshot from SBNViz AS edition.

<p>Sample screenshot from SBNViz AS edition.</p

Use of generic complexity management.

<p>Application of generic complexity management techniques without the use of domain specific knowledge typically results in invalid or incomplete process description maps. (A) An SBGN map for ATM mediated phosphorylation of repair proteins in the context of MRN complex, (B) The same map after NBN instances are selected and the rest (in this case, only one of the four processes in the map) are hidden using generic filtering, and (C) The same map when proper filtering that takes domain-specific information into account is applied.</p

A sample screenshot illustrating how genes may be inspected for details.

<p>A sample screenshot illustrating how genes may be inspected for details.</p