Semantic Lenses

Semantic Lenses are the UI and aggregator systems of Haystack. We expect the community to create, publish, and utilize lenses, based on their power and ease of use. A short guide on how to create and modify lenses is provided here.

Three initial viewing planes or canvases are provided with this version of BioDASH:

1.Topic Dashboard

This renders the therapeutic topic (RDF) and the underlying related information in a consolidated view:


The View is comprised of the following subviews/lenses:

2.BioPathways Viewer

Different views of selected pathways (hard-wired for the WNT-BioPAX file), that allow different pathway renderings.

·BioPAX lens (reaction view, signal transduction view)


This lens actually selects only the Component Entities that are related to interactions through the biopax:LEFT and biopax:RIGHT attributes, and connects them to each other. This way, the lens reduces the complexity inherent in a BioPAX model, to focus attention on only the elements a scientists needs at a give time. This is a useful paradigm when viewing any pathway model.

3.Chemical Canvas

This lens is designed to show a variety of relationships around aggregations of chemical entities and compounds. The relationships can be quite diverse (synthesized from, derived from, similar activity to, etc), originating from various different compound databases, as well as patent searches (concept from, patent covered by, etc). By representing multiple relations across different compound sets and libraries, it is possible to apply tools that can look for patterns in the relations that can enable chemists to find structure activity relations (SAR), alternative structures with minimal patent issues, and consolidate synthesis strategies for groups of compounds. The canvas includes:


  1. Relationship View
  2. Chemical Libraries View
  3. Relationships Editor
  4. Target Lists

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