Nexplorer3 (challenge entry)

[Arlin Stoltzfus]

Dear iEvoBio--

Please accept the enclosed challenge entry abstract with low-res screen shots.    

Arlin

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Arlin Stoltzfus (ar...@umd.edu)

Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST

IBBR, 9600 Gudelsky Drive, Rockville, MD

tel: 240 314 6208; web: www.molevol.org

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Nexplorer3: interactive visualization and querying of comparative data, built on the foundation of an ontology

Vivek Gopalan1, Qina Tan1, Yasmin Mohamoud1, Arlin Stoltzfus 2 and Yentram Huyen1

1Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

2 Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899.

Evolutionary comparative analysis is an example of a scientific domain in which the interoperability of software and resources is low.   For example, PFAM, PANDIT, TreeBASE, and  TreeFAM are online resources with comparative molecular data (trees and sequence alignments), but these data are stored in incompatible formats.  Hence, it is not easy for a phylogenetics researcher to use these resources in an integrative manner.  To address such challenges, members of the phylogenetics community are developing a Comparative Data Analysis Ontology (CDAO), which covers molecular and non-molecular characters. 

Nexplorer3 is an interactive viewer for phylogenies and associated character data, such as sequence alignments.   Like other available viewers, it supports some mouse-driven operations on trees and associated data.  However, unlike other phylogenetics software based on ad hoc data models or formats, Nexplorer3 is built on the foundation of CDAO.  The data model is populated by processing statements from a CDAO RDF file.  The front end of Nexplorer3 is a web client, built using GWT (Google web toolkit), that makes requests (RESTful) and gets responses (JSON) back from the server, which uses a CDAO API built on the Jena library.  In addition to implementing mouse-driven commands  (operating on the tree or character matrix), it provides a SPARQL query interface.  

An installation of Nexplorer3 is available at http://exon.niaid.nih.gov/nexplorer (click "Source" to select a data source). To build and install a local instance that will run as an embedded Tomcat server, follow the directions at http://nexplorer.svn.sourceforge.net/viewvc/nexplorer/trunk/nexplorer3/README.txt . 

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