Visualizing information across multidimensional post-genomic structured and textual databases

Abstract

Motivation: Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface.

Results: We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research.

Availability: PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/

Contact: Lussier@dbmi.columbia.edu.

Figure 1

Architecture of the Phenogenes Viewer

Figure 2

Query interface showing dimensions of the Human Genomics Dataset

Figure 3

Tree generated from data in Table 3

Figure 4

Query results displayed in the presentation interface of Phenogenes Viewer (Human Genomics Dataset, comprehensive dataset from of table 1, order of dimensions: GO, Gene, Disorder, PubMedID)

Figure 5

Tree view of gene location, disorder and gene (Human Genomics Dataset)

Figure 6

Tree view of GO term, disorder, gene and PubMed ID (Human Genomics Dataset). The tree structure we use represents an ordering or clustering of information, and should not be associated with a hierarchical classification, which is a typical use of a tree when specifying an ontology or taxonomy