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Open Access Highly Accessed Software

GeneNotes – A novel information management software for biologists

Pengyu Hong1 and Wing H Wong2

Author Affiliations

1 BioX program, Department of Statistics and HRP, Stanford University, Stanford, CA 94305-4065, USA

2 BioX program, Department of Statistics and HRP, Stanford University, Stanford, CA 94305-4065, USA

BMC Bioinformatics 2005, 6:20  doi:10.1186/1471-2105-6-20

Published: 1 February 2005

Abstract

Background

Collecting and managing information is a challenging task in a genome-wide profiling research project. Most databases and online computational tools require a direct human involvement. Information and computational results are presented in various multimedia formats (e.g., text, image, PDF, word files, etc.), many of which cannot be automatically processed by computers in biologically meaningful ways. In addition, the quality of computational results is far from perfect and requires nontrivial manual examination. The timely selection, integration and interpretation of heterogeneous biological information still heavily rely on the sensibility of biologists. Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information.

Description

We developed an information management application called GeneNotes. GeneNotes is the first application that allows users to collect and manage multimedia biological information about genes/ESTs. GeneNotes provides an integrated environment for users to surf the Internet, collect notes for genes/ESTs, and retrieve notes. GeneNotes is supported by a server that integrates gene annotations from many major databases (e.g., HGNC, MGI, etc.). GeneNotes uses the integrated gene annotations to (a) identify genes given various types of gene IDs (e.g., RefSeq ID, GenBank ID, etc.), and (b) provide quick views of genes. GeneNotes is free for academic usage. The program and the tutorials are available at: http://bayes.fas.harvard.edu/genenotes/ webcite.

Conclusions

GeneNotes provides a novel human-computer interface to assist researchers to collect and manage biological information. It also provides a platform for studying how users behave when they manipulate biological information. The results of such study can lead to innovation of more intelligent human-computer interfaces that greatly shorten the cycle of biology research.