PubNet a flexible system for visualizing literature derived networks 英文参考文献.docVIP

Open Access So are 2005DouglasetVoal.lumeftw6, Issue 9, Article R80 PubNet: a flexible system for visualizing literature derived networks Shawn M Douglas*, Gaetano T Montelione? and Mark Gerstein*? Addresses: *Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. ?Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers University and Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA. ?Department of Computer Science, Yale University, New Haven, CT 06520, USA. Correspondence: Mark Gerstein. E-mail: mark.gerstein@ Published: 16 August 2005 Received: 4 April 2005 Revised: 10 June 2005 Accepted: 12 July 2005 Genome Biology 2005, 6:R80 (doi:10.1186/gb-2005-6-9-r80) The electronic version of this article is the complete one and can be found online at /2005/6/9/R80 ? 2005 Douglas et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. VisualizingpPubNetliteratures a web-bderivedased toonetworksl to extract several types of relationships returned by PubMed queries and map them into networks./p Abstract We have developed PubNet, a web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors. This feature allows one to, for example, examine a literature derived network of genes based on functional similarity. Rationale Previous work has been done to augment or refi