Osprey: a network visualization system
© Breitkreutz et al.; licensee BioMed Central Ltd. 2003
Received: 8 November 2002
Accepted: 10 January 2003
Published: 27 February 2003
We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.
The rapidly expanding biological datasets of physical, genetic and functional interactions present a daunting task for data visualization and evaluation . Existing applications such as Pajek allow the user to visualize networks in a simple graphical format , but lack the necessary features needed for functional assessment and comparative analysis between datasets. Typically, interaction networks are viewed within a graphing application, but data is manipulated in other contexts, often manually.
To address these shortfalls, we developed a network visualization system called Osprey that not only represents interactions in a flexible and rapidly expandable graphical format, but also provides options for functional comparisons between datasets. Osprey was developed with the Sun Microsystems Java Standard Development Kit version 1.4.0_02 , which allows it to be used both in stand-alone form and as an add-on viewer for online interaction databases.
Searches and filters
Osprey allows user defined colors to indicate gene function, experimental systems and data sources. Genes are colored by their biological process as defined by standardized Gene Ontology (GO) annotations. Genes that have been assigned more than one process are represented as multicolored pie charts. Osprey currently recognizes 29 biological processes derived from the categories maintained by the GO Consortium . Interactions are colored by experimental system along the entire length of the edge between two nodes. If a given interaction is supported by multiple experimental systems, the edges are segmented into multiple colors to reflect each system. Alternatively, interactions can be colored by data source, again as multiply colored if more than one source supports the interaction. When combined with filter options, a network can be rapidly visualized according to any number of experimental parameters.
A personal copy of the Osprey network visualization system version 0.9.9 for use in not-for-profit organizations can be downloaded from the Osprey webpage at . Registration is required for the sole purpose of enabling notification of software fixes and updates. A limited version of Osprey used for online interaction viewing can be used at The GRID website . For implementation of Osprey as an online viewer for other online interaction databases please contact the authors.
We thank Hosam Abdulrrazek for contributions to our layout algorithms, and Lorrie Boucher, Ashton Breitkreutz and Paul Jorgensen for suggestions on Osprey features. Development of Osprey was supported by the Canadian Institutes of Health Research. M.T. is a Canada Research Chair in Biochemistry.
- Vidal M: A biological atlas of functional maps. Cell. 2001, 104: 333-339.PubMedView ArticleGoogle Scholar
- Batagelj V, Mrvar A: Pajek - program for large network analysis. Connections. 1998, 21: 47-57.Google Scholar
- Sun Microsystems Java Standard Development Kit 1.4.0_02. [http://java.sun.com]
- The Grid. [http://biodata.mshri.on.ca/grid]
- Batik SVG toolkit. [http://xml.apache.org/batik/]
- Adobe Illustrator 10. [http://www.adobe.com/products/illustrator/main.html]
- Cherry JM, Ball C, Dolinski K, Dwight S, Harris M, Matese JC, Sherlock G, Binkley G, Jin H, Weng S, Botstein D: Saccharomyces Genome Database June 2002. [ftp://genome-ftp.stanford.edu/pub/yeast/SacchDB/]
- The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nat Genet. 2000, 25: 25-29. 10.1038/75556.View ArticleGoogle Scholar
- Osprey. [http://biodata.mshri.on.ca/osprey]
- Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, et al: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002, 415: 141-147. 10.1038/415141a.PubMedView ArticleGoogle Scholar
- Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, et al: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002, 415: 180-183. 10.1038/415180a.PubMedView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.