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Bioinformatics Advance Access originally published online on August 12, 2004
Bioinformatics 2005 21(2):199-207; doi:10.1093/bioinformatics/bth465
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.

BioLingua: a programmable knowledge environment for biologists

J. P. Massar 1, Michael Travers 1, Jeff Elhai 3 and Jeff Shrager 1,2,*

1 Institute for Study of Learning and Expertise Palo Alto, CA, USA
2 Carnegie Institute of Washington, Department of Plant Biology Stanford, CA, USA
3 Virginia Commonwealth University, Center for the Study of Biological Complexity Richmond, VA, USA

*To whom correspondence should be addressed.

Summary: BioLingua is an interactive, web-based programming environment that enables biologists to analyze biological systems by combining knowledge and data through direct end-user programming. BioLingua embeds a mature symbolic programming language in a frame-based knowledge environment, integrating genomic and pathway knowledge about a class of similar organisms. The BioLingua language provides interfaces to numerous state-of-the-art bioinformatic tools, making these available as an integrated package through the novel use of web-based programmability and an integrated Wiki-based community code and data store. The pilot instantiation of BioLingua, which has been developed in collaboration with several cyanobacteriologists, integrates knowledge about a subset of cyanobacteria with the Gene Ontology, KEGG and BioCyc knowledge bases. We introduce the BioLingua concept, architecture and language, and give several examples of its use in complex analyses.

Availability: Extensive documentation is available online at http://nostoc.stanford.edu/Docs/index.html

Contact: JShrager{at}Stanford.edu


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