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Bioinformatics Advance Access published online on August 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth465
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 30, 2004
Revised July 22, 2004
Accepted August 2, 2004

Article

BioLingua: a programmable knowledge environment for biologists

J. P. Massar 1, Michael Travers 2, Jeff Elhai 3, Jeff Shrager 4*

1 Thinking Machines Corporation, Cambridge, MA, USA
2 MDL Information Systems, Inc., San Francisco, CA, USA
3 Department of Biology and Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
4 Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA, USA

* To whom correspondence should be addressed. E-mail: jshrager{at}stanford.edu.


  Abstract

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


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