BioLingua: a programmable knowledge environment for biologists.
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.


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


BACKGROUND
JShrager@Stanford.edu
Institute for Study of Learning and Expertise Palo Alto, CA, USA.
J P
JP
Massar
Michael
M
Travers
Jeff
J
Elhai
Jeff
J
Shrager
D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods; D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D008956:Models, Chemical; D011381:Programming Languages; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology; D012984:Software; D014584:User-Computer Interface
D011506:Proteins