BioLingua: a programmable knowledge environment for biologists Export

@article{massar:2005:biolingua, 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.}, author = {Massar, J. P. and Travers, Michael and Elhai, Jeff and Shrager, Jeff}, citeulike-article-id = {164363}, citeulike-linkout-0 = {http://bioinformatics.oupjournals.org/cgi/content/abstract/21/2/199}, eprint = {http://bioinformatics.oupjournals.org/cgi/reprint/21/2/199.pdf}, journal = {Bioinformatics}, keywords = {bibtex-import, bioinformatics, biolingua, commonlisp, dsl, lisp, littlelanguage}, number = {2}, pages = {199--207}, posted-at = {2005-04-19 10:16:50}, priority = {3}, title = {BioLingua: a programmable knowledge environment for biologists}, url = {http://bioinformatics.oupjournals.org/cgi/content/abstract/21/2/199}, volume = {21}, year = {2005} }

TY - JOUR ID - massar:2005:biolingua L3 - citeulike-article-id:164363 N2 - 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. IS - 2 JF - Bioinformatics EP - 207 TI - BioLingua: a programmable knowledge environment for biologists VL - 21 SP - 199 KW - bibtex-import KW - bioinformatics KW - biolingua KW - commonlisp KW - dsl KW - lisp KW - littlelanguage AU - Massar, JP AU - Travers, Michael AU - Elhai, Jeff AU - Shrager, Jeff PY - 2005/// UR - http://bioinformatics.oupjournals.org/cgi/content/abstract/21/2/199 ER -