{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T19:27:20Z","timestamp":1760297240570,"version":"3.30.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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.<\/jats:p><jats:p>Availability: Extensive documentation is available online at http:\/\/nostoc.stanford.edu\/Docs\/index.html<\/jats:p><jats:p>Contact: \u00a0JShrager@Stanford.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth465","type":"journal-article","created":{"date-parts":[[2004,8,13]],"date-time":"2004-08-13T00:15:36Z","timestamp":1092356136000},"page":"199-207","source":"Crossref","is-referenced-by-count":24,"title":["BioLingua: a programmable knowledge environment for biologists"],"prefix":"10.1093","volume":"21","author":[{"given":"J. P.","family":"Massar","sequence":"first","affiliation":[]},{"given":"Michael","family":"Travers","sequence":"additional","affiliation":[]},{"given":"Jeff","family":"Elhai","sequence":"additional","affiliation":[]},{"given":"Jeff","family":"Shrager","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,8,12]]},"reference":[{"key":"2023013107194029100_B1","unstructured":"Bay, S., Shrager, J., Pohorille, A., Langley, P. 2002Revising regulatory networks: from expression data to linear causal models. J. Biomed. Informa.35289\u2013297"},{"key":"2023013107194029100_B2","doi-asserted-by":"crossref","unstructured":"Cox, P.T., Giles, F.R., Pietrzykowski, T. 1989Prograph: a step towards liberating programming from textual conditioning. 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