title: Groups: knowledge spreadsheets for symbolic biocomputing.
abstract: Knowledge spreadsheets (KSs) are a visual tool for interactive data analysis and exploration. They differ from traditional spreadsheets in that rather than being oriented toward numeric data, they work with symbolic knowledge representation structures and provide operations that take into account the semantics of the application domain. 'Groups' is an implementation of KSs within the Pathway Tools system. Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database. Groups can be transformed (e.g. by transforming a metabolite group to the group of pathways in which those metabolites are substrates); combined through set operations; analysed (e.g. through enrichment analysis); and visualized (e.g. by painting onto a metabolic map diagram). Users of the Pathway Tools-based BioCyc.org website have made extensive use of Groups, and an informal survey of Groups users suggests that Groups has achieved the goal of allowing biologists themselves to perform some data manipulations that previously would have required the assistance of a programmer. Database URL: BioCyc.org.
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Travers
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Paley
authors.forename: Jeff
authors.initials: J
authors.lastname: Shrager
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Holland
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019992:Databases as Topic; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics; D006801:Humans; D019359:Knowledge; D051188:Knowledge Bases; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D012984:Software; D014157:Transcription Factors / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors
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