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Groups: knowledge spreadsheets for symbolic biocomputing
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DOI：10.1093/database/bat061.png)
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Abstract
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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.
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GENOME BIOLOGYIF9.4
OAAIShareSavePathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
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OAAIShareSaveThe MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databasesNUCLEIC ACIDS RESEARCHOAAI
NUCLEIC ACIDS RESEARCHIF13.1
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