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.
Highlights
A long-standing problem in computing is that of providing non-programmers with intuitive, yet powerful tools for manipulating and analysing sets of entities
Because building complex interactivity on the web is difficult, to speed implementation of Web Groups, we introduced two new layers to the Pathway Tools software infrastructure stack: AllegroServe, a commercially provided Lispbased web server that replaced the previous web server CWEST [19], and WuWei [20], a toolkit for building complex Ajax applications using Lisp continuations
That would permit users to perform what would amount to between-species metabolic or genomic ‘joins’. This would be an interesting computation, and raises the question of what common keys make sense between organisms; such keys would be likely to vary from case to case, but homologous genes at least, or those whose product proteins have the same biochemical function, would make sensible join keys
Summary
A long-standing problem in computing is that of providing non-programmers with intuitive, yet powerful tools for manipulating and analysing sets of entities. Traditional spreadsheets provide a compelling interaction model, and are excellent tools for the manipulation of the tables of numbers that are typical of accounting and data analysis problems, they are less used with the complex symbolic computations typical of symbolic biocomputing They cannot perform semantic transformations such as converting a gene list to the list of pathways the genes act in. Those features of Groups that respondents mentioned as being the most useful included its transformation and set operations, its over-representation analysis, its ability to share and download groups for further analysis, the ability to conduct metabolic pathway comparisons and the ability to view properties of different genes ‘all at once’. This would be an interesting computation, and raises the question of what common keys make sense between organisms; such keys would be likely to vary from case to case, but homologous genes at least, or those whose product proteins have the same biochemical function, would make sensible join keys
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