Abstract: An information management system for managing biochemical information (200). The biochemical information (200) comprises data sets (202) and each data set comprises a variable value matrix containing variable values organized as rows and columns; a row description list, in a variable description language, of the rows in the variable value matrix; a column description list, in a variable description language, of the columns in the variable value matrix; and a fixed dimension description, in a variable description language, of one or more fixed dimensions that are common to all values in the variable value matrix. A benefit achieved by storing the numerical values as a scalar matrix is that the matrix can be analyzed with many commercially available data-mining tools, such as self-organizing maps or other clustering algorithms, that do not readily process dimensioned values.

Abstract: An information management system for managing biological information (200). The information management system comprises by structured descriptions of biological pathways (700) that are formed of at least pathways (212), biochemical entities (218), connections (216) and interactions (222), such that each pathway (212) relates to one or more connections (216); each connection (216) joins one biochemical entity (218) and one interaction (222); and each pathway (212) relates to a specific location (214).

Abstract: A system for visualizing an information network. A database (DB) contains node descriptions and connection descriptions that collectively define the topology of the information network. A rule set (RS) relates at least to the topology of the information network. First user input means (IN) receive a navigation input (NI) and a definition a set of focus nodes. Second user input means receive filter settings (FS). Selection means (RE, FR) dynamically create one or more subnetworks based on the set of focus nodes, the topology of the information network, the rule set (RS) and the filter settings (FS). Layout generation means (LG, BF, ZP) dynamically generate a layout for the subnetworks.

Abstract: An information management system for managing workflows comprises a syntactic and semantic data entity type definition (1214) for each data entity type, and a data entity definition (1216) for each data entity (1250), each of which contains a subset of the information to be processed by a workflow. Tool definitions (1208) define tools (1254) that execute data processing tasks in a tool server (1222). Tool input binders (1210) and tool output binders (1212) bind tool inputs or outputs to a specific data entity type. A workflow definition (1202, 1202?) comprises one or more workflow input definitions (1204, 1204?) and workflow output definitions (1206, 1206?). The workflow input and output definitions collectively define a data flow network from the input of the workflow to the output of the workflow via one or more instances of tool definitions (1208).

Abstract: An information management system for managing biochemical information (200). The biochemical information (200) comprises data sets (202) and each data set comprises a variable value matrix containing variable values organized as rows and columns; a row description list, in a variable description language, of the rows in the variable value matrix; a column description list, in a variable description language, of the columns in the variable value matrix; and a fixed dimension description, in a variable description language, of one or more fixed dimensions that are common to all values in the variable value matrix. A benefit achieved by storing the numerical values as a scalar matrix is that the matrix can be analyzed with many commercially available data-mining tools, such as self-organizing maps or other clustering algorithms, that do not readily process dimensioned values.

Abstract: An information management system [=“IMS”] for managing biochemical information (200). The IMS comprises structured descriptions of biochemical pathways (700) that are formed of at least pathways (212), biochemical entities (218), connections (216) and interactions (222), such that each pathway (212) relates to one or more connections (216); each connection (216) joins one biochemical entity (218) and one interaction (222); and each pathway (212) relates to a specific location (214). The IMS also comprises means (220) for receiving genetic information from one or more sequence data bases, wherein the genetic information associations of an identifier of a gene and a coding area of the gene and a logic for automatically creating biochemical pathways from the genetic information.

Abstract: A piece of biochemical information may not be valid everywhere. Accordingly, an information management system for managing biological information is operable to store location information (214) that relates to at least one of biomaterial information (210) and pathway information (212), such that the location information (214) comprises a location hierarchy (214-1 . . . 214-6). By means of the location hierarchy, the system is able to store location information at widely different detail levels.

Abstract: An information management system (=“IMS”) for managing biochemical information has a first data structure for containing biochemical information as data sets for describing biomaterial and/or biochemical entities. The IMS also has a second data structure (900) for containing project information as data sets for describing experiments (904), each experiment having an experiment input (914) and experiment output (920). The experiment input (914) and experiment output (920) are instances of the data sets of the first data structure for describing biomaterial (210) and/or biochemical entities (218).