GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data

Abstract

The immense growth in the volume of research literature and experimental data in the field of molecular biology calls for efficient automatic methods to capture and store information. In recent years, several groups have worked on specific problems in this area, such as automated selection of articles pertinent to molecular biology, or automated extraction of information using natural-language processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing on multiple sources of information to infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information.

Infrastructure for Annotation-Driven Information Extraction from the Primary Scientific Literature: Principles and Practice

“…This system mines interaction-network-related data from a collection of over 250,000 full-text papers to construct a large-scale interaction database conforming to a locally built ontology [17]. Interestingly, this information then supports secondary studies concerned with the consistency of the information [18], methods to imitate manual curation [19] and the propagation of facts in the literature [20].…”

Hierarchical Biological Pathway Data Integration and Mining

“…Some of the data integration and management efforts are presented in [27][28][29][30][31][32]. Several major approaches have been proposed for data integration, which can be roughly classified into five groups [33][34] namely; data warehousing, federated databasing, serviceoriented integration, semantic integration and wiki-based integration.…”

Pathway information for systems biology

“…Some databases span multiple categories, such as Reactome [25], which we might classify as both a metabolic and a signaling database. Others do not fit into these categories, such as those that store genetic interactions [26], and databases that store literature co-cited gene name links [27] or more detailed literature extracted links [28]. While these databases may not be universally considered pathway databases, they contain valuable functional links between genes, many of which are not available in other pathway databases.…”