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GeneWays: A System for Extracting, Analyzing, Visualizing and Integrating Molecular Pathway Data (RRID:SCR_008368)Copy Citation Copied
URL: http://anya.igsb.anl.gov/Geneways/GeneWays.html
Proper Citation: GeneWays: A System for Extracting, Analyzing, Visualizing and Integrating Molecular Pathway Data (RRID:SCR_008368)
Description: A system for automatically extracting, analyzing, visualizing and integrating molecular pathway data from the research literature. The system focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as an open platform, allowing researchers to query, review and critique the integrated information. Knowledge integration in the domain of molecular biology is crucial for a deeper understanding of molecular cell functions. Integration can be accomplished by gathering research results published in the scientific literature. Unfortunately, researchers are facing a true challenge how to best integrate the sheer amount of scientific publications available. GeneWays is built to help integrating research results by providing automatic tools to gather knowledge from the scientific literature. The GeneWays project team comprises experts from biology, computer science and linguistics, who use natural language processing (NLP) to scan thousands of research articles in order to automatically extract relevant molecular knowledge. The key idea is rather simple: While a single author may be an ultimate expert on a specific molecular substance, the collective knowledge of the whole research community is currently unavailable in an integrated form. Molecular interactions are frequently represented in research articles by statements such as protein A activates protein B, which can be collected and integrated into knowledge about a complex molecular network consisting of thousands of genes, proteins, small molecules (along with other substances) and their interactions. GeneWays's architecture combines various modules designed to automatically gather knowledge on signal transduction pathways from online scientific journals. The core of the system is a knowledge base of molecular actions. The knowledge is provided by various system modules, which select scientific journals of interest, mark and identify substance names in the journal text and extract interactions between these substances and other actions by means of natural language processing (NLP). The integrated knowledge stored in a database can be queried, analyzed, critiqued and visualized by interested researchers.
Abbreviations: GeneWays
Synonyms: GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data, GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data
Resource Type: analysis service resource, production service resource, data or information resource, service resource, data analysis service, database
Defining Citation: PMID:15016385
Keywords: text mining, information extraction, molecular network, molecular interaction, artificial intelligence, knowledge engineering, machine learning, natural language processing
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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