%0 Journal Article %1 geneways.friedman. %A Rzhetsky, Andrey %A Krauthammer, Michael %A Koike, Tomohiro %A Kra1, Pauline %A Gomez, Shawn M. %A Yu, Hong %A Duboue, Pablo %A Weng, Wubin %A Johnson, Steven B. %A Hatzivassiloglou, Vasileios %A Friedman, Carol %D 2004 %J J. Biomed. Inform. %K CAT CAT-IE CAT-REL-NLP CAT-REL-RULE CAT-SIMILAR CAT-VIZ GeneWays %N 37 %P 43-53 %T GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data %U http://www.bioinfo.de/isb/gcb01/talks/rzhetsky/main.html %X INTRODUCTION Imagine a group of ignorant yet bright cavepeople who are trying to understand operation of a modern car by analyzing a several damaged cars that were produced by various makers. After many hours of hard manual labor, the cavepeople manage to disassemble the cars into myriad parts. Some parts are damaged and some are intact; some pairs of parts interact with each other whereas others do not; some parts are different in different cars yet apparently have the same function. The leap to understanding of whole from knowing the parts requires reduction of redundant or conflicting pieces of information to a consistent consensus model that can be used for analysis of dynamics. Researchers in post-genome-era molecular biology are in precisely the same situation as the cavepeople: They are contemplating a collection of diverse parts of cellular machinery, and are attempting to understand the whole cell properties. To make their problem more complex, a given part of the cellular machinery can play different roles in different cells of the same organism, or even within the same cell but under different environmental conditions. The number of nodes in human molecular networks is on the order of hundreds of thousands when all substances (genes, RNAs, proteins, and other molecules) are considered together. These numerous substances can be in turn present or absent in dozens of cell types in humans. Evidently, the problem is far too complex to be analyzed manually. With the aim of relieving the information overload that is currently assaulting our fellow scientists, we - in parallel with a few other groups - have developed a computer system, GeneWays, that comprises a battery of tools for automatic gathering and processing of knowledge about molecular pathways. Due to space limitations, we cannot provide here a comprehensive overview of related work; thus, we will reference related work as we describe GeneWays.

@article{geneways.friedman., abstract = {INTRODUCTION Imagine a group of ignorant yet bright cavepeople who are trying to understand operation of a modern car by analyzing a several damaged cars that were produced by various makers. After many hours of hard manual labor, the cavepeople manage to disassemble the cars into myriad parts. Some parts are damaged and some are intact; some pairs of parts interact with each other whereas others do not; some parts are different in different cars yet apparently have the same function. The leap to understanding of whole from knowing the parts requires reduction of redundant or conflicting pieces of information to a consistent consensus model that can be used for analysis of dynamics. Researchers in post-genome-era molecular biology are in precisely the same situation as the cavepeople: They are contemplating a collection of diverse parts of cellular machinery, and are attempting to understand the whole cell properties. To make their problem more complex, a given part of the cellular machinery can play different roles in different cells of the same organism, or even within the same cell but under different environmental conditions. The number of nodes in human molecular networks is on the order of hundreds of thousands when all substances (genes, RNAs, proteins, and other molecules) are considered together. These numerous substances can be in turn present or absent in dozens of cell types in humans. Evidently, the problem is far too complex to be analyzed manually. With the aim of relieving the information overload that is currently assaulting our fellow scientists, we - in parallel with a few other groups - have developed a computer system, GeneWays, that comprises a battery of tools for automatic gathering and processing of knowledge about molecular pathways. Due to space limitations, we cannot provide here a comprehensive overview of related work; thus, we will reference related work as we describe GeneWays. }, added-at = {2010-08-30T06:53:20.000+0200}, author = {Rzhetsky, Andrey and Krauthammer, Michael and Koike, Tomohiro and Kra1, Pauline and Gomez, Shawn M. and Yu, Hong and Duboue, Pablo and Weng, Wubin and Johnson, Steven B. and Hatzivassiloglou, Vasileios and Friedman, Carol}, biburl = {https://www.bibsonomy.org/bibtex/2faf70a4fbf456fe48beccc618379beb6/huiyangsfsu}, interhash = {0748906ba4183d7e9c401ff3d393081c}, intrahash = {faf70a4fbf456fe48beccc618379beb6}, journal = {J. Biomed. Inform. }, keywords = {CAT CAT-IE CAT-REL-NLP CAT-REL-RULE CAT-SIMILAR CAT-VIZ GeneWays}, number = 37, pages = {43-53}, timestamp = {2010-11-09T08:43:17.000+0100}, title = {GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data}, url = {http://www.bioinfo.de/isb/gcb01/talks/rzhetsky/main.html}, year = 2004 }