PathCase: Pathways database system

Brendan Elliott; Mustafa Kirac; Ali Cakmak; Gokhan Yavas; Stephen Mayes; En Cheng; Yuan Wang; Chirag Gupta; Gultekin Ozsoyoglu; Zehra Meral Ozsoyoglu

doi:10.1093/bioinformatics/btn459

PathCase: Pathways database system

Brendan Elliott^*, Mustafa Kirac, Ali Cakmak, Gokhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Ozsoyoglu, Zehra Meral Ozsoyoglu

^*Corresponding author for this work

Case Western Reserve University

Research output: Contribution to journal › Article › peer-review

38 Citations (Scopus)

Abstract

Motivation: As the blueprints of cellular actions, biological pathways characterize the roles of genomic entities in various cellular mechanisms, and as such, their availability, manipulation and queriability over the web is important to facilitate ongoing biological research. Results: In this article, we present the new features of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of genetic, molecular, biochemical and organismal detail. The new features include: (i) a web-based system with a new architecture, containing a server-side and a client-side, and promoting scalability, and flexible and easy adaptation of different pathway databases, (ii) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (iii) two distinct querying capabilities: an advanced querying interface for computer savvy users, and built-in queries for ease of use, that can be issued directly from pathway visualizations and (iv) a pathway functionality analysis tool. PathCase is now available for three different datasets, namely, KEGG pathways data, sample pathways from the literature and BioCyc pathways for humans.

Original language	English
Pages (from-to)	2526-2533
Number of pages	8
Journal	Bioinformatics
Volume	24
Issue number	21
DOIs	https://doi.org/10.1093/bioinformatics/btn459
Publication status	Published - Nov 2008
Externally published	Yes

Funding

Funding: National Science Foundation (DBI 0218061and CNS-0551603); Charles B. Wang Foundation to the Center for Computational Genomics, CWRU.

Funders	Funder number
Charles B. Wang Foundation
National Science Foundation	DBI 0218061and CNS-0551603
Case Western Reserve University
Center for Computational, Evolutionary and Human Genomics, Stanford University

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10.1093/bioinformatics/btn459

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title = "PathCase: Pathways database system",

abstract = "Motivation: As the blueprints of cellular actions, biological pathways characterize the roles of genomic entities in various cellular mechanisms, and as such, their availability, manipulation and queriability over the web is important to facilitate ongoing biological research. Results: In this article, we present the new features of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of genetic, molecular, biochemical and organismal detail. The new features include: (i) a web-based system with a new architecture, containing a server-side and a client-side, and promoting scalability, and flexible and easy adaptation of different pathway databases, (ii) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (iii) two distinct querying capabilities: an advanced querying interface for computer savvy users, and built-in queries for ease of use, that can be issued directly from pathway visualizations and (iv) a pathway functionality analysis tool. PathCase is now available for three different datasets, namely, KEGG pathways data, sample pathways from the literature and BioCyc pathways for humans.",

author = "Brendan Elliott and Mustafa Kirac and Ali Cakmak and Gokhan Yavas and Stephen Mayes and En Cheng and Yuan Wang and Chirag Gupta and Gultekin Ozsoyoglu and Ozsoyoglu, {Zehra Meral}",

year = "2008",

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AU - Kirac, Mustafa

AU - Cakmak, Ali

AU - Yavas, Gokhan

AU - Mayes, Stephen

AU - Cheng, En

AU - Wang, Yuan

AU - Gupta, Chirag

AU - Ozsoyoglu, Gultekin

AU - Ozsoyoglu, Zehra Meral

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PathCase: Pathways database system

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