Towards a Comprehensive Human Pathway Database For Systems Biology Applications
type: CreativeWork
description: A biological pathway is a series of reactions and molecular interactions. Pathway information provides a blueprint for biomedical researchers to devise new treatment and diagnostic solutions for human diseases. Pathway data are publicly available in many databases. Most of the databases however have only partial coverage of human biological pathways, especially for signal transduction and gene regulatory pathways. Comprehensive knowledge and a combined view for all types for biological pathways may lead to insights into the molecular physiology of cells and drug discovery. In this project, we collected human signaling pathway data from different database sources. The pathway data comes from the Biocarta, Protein Lounge, Resnet and NCI-Nature Curated databases. We analyzed the structures of collected data, and developed a comprehensive data model to manage integrated information of molecules, complexes, regulation relationships of molecules, and reactions involved in signaling and regulatory pathways. The integrated database, the Human Pathway database (HPD), is a data warehouse of a comprehensive collection of biological reactions, regulators, and metabolites, serving as a potential platform for future pathway analysis studies. We developed the database to manage integrated biomolecular information related to pathways. In HPD, which uses Oracle 10g, there are a total of 1,895 pathways, 10,631 molecular entities (proteins, complexes and compounds) and 4,370 reactions that were consolidated and integrated into a single relational database platform using Oracle 10g. We also developed a prototypical GUI for the navigation and querying of biological pathways. Such a system, when completed, and used in conjunction with future pathway data visualization and analysis tools, could provide a framework for systems biology studies. We developed HPD with comprehensive annotation data. For example, the kinase - disease association information and perturbation effect of several en…
abstract: A biological pathway is a series of reactions and molecular interactions. Pathway information provides a blueprint for biomedical researchers to devise new treatment and diagnostic solutions for human diseases. Pathway data are publicly available in many databases. Most of the databases however have only partial coverage of human biological pathways, especially for signal transduction and gene regulatory pathways. Comprehensive knowledge and a combined view for all types for biological pathways may lead to insights into the molecular physiology of cells and drug discovery. In this project, we collected human signaling pathway data from different database sources. The pathway data comes from the Biocarta, Protein Lounge, Resnet and NCI-Nature Curated databases. We analyzed the structures of collected data, and developed a comprehensive data model to manage integrated information of molecules, complexes, regulation relationships of molecules, and reactions involved in signaling and regulatory pathways. The integrated database, the Human Pathway database (HPD), is a data warehouse of a comprehensive collection of biological reactions, regulators, and metabolites, serving as a potential platform for future pathway analysis studies. We developed the database to manage integrated biomolecular information related to pathways. In HPD, which uses Oracle 10g, there are a total of 1,895 pathways, 10,631 molecular entities (proteins, complexes and compounds) and 4,370 reactions that were consolidated and integrated into a single relational database platform using Oracle 10g. We also developed a prototypical GUI for the navigation and querying of biological pathways. Such a system, when completed, and used in conjunction with future pathway data visualization and analysis tools, could provide a framework for systems biology studies. We developed HPD with comprehensive annotation data. For example, the kinase - disease association information and perturbation effect of several en…
author: Kasamsetty, Harini
language: en_US
keywords: Systems Biology Applications, Human Pathway, Database
date modified: 2026-07-24T02:41:41Z
provider: IUPUI
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: IUPUI

PropertyValue
property ID: Handle
value: https://hdl.handle.net/1805/2262

PropertyValue
property ID: DOI
value: 10.7912/C2/887