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The HumanCyc Pathway-Genome Database and Pathway Tools Software as Tools for Imaging and Analyzing Metabolomics Data

  • Pedro RomeroEmail author
Protocol
Part of the Methods in Pharmacology and Toxicology book series (MIPT)

Abstract

Metabolomics analysis provides a window to the phenotypic responses to stimuli, including disease states and drug interventions. These responses are the end result of complex processes encoded by the organism’s genome. This chapter describes a computational set of tools that can be of great assistance in all kinds of studies related to the metabolic network of an organism in the context of genomic information. These tools comprise (1) Pathway/Genome Databases (PGDBs) a high-level, last-generation database that relates metabolic information to an organism’s genome and (2) Pathway Tools, a software suite designed to access and facilitate analysis on the PGDB information. In particular, we describe HumanCyc, the human PGDB, and explore its usefulness in analyzing and extracting knowledge from the data produced by metabolomics, transcriptomics, and other systemic experiments. In the so-called postgenomic era, the lack of sophistication of many biological databases and resources has become a hurdle for the development of complex analytical tools, especially at the systems biology level, and a common complaint by computational molecular biologists. Resources such as HumanCyc and Pathway Tools can change this situation by providing the developer with a computable encoding of biological knowledge and a sophisticated collection of computational tools to access it.

Key words

HumanCyc Pathway-genome databases systems biology 

Notes

Glossary

API

Application program interface

DB

Data base

FRS

Frame representation system

GFP

Generic frame protocol

Isozyme

Variant form of an enzyme coded for by a separate allele. There is often tissue specific expression of isozymes, which may have significantly different kinetic properties from one another. In multisubunit enzymes, such as LDH two alleles give rise to a (statistical) mixture of enzymes, viz L4, L3M, L2M2, LM3, and M4, where L and M are the products of the two LDH genes.

MOD

Model organism database

Omics

The group of biological sub specialties whose descriptors end in “omics” such as genomics, proteomics and metabolomics spuriously described by adding this suffix to a field name such as gene → gene → genomics. The Omics refers to the systematic study of the phenomena: metabolomics is the study of the metabolome. Many possible subfields have been “omicized” (http://omics.org/index.php/Main_Page#Definition_of_Omics). A challenge is to integrate information and concepts obtained from these areas that frequently used very different platforms.

Ontology

The study of existence (philosophy). In informatics, and ontology is a data model that represents a set of concepts within a domain and the relationships between those concepts. It is used to reason about entities within that domain

PGDB

Pathway/genome database

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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.School of InformaticsIndiana University-Purdue UniversityIndianapolisUSA
  2. 2.Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisUSA

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