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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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iPathCons and iPathDB: an improved insect pathway construction tool and the database.
Zan Zhang1, Chuanlin Yin1, Ying Liu1
1Department of Entomology, College of Plant Protection, Nanjing Agricultural University and The Key laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Agriculture, No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China.
Database : the Journal of Biological Databases and Curation
|November 13, 2014
Summary
A new tool, iPathCons, aids entomological research by constructing molecular interaction pathways from insect genome and transcriptome data. This facilitates understanding insect biology and improving pest management strategies.
Area of Science:
- Entomology
- Bioinformatics
- Genomics
Background:
- Insects represent a highly successful animal group with significant ecological and economic impacts.
- The rapid accumulation of insect genomic and transcriptomic data necessitates advanced tools for pathway construction.
- Understanding molecular interactions is crucial for entomological research, including pest control and beneficial insect management.
Purpose of the Study:
- To develop an improved computational tool, iPathCons, for constructing molecular interaction pathways.
- To facilitate pathway construction from both genome and transcriptome data for diverse insect species.
- To create a centralized database (iPathDB) of insect molecular pathways.
Main Methods:
- Development of iPathCons, a tool utilizing a voting system for Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology assignment to accommodate insect evolutionary diversity.
- Application of iPathCons to construct pathways from 37 genome-sequenced and 15 transcriptome-sequenced insects.
- Establishment of the iPathDB database, offering search, web server, and data download functionalities.
Main Results:
- Successful construction of molecular interaction pathways for 52 insect species using iPathCons.
- The iPathDB database provides a valuable resource for the insect research community.
- iPathCons accommodates high evolutionary diversity in insects through its KEGG Orthology assignment method.
Conclusions:
- iPathCons is an effective tool for knowledge-based pathway construction in entomology.
- The iPathDB database significantly enhances the accessibility and utility of insect pathway data.
- This resource will accelerate research in insect biology, evolution, and applied entomology.
