Genewebex: Gene annotation Web extraction, aggregation, and updating from Web-interfaced biomolecular databanks

Marco Masseroli, Andrea Stella, Myriam Alcalay, Francesco Pinciroli

Research output: Contribution to journalArticle

Abstract

Numerous genomic annotations are currently stored in different Web-accessible databanks that scientists need to mine with user-defined queries and in a batch mode to orderly integrate the diverse extracted data in suitable user-customizable working environments. Unfortunately, to date, most accessible databanks can be interrogated only for a single gene or protein at a time and generally the data retrieved are available in HTML page format only. We developed GeneWebEx to effectively mine data of interest in different HTML pages of Web-interfaced databanks, and organize extracted data for further analyses. GeneWebEx utilizes user-defined templates to identify data to extract, and aggregates and structures them in a database designed to allocate the various extractions from distinct biomolecular databanks. Moreover, a template-based module enables automatic updating of extracted data. Validations performed on GeneWebEx allowed us to efficiently gather relevant annotations from various sources, and comprehensively query them to highlight significant biological characteristics.

Original languageEnglish
Pages (from-to)511-526
Number of pages16
JournalInternational Journal of Software Engineering and Knowledge Engineering
Volume15
Issue number3
DOIs
Publication statusPublished - Jun 2005

Keywords

  • Biomolecular database
  • Data extraction
  • Genomic information
  • Microarray data interpretation
  • Web wrapper

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Artificial Intelligence
  • Computer Graphics and Computer-Aided Design
  • Software

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