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 language | English |
|---|---|
| Pages (from-to) | 511-526 |
| Number of pages | 16 |
| Journal | International Journal of Software Engineering and Knowledge Engineering |
| Volume | 15 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - Jun 2005 |
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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
Cite this
Genewebex : Gene annotation Web extraction, aggregation, and updating from Web-interfaced biomolecular databanks. / Masseroli, Marco; Stella, Andrea; Alcalay, Myriam; Pinciroli, Francesco.
In: International Journal of Software Engineering and Knowledge Engineering, Vol. 15, No. 3, 06.2005, p. 511-526.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Genewebex
T2 - Gene annotation Web extraction, aggregation, and updating from Web-interfaced biomolecular databanks
AU - Masseroli, Marco
AU - Stella, Andrea
AU - Alcalay, Myriam
AU - Pinciroli, Francesco
PY - 2005/6
Y1 - 2005/6
N2 - 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.
AB - 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.
KW - Biomolecular database
KW - Data extraction
KW - Genomic information
KW - Microarray data interpretation
KW - Web wrapper
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U2 - 10.1142/S0218194005002403
DO - 10.1142/S0218194005002403
M3 - Article
AN - SCOPUS:22344433881
VL - 15
SP - 511
EP - 526
JO - International Journal of Software Engineering and Knowledge Engineering
JF - International Journal of Software Engineering and Knowledge Engineering
SN - 0218-1940
IS - 3
ER -