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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.
Alberto Anguita1, Luis Martin, Miguel Garcia-Remesal
1Biomedical Informatics Group, Artificial Intelligence Laboratory, School of Computer Science, Universidad Politécnica de Madrid, Campus de Montegancedo S/N, 28660 Boadilla del Monte, Madrid, Spain. aanguita@infomed.dia.fi.upm.es
Computer Methods and Programs in Biomedicine
|May 15, 2013
Summary
RDFBuilder provides RDF-based access to microarray databases, transforming MAGE-OM data into RDF format for efficient SPARQL querying. This tool enhances data retrieval from ArrayExpress, optimizing response times through caching.
Area of Science:
- Bioinformatics
- Genomics
- Data Management
Background:
- Microarray data is complex and often stored in MAGE-ML compliant formats.
- Accessing and querying diverse microarray datasets, like those in ArrayExpress, presents challenges.
- Existing initiatives may not fully address the need for flexible, programmatic data retrieval.
Purpose of the Study:
- To develop a tool, RDFBuilder, for seamless RDF-based access to MAGE-ML microarray databases.
- To enable automated transformation of MAGE-OM models and ArrayExpress data into RDF.
- To provide a SPARQL endpoint for efficient querying of microarray experimental data.
Main Methods:
- Automated transformation of the MAGE-OM model into RDF.
- Conversion of ArrayExpress database content into RDF format.
- Implementation of a SPARQL endpoint with query optimization via caching.
Main Results:
- RDFBuilder successfully transforms MAGE-OM and ArrayExpress data into RDF.
- A functional SPARQL endpoint is automatically enabled, allowing complex queries.
- Optimized response times for data retrieval through caching mechanisms.
Conclusions:
- RDFBuilder facilitates efficient, RDF-based access to microarray data.
- The system complements existing efforts like Bio2RDF for ArrayExpress data access.
- The tool empowers researchers to query and integrate microarray data more effectively.
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