A Temporal Database Mediator for Gene Expression Data
Location
Hager-Lubbers Exhibition Hall
Description
PURPOSE: Molecular biological research is often based on measurements that have been obtained at different points in time. The biologist looks at these values not as individual points, but as a progression over time. Our program (SPOT) helps the researcher find temporal patterns in large sets of microarray data. PROCEDURES: Temporal data maintenance is concerned with the storage and retrieval of temporal data, while temporal reasoning focuses on the use of temporal data for decision support. A temporal (database) mediator is a computer program that allows for integration of the two tasks. Critical to both areas is temporal modeling. One framework of temporal modeling is the KBTA (the knowledge-based temporal abstraction) framework. Temporal abstractions (TAs) enable the conversion of quantitative data to an interval-based qualitative representation. Examples of temporal abstractions are trend TAs that capture increasing/decreasing values in time series and state TAs that correspond to low, high, or normal values in the time series. Temporal abstractions (TAs) convert quantitative data to an interval-based qualitative representation. OUTCOME: We created a web based temporal database mediator using open-source platforms that supports the R statistical package, PHP, Bioconductor, and Web 2.0 knowledge representation standards using the open source Semantic Web tool Protégé-OWL. We report here on use of the web interface and challenges of using public databases. IMPACT: Analysis of temporal gene expression data presents a novel opportunity to identify new drug targets and is one potential step to evaluate drugs for their overall effects.
A Temporal Database Mediator for Gene Expression Data
Hager-Lubbers Exhibition Hall
PURPOSE: Molecular biological research is often based on measurements that have been obtained at different points in time. The biologist looks at these values not as individual points, but as a progression over time. Our program (SPOT) helps the researcher find temporal patterns in large sets of microarray data. PROCEDURES: Temporal data maintenance is concerned with the storage and retrieval of temporal data, while temporal reasoning focuses on the use of temporal data for decision support. A temporal (database) mediator is a computer program that allows for integration of the two tasks. Critical to both areas is temporal modeling. One framework of temporal modeling is the KBTA (the knowledge-based temporal abstraction) framework. Temporal abstractions (TAs) enable the conversion of quantitative data to an interval-based qualitative representation. Examples of temporal abstractions are trend TAs that capture increasing/decreasing values in time series and state TAs that correspond to low, high, or normal values in the time series. Temporal abstractions (TAs) convert quantitative data to an interval-based qualitative representation. OUTCOME: We created a web based temporal database mediator using open-source platforms that supports the R statistical package, PHP, Bioconductor, and Web 2.0 knowledge representation standards using the open source Semantic Web tool Protégé-OWL. We report here on use of the web interface and challenges of using public databases. IMPACT: Analysis of temporal gene expression data presents a novel opportunity to identify new drug targets and is one potential step to evaluate drugs for their overall effects.