Related Experiment Videos
semCDI: a query formulation for semantic data integration in caBIG
E Patrick Shironoshita1, Yves R Jean-Mary, Ray M Bradley
1INFOTECH Soft, Inc., 9200 Dadeland Blvd., Ste 620, Miami, FL 33156, USA.
Objectives:
To develop mechanisms to formulate queries over the semantic representation of cancer-related data services available through the cancer Biomedical Informatics Grid (caBIG).
Design:
The semCDI query formulation uses a view of caBIG semantic concepts, metadata, and data as an ontology, and defines a methodology to specify queries using the SPARQL query language, extended with Horn rules. semCDI enables the joining of data that represent different concepts through associations modeled as object properties, and the merging of data representing the same concept in different sources through Common Data Elements (CDE) modeled as datatype properties, using Horn rules to specify additional semantics indicating conditions for merging data. Validation In order to validate this formulation, a prototype has been constructed, and two queries have been executed against currently available caBIG data services.
Discussion:
The semCDI query formulation uses the rich semantic metadata available in caBIG to build queries and integrate data from multiple sources. Its promise will be further enhanced as more data services are registered in caBIG, and as more linkages can be achieved between the knowledge contained within caBIG's NCI Thesaurus and the data contained in the Data Services.
Conclusion:
semCDI provides a formulation for the creation of queries on the semantic representation of caBIG. This constitutes the foundation to build a semantic data integration system for more efficient and effective querying and exploratory searching of cancer-related data.
Related Concept Videos
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...
Couples: Scalar and Vector Formulation
A couple moment is a rotational force that tends to rotate the steering wheel. The wheel's rotation can either be in a clockwise or anticlockwise direction. The right-hand rule is a helpful method for determining the direction of a couple moment. To...
Tandem Mass Spectrometry
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
¹H NMR Signal Integration: Overview
ER Retrieval Pathway
The ER uses many checkpoints to prevent the entry of incorrectly folded or a resident protein as cargo onto a transport vesicle. These mechanisms...