HCLSIG BioRDF Subgroup/Tasks/SenseLab
- Understand how to map the relational database structure of SenseLab to the corresponding RDF/OWL structure
- Explore tools such as D2RQ to convert part of the SenseLab Oracle database into RDF/OWL
- Explore Oracle/RDF to store and query SenseLab data in RDF/OWL format
Task Status (Use Cases)
- SenselabUsecase1 -- OWL-based mapping between NeuronDB and CoCoDat
- SenselabUsecase2 -- RDF-based integration of BrainPharm (drug information) and SWAN (Alzforum's publications/hypotheses)
Rationale: We will use this project to explore the intersection of neuroscience and semantic web technology and demonstrate the potential benefits of semantic web in the neurosciences. In addition, we will interact with neuroscience experts (e.g., Gordon Shepherd who is the PI of SenseLab) to identify real use case(s).
Scope: We will demonstrate how to use existing semantic web tools to convert relational (Oracle) neuroscience databases into RDF/OWL as well as to store and query RDF/OWL data.
Participants: Kei Cheung, Susie Stephens
Use case context: We will explore how a variety of neuronal and pharmacological data can potentially be represented, queried, integrated, and possibly be linked to neurological disorders (e.g., Alzheimer's disease and Parkinson's disease) as well as drug abuse studies using RDF/OWL.
Problem statement for this use case: Integrative neuroscience involves integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases (which are mostly relational databases) do not expose their schemas (database structures) and their contents to web agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we initiate a pilot project that illustrates how neuroscience databases can be expressed using the RDF/OWL as the common data representation language to facilitate cross-database queries. As a pilot test, we will convert part of SenseLab into RDF/OWL. SenseLab is an Oracle neuroscience database listed in the SfN Neuroscience Database Gateway in RDF/OWL. We will explore the use of Oracle/RDF as a semantic web data warehouse in storing and querying the converted RDF/OWL datasets.
- RDF/OWL conversion
- Convert SenseLab data into RDF/OWL format
- Make such RDF/OWL datasets available to the community
- Load the RDF/OWL datasets into Oracle/RDF
- Demonstrate how to use Oracle/RDF to query and integrate such RDF datasets.
- Publish the results
Mapping to existing standard ontologies
Some of the SenseLab concepts such as receptors, transmitters and neurons can be mapped to UMLS concepts. For example, the receptor "glycine" in SenseLab maps to the UMLS concept "glycine receptors" (C0061605)
Other possible ontologies include:
2. BrainML (http://brainml.org/). For example, some of the terms describing experimental recording techniques can be borrowed from BrainML (e.g., extracellular multielectrode array).
- NIH Neuroscience Microarray Consortium (http://arrayconsortium.tgen.org/np2/home.do)
- GeneNetwork brain expression data (http://www.genenetwork.org)
- SfN Neuroscience Database Gateway (http://big.sfn.org/NDG/site/)
Task supports and dependencies
Tools and Services
- D2RQ (http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/)
- Oracle/RDF (http://www.oracle.com/technology/tech/semantic_technologies/index.html)
Timeline for Task Completion
- Stage 1 (3 month goals)
- study how to convert SenseLab data from the Oracle database to RDF/OWL format
- install, set up and learn how to use Oracle/RDF
- Stage 2 (6 months goals)
- Perform the RDF/OWL conversion
- Use Oracle/RDF to load, query, integrate the converted RDF datasets
- Build a prototype web application to allow access to and queries of the SenseLab data stored in Oracle/RDF
For more info on Oracle see http://www.orafaq.com/