FedViz: A Visual Interface for SPARQL Queries Formulation

and ExecutionSyeda Sana e Zainab, Muhammad Saleem, Qaiser

Mehmood, Durre Zehra, Stefan Decker, and Ali Hasnain

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Outline•Introduction Motivation and Challenges Related Work•Methods FedViz System Architecture Datasets Connectivity•Results Visual Query Formulation and Execution through FedViz•Evaluation System Usability Scale Survey Custom Survey

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Motivation•Drug-Drug Interaction for Medication of Certain Disease Example: For disease Hypothyroidism how Levothyroxine drug interacts with Acenocoumarol drug as both are for its curing.

•Drug-Disease InteractionExample: Drugs having molecular weight less than 500 for curing disease Anemia.

•Drug-Side Effect InteractionExamples: Side Effect of drug “Retinol”, List of drugs having side effect “Insomnia”.

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Challenges•To draw any biological correlation or to answer a biological questions involve querying multiple data source, provided by different providers, sometimes available in different format with different accessing mechanism.

•Assembling a federated SPARQL query is time-consuming and technical process since it requires the knowledge of underlying datasets schema and the connectivity between the datasets.

•Due to less SPARQL knowledge the ultimate end-users and the domain experts either biologists or clinical researchers, remain unable to assemble complex queries in order to access such data.

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FedViz System Architecture

FedViz is an online application that provides Biologist a flexible visual interface to formulate and execute both federated and non-federated, SPARQL queries.

It translates the visually assembled queries into SPARQL equivalent and execute using query engine (FedX).

http://srvgal86.deri.ie/FedViz/index.html

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Datasets ConnectivityCurrent version of FedViz supports 6 Life Sciences domain datasets namely:

1. Drugbank 2. Kegg Kyoto Encyclopedia of Genes

and Genomes (KEGG)3. Sider4. Medicare5. Diseasome6. Dailymed

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Scenario“Drug-Disease and Drug-Compound interaction”Drugs with their compound mass for curing disease Anemia.Datasets Involves: Drugbank, Diseasome and Kegg.

Drug(Drugbank)

Disease(Diseasome)

Compound(Kegg)

Result

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FedViz Visual Query Building(Step by Step Approach)

1. Dataset Selection

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Drugbank Concept and Properties Selection

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Diseasome Concept and Properties Selection

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Kegg Concept and Properties Selection

5. Selected Concepts

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SPARQL Query Editor

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Formulated Query

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Results

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Instance Data Exploration

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Evaluation- System Usability Scale

System Usability Scale Survey

The SUS is a simple, low-cost, reliable 10 item scale that can be used for global assessments of systems usability.

In this survey, 15 users including researchers and engineers in Semantic Web were participated.

FedViz achieved a mean usability score of 74.16% indicating a high level of usability according to the SUS score.

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Evaluation- Custom Survey

Customised SurveyThis survey was particularly designed to measure the usability and usefulness of the different functionalists provided by FedViz. In particular, we asked users to formulate both federated and non-federated SPARQL queries and share their experience.Researchers including Computer Scientist and Bioinformaticians were participated in survey. The average scores for simple query(i.e., 4.2 ± 0.91) and federated query(i.e., 3.9 ± 0.73) questions show that most of the user feel confident in formulating simple and federated queries, respectively.

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Conclusion and Future Work

•FedViz is an online interface for SPARQL query formulation and execution.

•FedViz has evaluated using the standard system usability scale (SUS) as well as through domain experts.

•Preliminary analysis and evaluation revels the overall usability score of 74.16%, concluding FedViz an interface, easy to learn and help users formulating complex SPARQL queries intuitively.

•In future FedViz will be improved with Faceted browsing and visualization at entity level e.g, Genes and Molecules where user can see the Gene sequences and 3D structure for Molecules.

Thank you

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