Ali Hasnain

A fine-grained evaluation of SPARQL endpoint federation systems

The Web of Data has grown enormously over the last years. Currently, it comprises a large compendium of interlinked and distributed datasets from multiple domains. Running complex queries on this compendium often requires accessing data from different endpoints within one query. The abundance of datasets and the need for running complex query has thus motivated a considerable body of work on SPARQL query federation systems, the dedicated means to access data distributed over the Web of Data. However, the granularity of previous evaluations of such systems has not allowed deriving of insights concerning their behavior in different steps involved during federated query processing. In this work, we perform extensive experiments to compare state-of-the-art SPARQL endpoint federation systems using the comprehensive performance evaluation framework Fed- Bench. In addition to considering the tradition query runtime as an evaluation criterion, we extend the scope of our performance evaluation by considering criteria, which have not been paid much attention to in previous studies. In particular, we consider the number of sources selected, the total number of SPARQL ASK requests used, the completeness of answers as well as the source selection time. Yet, we show that they have a significant impact on the overall query runtime of existing systems. Moreover, we extend FedBench to mirror a highly distributed data environment and assess the behavior of existing systems by using the same performance criteria. As the result we provide a detailed analysis of the experimental outcomes that reveal novel insights for improving current and future SPARQL federation systems.

Linked Biomedical Dataspace: Lessons Learned Integrating Data for Drug Discovery

The increase in the volume and heterogeneity of biomedical data sources has motivated researchers to embrace Linked Data (LD) technologies to solve the ensuing integration challenges and enhance information discovery. As an integral part of the EU GRANATUM project, a Linked Biomedical Dataspace (LBDS) was developed to semantically interlink data from multiple sources and augment the design of in silico experiments for cancer chemoprevention drug discovery. The different components of the LBDS facilitate both the bioinformaticians and the biomedical researchers to publish, link, query and visually explore the heterogeneous datasets. We have extensively evaluated the usability of the entire platform. In this paper, we showcase three different workflows depicting real-world scenarios on the use of LBDS by the domain users to intuitively retrieve meaningful information from the integrated sources. We report the important lessons that we learned through the challenges encountered and our accumulated experience during the collaborative processes which would make it easier for LD practitioners to create such dataspaces in other domains. We also provide a concise set of generic recommendations to develop LD platforms useful for drug discovery.

ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research

Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biomedical discovery. Despite the popularity of semantic web technologies in tackling the integrative bioinformatics challenge, there are many obstacles towards its usage by non-technical research audiences. In particular, the ability to fully exploit integrated information needs using improved interactive methods intuitive to the biomedical experts. In this report we present ReVeaLD (a Real-time Visual Explorer and Aggregator of Linked Data), a user-centered visual analytics platform devised to increase intuitive interaction with data from distributed sources. ReVeaLD facilitates query formulation using a domain-specific language (DSL) identified by biomedical experts and mapped to a self-updated catalogue of elements from external sources. ReVeaLD was implemented in a cancer research setting; queries included retrieving data from in silico experiments, protein modeling and gene expression. ReVeaLD was developed using Scalable Vector Graphics and JavaScript and a demo with explanatory video is available at http://www.srvgal78.deri.ie:8080/explorer. A set of user-defined graphic rules controls the display of information through media-rich user interfaces. Evaluation of ReVeaLD was carried out as a game: biomedical researchers were asked to assemble a set of 5 challenge questions and time and interactions with the platform were recorded. Preliminary results indicate that complex queries could be formulated under less than two minutes by unskilled researchers. The results also indicate that supporting the identification of the elements of a DSL significantly increased intuitiveness of the platform and usability of semantic web technologies by domain users.

A Roadmap for Navigating the Life Sciences Linked Open Data Cloud

Multiple datasets that add high value to biomedical research have been exposed on the web as a part of the Life Sciences Linked Open Data (LSLOD) Cloud. The ability to easily navigate through these datasets is crucial for personalized medicine and the improvement of drug discovery process. However, navigating these multiple datasets is not trivial as most of these are only available as isolated SPARQL endpoints with very little vocabulary reuse. The content that is indexed through these endpoints is scarce, making the indexed dataset opaque for users. In this paper, we propose an approach for the creation of an active Linked Life Sciences Data Roadmap, a set of congurable rules which can be used to discover links (roads) between biological entities (cities) in the LSLOD cloud. We have catalogued and linked concepts and properties from 137 public SPARQL endpoints. Our Roadmap is primarily used to dynamically assemble queries retrieving data from multiple SPARQL endpoints simultaneously. We also demonstrate its use in conjunction with other tools for selective SPARQL querying, semantic annotation of experimental datasets and the visualization of the LSLOD cloud. We have evaluated the performance of our approach in terms of the time taken and entity capture. Our approach, if generalized to encompass other domains, can be used for road-mapping the entire LOD cloud.

BioFed: federated query processing over life sciences linked open data

BackgroundBiomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to biological data sets, but this still requires solutions to query multiple endpoints for their heterogeneous data to eventually retrieve all the meaningful information. Suggested solutions are based on query federation approaches, which require the submission of SPARQL queries to endpoints. Due to the size and complexity of available data, these solutions have to be optimised for efficient retrieval times and for users in life sciences research. Last but not least, over time, the reliability of data resources in terms of access and quality have to be monitored. Our solution (BioFed) federates data over 130 SPARQL endpoints in life sciences and tailors query submission according to the provenance information. BioFed has been evaluated against the state of the art solution FedX and forms an important benchmark for the life science domain.MethodsThe efficient cataloguing approach of the federated query processing system ’BioFed’, the triple pattern wise source selection and the semantic source normalisation forms the core to our solution. It gathers and integrates data from newly identified public endpoints for federated access. Basic provenance information is linked to the retrieved data. Last but not least, BioFed makes use of the latest SPARQL standard (i.e., 1.1) to leverage the full benefits for query federation. The evaluation is based on 10 simple and 10 complex queries, which address data in 10 major and very popular data sources (e.g., Dugbank, Sider).ResultsBioFed is a solution for a single-point-of-access for a large number of SPARQL endpoints providing life science data. It facilitates efficient query generation for data access and provides basic provenance information in combination with the retrieved data. BioFed fully supports SPARQL 1.1 and gives access to the endpoint’s availability based on the EndpointData graph. Our evaluation of BioFed against FedX is based on 20 heterogeneous federated SPARQL queries and shows competitive execution performance in comparison to FedX, which can be attributed to the provision of provenance information for the source selection.ConclusionDeveloping and testing federated query engines for life sciences data is still a challenging task. According to our findings, it is advantageous to optimise the source selection. The cataloguing of SPARQL endpoints, including type and property indexing, leads to efficient querying of data resources over the Web of Data. This could even be further improved through the use of ontologies, e.g., for abstract normalisation of query terms.

SPORTAL: Profiling the Content of Public SPARQL Endpoints

This publication was supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2289, by the Millennium Nucleus Center for Semantic Web Research under Grant NC120004, and by Fondecyt Grant No. 11140900

A Comparison of Federation over SPARQL Endpoints Frameworks

The increasing amount of Linked Data and its inherent distributed nature have attracted significant attention throughout the research community and amongst practitioners to search data, in the past years. Inspired by research results from traditional distributed databases, different approaches for managing federation over SPARQL Endpoints have been introduced. SPARQL is the standardised query language for RDF, the default data model used in Linked Data deployments and SPARQL Endpoints are a popular access mechanism provided by many Linked Open Data (LOD) repositories. In this paper, we initially give an overview of the federation framework infrastructure and then proceed with a comparison of existing SPARQL federation frameworks. Finally, we highlight shortcomings in existing frameworks, which we hope helps spawning new research directions.

SPORTAL: Searching for Public SPARQL Endpoints

There are hundreds of SPARQL endpoints on the Web, but finding an endpoint relevant to a client’s needs is difficult: each endpoint acts like a black box, often without a description of its content. Herein we briefly describe Sportal: a system that collects meta-data about the content of endpoints and collects them into a central catalogue over which clients can search. Sportal sends queries to individual endpoints offline to learn about their content, generating a best-effort VoID description for each endpoint. These descriptions can then be searched and queried over by clients in the Sportal user interface, for example, to find endpoints that contain instances of a given class, or triples with a given predicate, or more complex requests such as endpoints with at least 1,000 images of people. Herein we give a brief overview of Sportal, its design and functionality, and the features that shall be demoed at the conference.

A Provenance Assisted Roadmap for Life Sciences Linked Open Data Cloud

A significant portion of Web of Data is composed of multiple datasets that add high value to biomedical research. These datasets have been exposed on the web as a part of the Life Sciences Linked Open Data (LSLOD) Cloud. Different initiatives have been proposed for navigating through these datasets with or without vocabulary reuse. The significance of provenance information regarding life sciences data is great as compared to any other domain. With the provenance information, user becomes aware regarding the source, size, format along with authorization and privilege associated with the data. Previously, we proposed an approach for the creation of an active Linked Life Sciences Data Roadmap, that catalogues and links concepts as well as properties from 137 public SPARQL endpoints. In this work we extend the Roadmap with the provenance information collected directly by querying datasets. We designed a set of queries and the results were catalouged. This extended Roadmap is useful for dynamically assembling queries for retrieving data along with the provenance from multiple SPARQL endpoints. We also demonstrate its use in conjunction with other tools for selective SPARQL querying and the visualization of the LSLOD cloud. We have evaluated the performance of our approach in terms of time taken and success rates of data retrieved.

Assessing FAIR Data Principles Against the 5-Star Open Data Principles

Access to biomedical data is increasingly important to enable data driven science in the research community. The Linked Open Data (LOD) principles (by Tim Berner-Lee) have been suggested to judge the quality of data by its accessibility (open data access), by its format and structures, and by its interoperability with other data sources. The objective is to use interoperable data sources across the Web with ease.