Aftab Iqbal

Big linked cancer data

The amount of bio-medical data available on the Web grows exponentially with time. The resulting large volume of data makes manual exploration very tedious. Moreover, the velocity at which this data changes and the variety of formats in which bio-medical data is published makes it difficult to access them in an integrated form. Finally, the lack of an integrated vocabulary makes querying this data more difficult. In this paper, we advocate the use of Linked Data to integrate, query and visualize bio-medical data. The resulting Big Linked Data allows discovering knowledge distributed across manifold sources, making it viable for the serendipitous discovery of novel knowledge. We present the concept of Big Linked Data by showing how the constant stream of new bio-medical publications can be integrated with the Linked Cancer Genome Atlas dataset (TCGA) within a virtual integration scenario. We ensure the scalability of our approach through the novel TopFed federated query engine, which we evaluate by comparing the query execution time of our system with that of FedX on Linked TCGA. Then, we show how we can harness the value hidden in the underlying integrated data by making it easier to explore through a user-friendly interface. We evaluate the usability of the interface by using the standard system usability questionnaire as well as a customized questionnaire designed for the users of our system. Our overall result of 77 suggests that our interface is easy to use and can thus lead to novel insights.

Integrating developer-related information across open source repositories

Software developers use various software repositories in order to interact with each other or to solve software related problems. They are required to adopt an identity for each of the software repositories they wanted to use. Quite often developers are also found on different code forges developing open source projects. It is worth mentioning that the information relevant to the developers are distributed on the Web among different data sources each requires an ID and an authentication mechanism. In this paper, we propose to interlink the identities of a developer across different data sources on the Web. Further, we show the benefit of integrating developer-related information from different data sources using some real-world scenarios.

Integrating Open Source Software Repositories on the Web through Linked Data

In this paper, we propose a novel approach to the problem of integrating code forges based on metadata (e.g., programming language, database, intended audience, operating system), similar software projects and software developers. We review the current problems in integrating metadata of different code forges and argue that Semantic Web technologies are suitable for representing and integrating knowledge contained inside these code forges. Further, we show the advantages of interlinking metadata of software projects to other relevant data sources on the Web, which will enable querying more information from the Web. Moreover, we compute the overlapping between code forges based on similar software developers and argue the benefit of interlinking similar software developers and software projects across different code forges through examples.

Querying phenotype-genotype associations across multiple knowledge bases using Semantic Web technologies

Biomedical and genomic data are inherently heterogeneous and their recent proliferation over the Web has demanded innovative querying methods to help domain experts in their clinical and research studies. In this paper we present the use of Semantic Web technologies in querying diverse phenotype-genotype associations for supporting personalized medicine and potentially helping to discover new associations. Our initial results suggest that Semantic Web technologies has competitive advantages in extracting, consolidating and presenting phenotype-genotype associations that resides in various bioinformatics resources. The developed querying method could support researchers and medical professionals in discovering and utilizing information on published associations relating disease, treatment, adverse events and environmental factors to genetic markers from multiple repositories.

On the Need of Integrating Social Media Channels and Open Source Software Repositories

The growing interest in the usage of social media channels have attracted the open source software community to adopt an identity in order to disseminate project-related information to a wider audience. We foresee the need to integrate social media channels and open source software repositories in order to get an integrated view on the software project not only from the software development perspective but also from social perspective. Therefore, in this paper we study the usage of Twitter by software developers through harvesting their project-related activities on Twitter. In particular, we present the most frequently used hashtags by software developers and further investigate if project-related hashtags are the most frequent and commonly used hashtags by software developers. Based on our findings, we argue that relevant information from social media channels should be integrated with the open source software repositories in order to provide a homogeneous view on a software project.