Aggregation of biological knowledge for immunological and virological applications

Ph.DDOCTOR OF PHILOSOPH

A standards-based ICT framework to enable a service-oriented approach to clinical decision support

This research provides evidence that standards based Clinical Decision Support (CDS) at the point of care is an essential ingredient of electronic healthcare service delivery. A Service Oriented Architecture (SOA) based solution is explored, that serves as a task management system to coordinate complex distributed and disparate IT systems, processes and resources (human and computer) to provide standards based CDS. This research offers a solution to the challenges in implementing computerised CDS such as integration with heterogeneous legacy systems. Reuse of components and services to reduce costs and save time. The benefits of a sharable CDS service that can be reused by different healthcare practitioners to provide collaborative patient care is demonstrated. This solution provides orchestration among different services by extracting data from sources like patient databases, clinical knowledge bases and evidence-based clinical guidelines (CGs) in order to facilitate multiple CDS requests coming from different healthcare settings. This architecture aims to aid users at different levels of Healthcare Delivery Organizations (HCOs) to maintain a CDS repository, along with monitoring and managing services, thus enabling transparency. The research employs the Design Science research methodology (DSRM) combined with The Open Group Architecture Framework (TOGAF), an open source group initiative for Enterprise Architecture Framework (EAF). DSRM’s iterative capability addresses the rapidly evolving nature of workflows in healthcare. This SOA based solution uses standards-based open source technologies and platforms, the latest healthcare standards by HL7 and OMG, Decision Support Service (DSS) and Retrieve, Update Locate Service (RLUS) standard. Combining business process management (BPM) technologies, business rules with SOA ensures the HCO’s capability to manage its processes. This architectural solution is evaluated by successfully implementing evidence based CGs at the point of care in areas such as; a) Diagnostics (Chronic Obstructive Disease), b) Urgent Referral (Lung Cancer), c) Genome testing and integration with CDS in screening (Lynch’s syndrome). In addition to medical care, the CDS solution can benefit organizational processes for collaborative care delivery by connecting patients, physicians and other associated members. This framework facilitates integration of different types of CDS ideal for the different healthcare processes, enabling sharable CDS capabilities within and across organizations

Enabling Complex Semantic Queries to Bioinformatics Databases through Intuitive Search Over Data

Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data already available publicly. However, the heterogene- ity of the existing data sources still poses significant challenges for achieving interoperability among biological databases. Furthermore, merely solving the technical challenges of data in- tegration, for example through the use of common data representation formats, leaves open the larger problem. Namely, the steep learning curve required for understanding the data models of each public source, as well as the technical language through which the sources can be queried and joined. As a consequence, most of the available biological data remain practically unexplored today. In this thesis, we address these problems jointly, by first introducing an ontology-based data integration solution in order to mitigate the data source heterogeneity problem. We illustrate through the concrete example of Bgee, a gene expression data source, how relational databases can be exposed as virtual Resource Description Framework (RDF) graphs, through relational-to-RDF mappings. This has the important advantage that the original data source can remain unmodified, while still becoming interoperable with external RDF sources. We complement our methods with applied case studies designed to guide domain experts in formulating expressive federated queries targeting the integrated data across the domains of evolutionary relationships and gene expression. More precisely, we introduce two com- parative analyses, first within the same domain (using orthology data from multiple, inter- operable, data sources) and second across domains, in order to study the relation between expression change and evolution rate following a duplication event. Finally, in order to bridge the semantic gap between users and data, we design and im- plement Bio-SODA, a question answering system over domain knowledge graphs, that does not require training data for translating user questions to SPARQL. Bio-SODA uses a novel ranking approach that combines syntactic and semantic similarity, while also incorporating node centrality metrics to rank candidate matches for a given user question. Our results in testing Bio-SODA across several real-world databases that span multiple domains (both within and outside bioinformatics) show that it can answer complex, multi-fact queries, be- yond the current state-of-the-art in the more well-studied open-domain question answering. -- L’intégration des données promet d’être l’un des principaux catalyseurs permettant d’extraire des nouveaux aperçus de la richesse des données biologiques déjà disponibles publiquement. Cependant, l’hétérogénéité des sources de données existantes pose encore des défis importants pour parvenir à l’interopérabilité des bases de données biologiques. De plus, en surmontant seulement les défis techniques de l’intégration des données, par exemple grâce à l’utilisation de formats standard de représentation de données, on laisse ouvert un problème encore plus grand. À savoir, la courbe d’apprentissage abrupte nécessaire pour comprendre la modéli- sation des données choisie par chaque source publique, ainsi que le langage technique par lequel les sources peuvent être interrogés et jointes. Par conséquent, la plupart des données biologiques publiquement disponibles restent pratiquement inexplorés aujourd’hui. Dans cette thèse, nous abordons l’ensemble des deux problèmes, en introduisant d’abord une solution d’intégration de données basée sur ontologies, afin d’atténuer le problème d’hété- rogénéité des sources de données. Nous montrons, à travers l’exemple de Bgee, une base de données d’expression de gènes, une approche permettant les bases de données relationnelles d’être publiés sous forme de graphes RDF (Resource Description Framework) virtuels, via des correspondances relationnel-vers-RDF (« relational-to-RDF mappings »). Cela présente l’important avantage que la source de données d’origine peut rester inchangé, tout en de- venant interopérable avec les sources RDF externes. Nous complétons nos méthodes avec des études de cas appliquées, conçues pour guider les experts du domaine dans la formulation de requêtes fédérées expressives, ciblant les don- nées intégrées dans les domaines des relations évolutionnaires et de l’expression des gènes. Plus précisément, nous introduisons deux analyses comparatives, d’abord dans le même do- maine (en utilisant des données d’orthologie provenant de plusieurs sources de données in- teropérables) et ensuite à travers des domaines interconnectés, afin d’étudier la relation entre le changement d’expression et le taux d’évolution suite à une duplication de gène. Enfin, afin de mitiger le décalage sémantique entre les utilisateurs et les données, nous concevons et implémentons Bio-SODA, un système de réponse aux questions sur des graphes de connaissances domaine-spécifique, qui ne nécessite pas de données de formation pour traduire les questions des utilisateurs vers SPARQL. Bio-SODA utilise une nouvelle ap- proche de classement qui combine la similarité syntactique et sémantique, tout en incorporant des métriques de centralité des nœuds, pour classer les possibles candidats en réponse à une question utilisateur donnée. Nos résultats suite aux tests effectués en utilisant Bio-SODA sur plusieurs bases de données à travers plusieurs domaines (tantôt liés à la bioinformatique qu’extérieurs) montrent que Bio-SODA réussit à répondre à des questions complexes, en- gendrant multiples entités, au-delà de l’état actuel de la technique en matière de systèmes de réponses aux questions sur les données structures, en particulier graphes de connaissances

ICSEA 2021: the sixteenth international conference on software engineering advances

The Sixteenth International Conference on Software Engineering Advances (ICSEA 2021), held on October 3 - 7, 2021 in Barcelona, Spain, continued a series of events covering a broad spectrum of software-related topics. The conference covered fundamentals on designing, implementing, testing, validating and maintaining various kinds of software. The tracks treated the topics from theory to practice, in terms of methodologies, design, implementation, testing, use cases, tools, and lessons learnt. The conference topics covered classical and advanced methodologies, open source, agile software, as well as software deployment and software economics and education. The conference had the following tracks: Advances in fundamentals for software development Advanced mechanisms for software development Advanced design tools for developing software Software engineering for service computing (SOA and Cloud) Advanced facilities for accessing software Software performance Software security, privacy, safeness Advances in software testing Specialized software advanced applications Web Accessibility Open source software Agile and Lean approaches in software engineering Software deployment and maintenance Software engineering techniques, metrics, and formalisms Software economics, adoption, and education Business technology Improving productivity in research on software engineering Trends and achievements Similar to the previous edition, this event continued to be very competitive in its selection process and very well perceived by the international software engineering community. As such, it is attracting excellent contributions and active participation from all over the world. We were very pleased to receive a large amount of top quality contributions. We take here the opportunity to warmly thank all the members of the ICSEA 2021 technical program committee as well as the numerous reviewers. The creation of such a broad and high quality conference program would not have been possible without their involvement. We also kindly thank all the authors that dedicated much of their time and efforts to contribute to the ICSEA 2021. We truly believe that thanks to all these efforts, the final conference program consists of top quality contributions. This event could also not have been a reality without the support of many individuals, organizations and sponsors. We also gratefully thank the members of the ICSEA 2021 organizing committee for their help in handling the logistics and for their work that is making this professional meeting a success. We hope the ICSEA 2021 was a successful international forum for the exchange of ideas and results between academia and industry and to promote further progress in software engineering research

Data management and Data Pipelines: An empirical investigation in the embedded systems domain

Context: Companies are increasingly collecting data from all possible sources to extract insights that help in data-driven decision-making. Increased data volume, variety, and velocity and the impact of poor quality data on the development of data products are leading companies to look for an improved data management approach that can accelerate the development of high-quality data products. Further, AI is being applied in a growing number of fields, and thus it is evolving as a horizontal technology. Consequently, AI components are increasingly been integrated into embedded systems along with electronics and software. We refer to these systems as AI-enhanced embedded systems. Given the strong dependence of AI on data, this expansion also creates a new space for applying data management techniques. Objective: The overall goal of this thesis is to empirically identify the data management challenges encountered during the development and maintenance of AI-enhanced embedded systems, propose an improved data management approach and empirically validate the proposed approach.Method: To achieve the goal, we conducted this research in close collaboration with Software Center companies using a combination of different empirical research methods: case studies, literature reviews, and action research.Results and conclusions: This research provides five main results. First, it identifies key data management challenges specific to Deep Learning models developed at embedded system companies. Second, it examines the practices such as DataOps and data pipelines that help to address data management challenges. We observed that DataOps is the best data management practice that improves the data quality and reduces the time tdevelop data products. The data pipeline is the critical component of DataOps that manages the data life cycle activities. The study also provides the potential faults at each step of the data pipeline and the corresponding mitigation strategies. Finally, the data pipeline model is realized in a small piece of data pipeline and calculated the percentage of saved data dumps through the implementation.Future work: As future work, we plan to realize the conceptual data pipeline model so that companies can build customized robust data pipelines. We also plan to analyze the impact and value of data pipelines in cross-domain AI systems and data applications. We also plan to develop AI-based fault detection and mitigation system suitable for data pipelines

Planning for the Lifecycle Management and Long-Term Preservation of Research Data: A Federated Approach

Outcomes of the grant are archived here.The “data deluge” is a recent but increasingly well-understood phenomenon of scientific and social inquiry. Large-scale research instruments extend our observational power by many orders of magnitude but at the same time generate massive amounts of data. Researchers work feverishly to document and preserve changing or disappearing habitats, cultures, languages, and artifacts resulting in volumes of media in various formats. New software tools mine a growing universe of historical and modern texts and connect the dots in our semantic environment. Libraries, archives, and museums undertake digitization programs creating broad access to unique cultural heritage resources for research. Global-scale research collaborations with hundreds or thousands of participants, drive the creation of massive amounts of data, most of which cannot be recreated if lost. The University of Kansas (KU) Libraries in collaboration with two partners, the Greater Western Library Alliance (GWLA) and the Great Plains Network (GPN), received an IMLS National Leadership Grant designed to leverage collective strengths and create a proposal for a scalable and federated approach to the lifecycle management of research data based on the needs of GPN and GWLA member institutions.Institute for Museum and Library Services LG-51-12-0695-1

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here