Discovering information from an integrated graph database

The information explosion in science has become a different problem, not the sheer amount per se, but the multiplicity and heterogeneity of massive sets of data sources. Relations mined from these heterogeneous sources, namely texts, database records, and ontologies have been mapped to Resource Description Framework (RDF) triples in an integrated database. The subject and object resources are expressed as references to concepts in a biomedical ontology consisting of the Unified Medical Language System (UMLS), UniProt and EntrezGene and for the predicate resource to a predicate thesaurus. All RDF triples have been stored in a graph database, including provenance. For evaluation we used an actual formal PRISMA literature study identifying 61 cerebral spinal fluid biomarkers and 200 blood biomarkers for migraine. These biomarkers sets could be retrieved with weighted mean average precision values of 0.32 and 0.59, respectively, and can be used as a first reference for further refinements

Graphical Database Architecture For Clinical Trials

The general area of the research is Health Informatics. The research focuses on creating an innovative and novel solution to manage and analyze clinical trials data. It constructs a Graphical Database Architecture (GDA) for Clinical Trials (CT) using New Technology for Java (Neo4j) as a robust, a scalable and a high-performance database. The purpose of the research project is to develop concepts and techniques based on architecture to accelerate the processing time of clinical data navigation at lower cost. The research design uses a positivist approach to empirical research. The research is significant because it proposes a new approach of clinical trials through graph theory and designs a responsive structure of clinical data that can be deployed across all the health informatics landscape. It uniquely contributes to scholarly literature of the phenomena of Not only SQL (NoSQL) graph databases, mainly Neo4j in CT, for future research of clinical informatics. A prototype is created and examined to validate the concepts, taking advantage of Neo4j’s high availability, scalability, and powerful graph query language (Cypher). This research study finds that integration of search methodologies and information retrieval with the graphical database provides a solid starting point to manage, query, and analyze the clinical trials data, furthermore the design and the development of a prototype demonstrate the conceptual model of this study. Likewise the proposed clinical trials ontology (CTO) incorporates all data elements of a standard clinical study which facilitate a heuristic overview of treatments, interventions, and outcome results of these studies

Enhancing cyber assets visibility for effective attack surface management : Cyber Asset Attack Surface Management based on Knowledge Graph

The contemporary digital landscape is filled with challenges, chief among them being the management and security of cyber assets, including the ever-growing shadow IT. The evolving nature of the technology landscape has resulted in an expansive system of solutions, making it challenging to select and deploy compatible solutions in a structured manner. This thesis explores the critical role of Cyber Asset Attack Surface Management (CAASM) technologies in managing cyber attack surfaces, focusing on the open-source CAASM tool, Starbase, by JupiterOne. It starts by underlining the importance of comprehending the cyber assets that need defending. It acknowledges the Cyber Defense Matrix as a methodical and flexible approach to understanding and addressing cyber security challenges. A comprehensive analysis of market trends and business needs validated the necessity of asset security management tools as fundamental components in firms' security journeys. CAASM has been selected as a promising solution among various tools due to its capabilities, ease of use, and seamless integration with cloud environments using APIs, addressing shadow IT challenges. A practical use case involving the integration of Starbase with GitHub was developed to demonstrate the CAASM's usability and flexibility in managing cyber assets in organizations of varying sizes. The use case enhanced the knowledge graph's aesthetics and usability using Neo4j Desktop and Neo4j Bloom, making it accessible and insightful even for non-technical users. The thesis concludes with practical guidelines in the appendices and on GitHub for reproducing the use case

Representing and querying disease networks using graph databases

BACKGROUND: Systems biology experiments generate large volumes of data of multiple modalities and this information presents a challenge for integration due to a mix of complexity together with rich semantics. Here, we describe how graph databases provide a powerful framework for storage, querying and envisioning of biological data. RESULTS: We show how graph databases are well suited for the representation of biological information, which is typically highly connected, semi-structured and unpredictable. We outline an application case that uses the Neo4j graph database for building and querying a prototype network to provide biological context to asthma related genes. CONCLUSIONS: Our study suggests that graph databases provide a flexible solution for the integration of multiple types of biological data and facilitate exploratory data mining to support hypothesis generation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13040-016-0102-8) contains supplementary material, which is available to authorized users