Scalable Knowledge Graph Construction and Inference on Human Genome Variants

Real-world knowledge can be represented as a graph consisting of entities and relationships between the entities. The need for efficient and scalable solutions arises when dealing with vast genomic data, like RNA-sequencing. Knowledge graphs offer a powerful approach for various tasks in such large-scale genomic data, such as analysis and inference. In this work, variant-level information extracted from the RNA-sequences of vaccine-na\"ive COVID-19 patients have been represented as a unified, large knowledge graph. Variant call format (VCF) files containing the variant-level information were annotated to include further information for each variant. The data records in the annotated files were then converted to Resource Description Framework (RDF) triples. Each VCF file obtained had an associated CADD scores file that contained the raw and Phred-scaled scores for each variant. An ontology was defined for the VCF and CADD scores files. Using this ontology and the extracted information, a large, scalable knowledge graph was created. Available graph storage was then leveraged to query and create datasets for further downstream tasks. We also present a case study using the knowledge graph and perform a classification task using graph machine learning. We also draw comparisons between different Graph Neural Networks (GNNs) for the case study

Building a Knowledge Graph for Food, Energy, and Water Systems

Title from PDF of title page viewed January 30, 2018Thesis advisor: Praveen R. RaoVitaIncludes bibliographical references (pages 41-44)Thesis (M.S.)--School of Computing and Engineering. University of Missouri--Kansas City, 2017A knowledge graph represents millions of facts and reliable information about people, places, and things. Several companies like Microsoft, Amazon, and Google have developed knowledge graphs to better customer experience. These knowledge graphs have proven their reliability and their usage for providing better search results; answering ambiguous questions regarding entities; and training semantic parsers to enhance the semantic relationships over the Semantic Web. Motivated by these reasons, in this thesis, we develop an approach to build a knowledge graph for the Food, Energy, and Water (FEW) systems given the vast amount of data that is available from federal agencies like the United States Department of Agriculture (USDA), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Geological Survey (USGS), and the National Drought Mitigation Center (NDMC). Our goal is to facilitate better analytics for FEW and enable domain experts to conduct data-driven research. To construct the knowledge graph, we employ Semantic Web technologies, namely, the Resource Description Framework (RDF), the Web Ontology Language (OWL), and SPARQL. Starting with raw data (e.g., CSV files), we construct entities and relationships and extend them semantically using a tool called Karma. We enhance this initial knowledge graph by adding new relationships across entities by extracting information from ConceptNet via an efficient similarity searching algorithm. We show initial performance results and discuss the quality of the knowledge graph on several datasets from the USDA.Introduction -- Challenges -- Background and related work -- Approach -- Evaluation -- Conclusion and future wor

Knowledge hypergraph based-approach for multi-source data integration and querying : Application for Earth Observation domain

Early warning against natural disasters to save lives and decrease damages has drawn increasing interest to develop systems that observe, monitor, and assess the changes in the environment. Over the last years, numerous environmental monitoring systems and Earth Observation (EO) programs were implemented. Nevertheless, these systems generate a large amount of EO data while using different vocabularies and different conceptual schemas. Accordingly, data resides in many siloed systems and are mainly untapped for integrated operations, insights, and decision making situations. To overcome the insufficient exploitation of EO data, a data integration system is crucial to break down data silos and create a common information space where data will be semantically linked. Within this context, we propose a semantic data integration and querying approach, which aims to semantically integrate EO data and provide an enhanced query processing in terms of accuracy, completeness, and semantic richness of response. . To do so, we defined three main objectives. The first objective is to capture the knowledge of the environmental monitoring domain. To do so, we propose MEMOn, a domain ontology that provides a common vocabulary of the environmental monitoring domain in order to support the semantic interoperability of heterogeneous EO data. While creating MEMOn, we adopted a development methodology, including three fundamental principles. First, we used a modularization approach. The idea is to create separate modules, one for each context of the environment domain in order to ensure the clarity of the global ontology’s structure and guarantee the reusability of each module separately. Second, we used the upper-level ontology Basic Formal Ontology and the mid-level ontologies, the Common Core ontologies, to facilitate the integration of the ontological modules in order to build the global one. Third, we reused existing domain ontologies such as ENVO and SSN, to avoid creating the ontology from scratch, and this can improve its quality since the reused components have already been evaluated. MEMOn is then evaluated using real use case studies, according to the Sahara and Sahel Observatory experts’ requirements. The second objective of this work is to break down the data silos and provide a common environmental information space. Accordingly, we propose a knowledge hypergraphbased data integration approach to provide experts and software agents with a virtual integrated and linked view of data. This approach generates RML mappings between the developed ontology and metadata and then creates a knowledge hypergraph that semantically links these mappings to identify more complex relationships across data sources. One of the strengths of the proposed approach is it goes beyond the process of combining data retrieved from multiple and independent sources and allows the virtual data integration in a highly semantic and expressive way, using hypergraphs. The third objective of this thesis concerns the enhancement of query processing in terms of accuracy, completeness, and semantic richness of response in order to adapt the returned results and make them more relevant and richer in terms of relationships. Accordingly, we propose a knowledge-hypergraph based query processing that improves the selection of sources contributing to the final result of an input query. Indeed, the proposed approach moves beyond the discovery of simple one-to-one equivalence matches and relies on the identification of more complex relationships across data sources by referring to the knowledge hypergraph. This enhancement significantly showcases the increasing of answer completeness and semantic richness. The proposed approach was implemented in an open-source tool and has proved its effectiveness through a real use case in the environmental monitoring domain