scholarly journals Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface (Preprint)

2020 ◽  
Author(s):  
Steven Cox ◽  
Stanley C Ahalt ◽  
James Balhoff ◽  
Chris Bizon ◽  
Karamarie Fecho ◽  
...  
Keyword(s):  
Web Application ◽  
Query Language ◽  
Environmental Data ◽  
Use Cases ◽  
Knowledge Graph ◽  
Translational Science ◽  
Knowledge Sources ◽  
Public Data ◽  
Knowledge Graphs ◽  
Upper Level

BACKGROUND Efforts are underway to semantically integrate large biomedical knowledge graphs using common upper-level ontologies to federate graph-oriented application programming interfaces (APIs) to the data. However, federation poses several challenges, including query routing to appropriate knowledge sources, generation and evaluation of answer subsets, semantic merger of those answer subsets, and visualization and exploration of results. OBJECTIVE We aimed to develop an interactive environment for query, visualization, and deep exploration of federated knowledge graphs. METHODS We developed a biomedical query language and web application interphase—termed as Translator Query Language (TranQL)—to query semantically federated knowledge graphs and explore query results. TranQL uses the Biolink data model as an upper-level biomedical ontology and an API standard that has been adopted by the Biomedical Data Translator Consortium to specify a protocol for expressing a query as a graph of Biolink data elements compiled from statements in the TranQL query language. Queries are mapped to federated knowledge sources, and answers are merged into a knowledge graph, with mappings between the knowledge graph and specific elements of the query. The TranQL interactive web application includes a user interface to support user exploration of the federated knowledge graph. RESULTS We developed 2 real-world use cases to validate TranQL and address biomedical questions of relevance to translational science. The use cases posed questions that traversed 2 federated Translator API endpoints: Integrated Clinical and Environmental Exposures Service (ICEES) and Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP). ICEES provides open access to observational clinical and environmental data, and ROBOKOP provides access to linked biomedical entities, such as “gene,” “chemical substance,” and “disease,” that are derived largely from curated public data sources. We successfully posed queries to TranQL that traversed these endpoints and retrieved answers that we visualized and evaluated. CONCLUSIONS TranQL can be used to ask questions of relevance to translational science, rapidly obtain answers that require assertions from a federation of knowledge sources, and provide valuable insights for translational research and clinical practice.

scholarly journals Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface

10.2196/17964 ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. e17964
Author(s):  
Steven Cox ◽  
Stanley C Ahalt ◽  
James Balhoff ◽  
Chris Bizon ◽  
Karamarie Fecho ◽  
...  
Keyword(s):  
Web Application ◽  
Query Language ◽  
Environmental Data ◽  
Use Cases ◽  
Knowledge Graph ◽  
Translational Science ◽  
Knowledge Sources ◽  
Public Data ◽  
Knowledge Graphs ◽  
Upper Level

Background Efforts are underway to semantically integrate large biomedical knowledge graphs using common upper-level ontologies to federate graph-oriented application programming interfaces (APIs) to the data. However, federation poses several challenges, including query routing to appropriate knowledge sources, generation and evaluation of answer subsets, semantic merger of those answer subsets, and visualization and exploration of results. Objective We aimed to develop an interactive environment for query, visualization, and deep exploration of federated knowledge graphs. Methods We developed a biomedical query language and web application interphase—termed as Translator Query Language (TranQL)—to query semantically federated knowledge graphs and explore query results. TranQL uses the Biolink data model as an upper-level biomedical ontology and an API standard that has been adopted by the Biomedical Data Translator Consortium to specify a protocol for expressing a query as a graph of Biolink data elements compiled from statements in the TranQL query language. Queries are mapped to federated knowledge sources, and answers are merged into a knowledge graph, with mappings between the knowledge graph and specific elements of the query. The TranQL interactive web application includes a user interface to support user exploration of the federated knowledge graph. Results We developed 2 real-world use cases to validate TranQL and address biomedical questions of relevance to translational science. The use cases posed questions that traversed 2 federated Translator API endpoints: Integrated Clinical and Environmental Exposures Service (ICEES) and Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP). ICEES provides open access to observational clinical and environmental data, and ROBOKOP provides access to linked biomedical entities, such as “gene,” “chemical substance,” and “disease,” that are derived largely from curated public data sources. We successfully posed queries to TranQL that traversed these endpoints and retrieved answers that we visualized and evaluated. Conclusions TranQL can be used to ask questions of relevance to translational science, rapidly obtain answers that require assertions from a federation of knowledge sources, and provide valuable insights for translational research and clinical practice.

Mobile Software Assurance Informed through Knowledge Graph Construction: The OWASP Threat of Insecure Data Storage

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Suzanna Schmeelk ◽  
Lixin Tao
Keyword(s):  
Data Storage ◽  
Program Analysis ◽  
Web Application ◽  
Security Analysis ◽  
Knowledge Graph ◽  
Healthcare Applications ◽  
Sensitive Data ◽  
Knowledge Graphs ◽  
Mobile Malware Detection ◽  
Software Assurance

Many organizations, to save costs, are movinheg to t Bring Your Own Mobile Device (BYOD) model and adopting applications built by third-parties at an unprecedented rate.  Our research examines software assurance methodologies specifically focusing on security analysis coverage of the program analysis for mobile malware detection, mitigation, and prevention.  This research focuses on secure software development of Android applications by developing knowledge graphs for threats reported by the Open Web Application Security Project (OWASP).  OWASP maintains lists of the top ten security threats to web and mobile applications.  We develop knowledge graphs based on the two most recent top ten threat years and show how the knowledge graph relationships can be discovered in mobile application source code.  We analyze 200+ healthcare applications from GitHub to gain an understanding of their software assurance of their developed software for one of the OWASP top ten moble threats, the threat of “Insecure Data Storage.”  We find that many of the applications are storing personally identifying information (PII) in potentially vulnerable places leaving users exposed to higher risks for the loss of their sensitive data.

scholarly journals Virtual Knowledge Graphs: An Overview of Systems and Use Cases

2019 ◽  
Vol 1 (3) ◽  
pp. 201-223 ◽  
Author(s):  
Guohui Xiao ◽  
Linfang Ding ◽  
Benjamin Cogrel ◽  
Diego Calvanese
Keyword(s):  
Data Integration ◽  
Domain Knowledge ◽  
Data Access ◽  
Use Cases ◽  
Future Research ◽  
Knowledge Graph ◽  
Research Directions ◽  
Wide Range ◽  
Future Research Directions ◽  
Knowledge Graphs

In this paper, we present the virtual knowledge graph (VKG) paradigm for data integration and access, also known in the literature as Ontology-based Data Access. Instead of structuring the integration layer as a collection of relational tables, the VKG paradigm replaces the rigid structure of tables with the flexibility of graphs that are kept virtual and embed domain knowledge. We explain the main notions of this paradigm, its tooling ecosystem and significant use cases in a wide range of applications. Finally, we discuss future research directions.

scholarly journals Biological Insights Knowledge Graph: an integrated knowledge graph to support drug development

2021 ◽  
Author(s):  
David Geleta ◽  
Andriy Nikolov ◽  
Gavin Edwards ◽  
Anna Gogleva ◽  
Richard Jackson ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Development ◽  
Use Cases ◽  
Knowledge Graph ◽  
Multiple Use ◽  
Organisational Knowledge ◽  
Data Source ◽  
The Common ◽  
Knowledge Graphs ◽  
Use Of Knowledge

The use of knowledge graphs as a data source for machine learning methods to solve complex problems in life sciences has rapidly become popular in recent years. Our Biological Insights Knowledge Graph (BIKG) combines relevant data for drug development from public as well as internal data sources to provide insights for a range of tasks: from identifying new targets to repurposing existing drugs. Besides the common requirements to organisational knowledge graphs such as being able to capture the domain precisely and give the users the ability to search and query the data, the focus on handling multiple use cases and supporting use case-specific machine learning models presents additional challenges: the data models must also be streamlined for the performance of downstream tasks; graph content must be easily customisable for different use cases; different projections of the graph content are required to support a wider range of different consumption modes. In this paper we describe our main design choices in implementation of the BIKG graph and discuss different aspects of its life cycle: from graph construction to exploitation.

scholarly journals TransET: Knowledge Graph Embedding with Entity Types

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1407
Author(s):  
Peng Wang ◽  
Jing Zhou ◽  
Yuzhang Liu ◽  
Xingchen Zhou
Keyword(s):  
Link Prediction ◽  
State Of The Art ◽  
Score Function ◽  
Graph Embedding ◽  
Vector Spaces ◽  
Knowledge Graph ◽  
Semantic Features ◽  
Knowledge Graphs ◽  
Real World Datasets ◽  
Low Dimensional

Knowledge graph embedding aims to embed entities and relations into low-dimensional vector spaces. Most existing methods only focus on triple facts in knowledge graphs. In addition, models based on translation or distance measurement cannot fully represent complex relations. As well-constructed prior knowledge, entity types can be employed to learn the representations of entities and relations. In this paper, we propose a novel knowledge graph embedding model named TransET, which takes advantage of entity types to learn more semantic features. More specifically, circle convolution based on the embeddings of entity and entity types is utilized to map head entity and tail entity to type-specific representations, then translation-based score function is used to learn the presentation triples. We evaluated our model on real-world datasets with two benchmark tasks of link prediction and triple classification. Experimental results demonstrate that it outperforms state-of-the-art models in most cases.

scholarly journals Development of Knowledge Graph for Data Management Related to Flooding Disasters Using Open Data

2021 ◽  
Vol 13 (5) ◽  
pp. 124
Author(s):  
Jiseong Son ◽  
Chul-Su Lim ◽  
Hyoung-Seop Shim ◽  
Ji-Sun Kang
Keyword(s):  
Artificial Intelligence ◽  
Domain Knowledge ◽  
Open Data ◽  
Heterogeneous Data ◽  
Big Data Analysis ◽  
Knowledge Graph ◽  
Cross Domain ◽  
Disaster Data ◽  
Knowledge Graphs ◽  
Open Datasets

Despite the development of various technologies and systems using artificial intelligence (AI) to solve problems related to disasters, difficult challenges are still being encountered. Data are the foundation to solving diverse disaster problems using AI, big data analysis, and so on. Therefore, we must focus on these various data. Disaster data depend on the domain by disaster type and include heterogeneous data and lack interoperability. In particular, in the case of open data related to disasters, there are several issues, where the source and format of data are different because various data are collected by different organizations. Moreover, the vocabularies used for each domain are inconsistent. This study proposes a knowledge graph to resolve the heterogeneity among various disaster data and provide interoperability among domains. Among disaster domains, we describe the knowledge graph for flooding disasters using Korean open datasets and cross-domain knowledge graphs. Furthermore, the proposed knowledge graph is used to assist, solve, and manage disaster problems.

Improvements for research data repositories: The case of text spam

2021 ◽  
pp. 016555152199863
Author(s):  
Ismael Vázquez ◽  
María Novo-Lourés ◽  
Reyes Pavón ◽  
Rosalía Laza ◽  
José Ramón Méndez ◽  
...  
Keyword(s):  
Web Application ◽  
Research Data ◽  
Data Sets ◽  
Data Repositories ◽  
Software Applications ◽  
Public Data ◽  
Protection Mechanisms ◽  
Experimental Protocols ◽  
Learning Research ◽  
Processing Steps

Current research has evolved in such a way scientists must not only adequately describe the algorithms they introduce and the results of their application, but also ensure the possibility of reproducing the results and comparing them with those obtained through other approximations. In this context, public data sets (sometimes shared through repositories) are one of the most important elements for the development of experimental protocols and test benches. This study has analysed a significant number of CS/ML ( Computer Science/ Machine Learning) research data repositories and data sets and detected some limitations that hamper their utility. Particularly, we identify and discuss the following demanding functionalities for repositories: (1) building customised data sets for specific research tasks, (2) facilitating the comparison of different techniques using dissimilar pre-processing methods, (3) ensuring the availability of software applications to reproduce the pre-processing steps without using the repository functionalities and (4) providing protection mechanisms for licencing issues and user rights. To show the introduced functionality, we created STRep (Spam Text Repository) web application which implements our recommendations adapted to the field of spam text repositories. In addition, we launched an instance of STRep in the URL https://rdata.4spam.group to facilitate understanding of this study.

scholarly journals Research of Personalized Recommendation Technology Based on Knowledge Graphs

2021 ◽  
Vol 11 (15) ◽  
pp. 7104
Author(s):  
Xu Yang ◽  
Ziyi Huan ◽  
Yisong Zhai ◽  
Ting Lin
Keyword(s):  
Neural Network ◽  
Hot Spot ◽  
Experimental Results ◽  
Graph Representation ◽  
Personalized Recommendation ◽  
Knowledge Graph ◽  
Learning Technology ◽  
Data Set ◽  
Model Based ◽  
Knowledge Graphs

Nowadays, personalized recommendation based on knowledge graphs has become a hot spot for researchers due to its good recommendation effect. In this paper, we researched personalized recommendation based on knowledge graphs. First of all, we study the knowledge graphs’ construction method and complete the construction of the movie knowledge graphs. Furthermore, we use Neo4j graph database to store the movie data and vividly display it. Then, the classical translation model TransE algorithm in knowledge graph representation learning technology is studied in this paper, and we improved the algorithm through a cross-training method by using the information of the neighboring feature structures of the entities in the knowledge graph. Furthermore, the negative sampling process of TransE algorithm is improved. The experimental results show that the improved TransE model can more accurately vectorize entities and relations. Finally, this paper constructs a recommendation model by combining knowledge graphs with ranking learning and neural network. We propose the Bayesian personalized recommendation model based on knowledge graphs (KG-BPR) and the neural network recommendation model based on knowledge graphs(KG-NN). The semantic information of entities and relations in knowledge graphs is embedded into vector space by using improved TransE method, and we compare the results. The item entity vectors containing external knowledge information are integrated into the BPR model and neural network, respectively, which make up for the lack of knowledge information of the item itself. Finally, the experimental analysis is carried out on MovieLens-1M data set. The experimental results show that the two recommendation models proposed in this paper can effectively improve the accuracy, recall, F1 value and MAP value of recommendation.

scholarly journals Pattern-based design applied to cultural heritage knowledge graphs

Semantic Web ◽  
2020 ◽  
pp. 1-45
Author(s):  
Valentina Anita Carriero ◽  
Aldo Gangemi ◽  
Maria Letizia Mancinelli ◽  
Andrea Giovanni Nuzzolese ◽  
Valentina Presutti ◽  
...  
Keyword(s):  
Cultural Heritage ◽  
Design Patterns ◽  
Lessons Learned ◽  
Knowledge Graph ◽  
Unit Testing ◽  
Domain Specific ◽  
Rigorous Testing ◽  
Ontology Design ◽  
Domain Specific Knowledge ◽  
Knowledge Graphs

Ontology Design Patterns (ODPs) have become an established and recognised practice for guaranteeing good quality ontology engineering. There are several ODP repositories where ODPs are shared as well as ontology design methodologies recommending their reuse. Performing rigorous testing is recommended as well for supporting ontology maintenance and validating the resulting resource against its motivating requirements. Nevertheless, it is less than straightforward to find guidelines on how to apply such methodologies for developing domain-specific knowledge graphs. ArCo is the knowledge graph of Italian Cultural Heritage and has been developed by using eXtreme Design (XD), an ODP- and test-driven methodology. During its development, XD has been adapted to the need of the CH domain e.g. gathering requirements from an open, diverse community of consumers, a new ODP has been defined and many have been specialised to address specific CH requirements. This paper presents ArCo and describes how to apply XD to the development and validation of a CH knowledge graph, also detailing the (intellectual) process implemented for matching the encountered modelling problems to ODPs. Relevant contributions also include a novel web tool for supporting unit-testing of knowledge graphs, a rigorous evaluation of ArCo, and a discussion of methodological lessons learned during ArCo’s development.

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