Article
Biochemistry & Molecular Biology
Simon Mendelsohn, David Froelicher, Denis Loginov, David Bernick, Bonnie Berger, Hyunghoon Cho
Summary: Advances in genomics are increasingly dependent on the ability to analyze large and diverse genomic data collections while preserving privacy. However, the complexities of setup and coordination among parties have made existing tools challenging to use. To address this, sfkit is presented as a secure and federated toolkit for collaborative genomic studies, offering collaborative workflows for essential tasks such as GWAS and PCA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Ziyin Xin, Yujun Cai, Louis T. Dang, Hannah M. S. Burke, Jerico Revote, Natalie Charitakis, Denis Bienroth, Hieu T. Nim, Yuan-Fang Li, Mirana Ramialison
Summary: MonaGO is a web-based visualization system that allows biologists to perform GO enrichment analysis and visualize the results in an intuitive, interactive, and responsive manner. It supports various input formats and provides customizable display options.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Wen Chen, Jing Li, Shulan Huang, Xiaodeng Li, Xuan Zhang, Xiang Hu, Shuanglin Xiang, Changning Liu
Summary: Gene co-expression network analysis is widely used in gene function annotation, but there is a lack of effective cross-platform analysis tools. To address this issue and make it easier for biologists to build and predict gene co-expression networks, a command-line toolkit called GCEN has been developed using C++. With its efficient and user-friendly design, GCEN allows researchers to perform gene co-expression network analysis without requiring sophisticated programming skills, especially in the context of RNA-Seq research and lncRNA function annotation.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Inigo Fernandez del Amo, John Ahmet Erkoyuncu, Maryam Farsi, Dedy Ariansyah
Summary: This paper proposes dynamic authoring and hybrid recommender methods for accurate AR-based reporting in maintenance operations. Experimental results show that the proposed methods can improve the efficiency and effectiveness of reporting tasks.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Engineering, Marine
Hao Zhang, Anmin Zhang, Chenxu Wang, Liuyang Zhang, Shuai Liu
Summary: This paper proposes an ontological theory and methodology based on a comprehensive analysis of domain knowledge to address the issue of ambiguity and diversity in the semantic expression of ocean circulation. Through a comprehensive analysis of different elements, classes, properties, spatiotemporal relationships, and inference conditions are defined to complete the construction of ocean circulation ontology. The effectiveness of ontological construction is validated through the formal expression of the Equatorial Counter Current, and an ontology-based knowledge base of ocean circulation is proposed.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Thermodynamics
Bruno Veiga, Gabriel Santos, Tiago Pinto, Ricardo Faia, Carlos Ramos, Zita Vale
Summary: The increasing share of renewable generation globally has led to a need for new electricity markets suited to this new reality. Simulation tools can be used to analyze the impacts of new solutions and this work introduces two web services for electricity market simulation. These services enable the simulation of different algorithms and the evaluation of electrical grids, facilitating integration with other systems. A case study demonstrates the accuracy and usefulness of the proposed services.
Article
Computer Science, Information Systems
Andy Neumann, Nuno Laranjeiro, Jorge Bernardino
Summary: An analysis of 500 websites claiming to provide REST web service APIs revealed trends and discrepancies, with only a small percentage strictly adhering to all REST principles. The results can assist practitioners in developing guidelines for higher quality services and identifying deficiencies in current deployments.
IEEE TRANSACTIONS ON SERVICES COMPUTING
(2021)
Article
Biochemistry & Molecular Biology
Lan-Yun Chang, Meng-Zhan Lee, Yujia Wu, Wen-Kai Lee, Chia-Liang Ma, Jun-Mao Chang, Ciao-Wen Chen, Tzu-Chun Huang, Chia-Hwa Lee, Jih-Chin Lee, Yu-Yao Tseng, Chun-Yu Lin
Summary: Gscore is a powerful analytical method based on expression data that accurately identifies target pathways, reveals clinical outcomes, and is used to study COVID-19-related pathways.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Computer Science, Information Systems
Fahad Qaswar, M. Rahmah, Muhammad Ahsan Raza, A. Noraziah, Basem Alkazemi, Z. Fauziah, Mohd. Khairul Azmi Hassan, Ahmed Sharaf
Summary: This research conducted a systematic literature review to analyze the use of ontology in the Internet of Things (IoT). The findings show that ontologies are needed in the IoT field to minimize interoperability and integration issues, and there are existing ontologies that can be used for this purpose. Therefore, ontology is beneficial for achieving interoperability, integration, and privacy in the IoT.
Article
Biochemical Research Methods
Arya R. Massarat, Michael Lamkin, Ciara Reeve, Amy L. Williams, Matteo D'Antonio, Melissa Gymrek
Summary: This article introduces an open-source toolkit called haptools for performing local ancestry aware and haplotype-based analysis of complex traits in genome-wide association studies and downstream analyses. Haptools supports fast simulation of admixed genomes, visualization of admixture tracks, simulation of haplotype- and local ancestry-specific phenotype effects, and a variety of file operations and statistics computed in a haplotype-aware manner.
Article
Computer Science, Artificial Intelligence
Nicolas Ferranti, Jairo Francisco de Souza, Stenio Sa Rosario Furtado Soares
Summary: New ontology matching approaches are published every year to address the heterogeneity problem. Combining different alignment techniques can improve accuracy by capturing more entity characteristics. Local search-based meta-heuristics show good performance and accuracy compared to global optimization meta-heuristics.
KNOWLEDGE AND INFORMATION SYSTEMS
(2021)
Article
Biochemistry & Molecular Biology
Yali Wang, Kun Zheng, Xiuqiong Chen, Rui Chen, Yanmei Zou
Summary: The study identified pivotal genes associated with gastric cancer and explored their prognostic significance. COL1A1, THBS2, and SPP1 were found to potentially predict immunotherapy response in GC patients.
BIOSCIENCE REPORTS
(2021)
Article
Computer Science, Interdisciplinary Applications
Misty E. Porter, Mary C. Hill, Ted Harris, Andrea Brookfield, Xingong Li
Summary: DiscoverFramework is a freeware tool that helps users build spatial and temporal data visualization applications to increase public awareness and promote responsible use of complex environmental systems.
ENVIRONMENTAL MODELLING & SOFTWARE
(2021)
Article
Computer Science, Theory & Methods
Wardani Muhamad, Suhardi, Yoanes Bandung
Summary: This study aims to develop a system that can transform resources in OAS documents into RDF-based semantic web services. By creating a relational database schema, ontology, and using R2RML to generate triple RDF, this goal can be achieved. Through testing and using a dataset of OAS documents, the system has been proven to be effective in providing understandable and reusable services.
JOURNAL OF BIG DATA
(2022)
Article
Mathematical & Computational Biology
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, HyeongSik Kim, Huseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Ray Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona Walls, Christopher J. Mungall, David Osumi-Sutherland
Summary: This article discusses the complex workflows involved in managing the ontology life cycle and the diverse set of tools required for this process. Standardizing release practices and quality standards are crucial in the biomedical domain to enable interoperability. The article also provides an overview of the Ontology Development Kit (ODK) and its practical applications.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
