Comprehensive Knowledge Base Research Articles

Nurse-led multi-component behavioural activation programme to improve health outcomes in patients with atrial fibrillation: a mixed-methods study and feasibility analysis.

Patients with atrial fibrillation (AF) play passive roles in disease management. This study aimed to examine the feasibility and preliminary effects of an empowerment-based care model, titled 'the nurse-led multi-component behavioural activation (N-MBA) programme', on health-related quality of life, AF knowledge, psychological outcomes, medication adherence, and treatment decision-making in patients with AF. This mixed-methods study comprised a pilot randomized controlled trial and a qualitative study. Patients with AF who had a moderate-to-high risk of stroke but were not prescribed oral anticoagulants were recruited. Forty participants were recruited and randomized in a 1:1 ratio to receive either the N-MBA programme or standard care. The 13-week programme comprised care components that prepared patients for shared decision-making, an empowerment-based educational module on AF self-care, and continuous support through telephone calls. The programme was feasible, and the overall attendance rate was 82.5%. The participants gave excellent ratings in the satisfaction survey. The N-MBA group showed greater improvements in health-related quality of life (HRQoL) and AF knowledge than the standard care group at the immediate post intervention and 6-month follow-up time points. No significant between-group changes in medication adherence, anxiety, and depression were detected. Participants in the N-MBA group actively raised concerns about AF and its treatment with their attending doctors. The qualitative data were consistent with the quantitative data, indicating that the programme built a comprehensive knowledge base of AF and self-care behaviours. The N-MBA programme is feasible and acceptable to patients with AF. It improved patients' AF knowledge, treatment-related decision-making, and HRQoL. ClinicalTrials.gov NCT03924739.

Ec-Funded Projects’ Lessons Learned In Earth Friendly Freight Transportation

Abstract The paper is based on the research project ePIcenter (www.ePIcenterproject.eu) supported by the EU HORIZON 2020 Programme. ePIcenter connects thirty-six partners: port authorities, logistic service providers, manufacturers, academic institutions, and technology partners. The main goal is to develop and test AI driven logistic software solutions, apply new technologies and methodologies to increase the efficiency of global supply chains and reduce their environmental impact. One of the significant aspect the project focusses on is optimisation, using AI, digitalisation, automation and innovations in freight transport and handling technologies. Finally, modelling powerful solutions to enable resilient, efficient and environment friendly supply chains. Knowledge sharing is one of powerful tool for researchers, policymakers, service providers and other stakeholders to develop a holistic and comprehensive common knowledge base. First, a theoretical framework had been developed through identification and review knowledge available from previous projects funded through the European Commission as well as other international funding projects. Second, lessons learned and success stories from previous EC-funded projects and other international research programmes were reviewed and provided in the first year of project implementation.

ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers.

Alternative splicing (AS) is a fundamental process that governs almost all aspects of cellular functions, and dysregulation in this process has been implicated in tumor initiation, progression and treatment resistance. With accumulating studies of carcinogenic mis-splicing in cancers, there is an urgent demand to integrate cancer-associated splicing changes to better understand their internal cross-talks and functional consequences from a global view. However, a resource of key functional AS events in human cancers is still lacking. To fill the gap, we developed ASCancer Atlas (https://ngdc.cncb.ac.cn/ascancer), a comprehensive knowledgebase of aberrant splicing in human cancers. Compared to extant databases, ASCancer Atlas features a high-confidence collection of 2006 cancer-associated splicing events experimentally proved to promote tumorigenesis, a systematic splicing regulatory network, and a suit of multi-scale online analysis tools. For each event, we manually curated the functional axis including upstream splicing regulators, splicing event annotations, downstream oncogenic effects, and possible therapeutic strategies. ASCancer Atlas also houses about 2 million computationally putative splicing events. Additionally, a user-friendly web interface was built to enable users to easily browse, search, visualize, analyze, and download all splicing events. Overall, ASCancer Atlas provides a unique resource to study the functional roles of splicing dysregulation in human cancers.

Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy.

Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three official fungal nomenclatural repositories authorized by the International Nomenclature Committee for Fungi (NCF). Currently, FN includes >567 000 taxon names from >10 000 related journals and books published since 1596 and covers >147 000 collection records of type specimens/illustrations from >5000 preserving agencies. FN is also a knowledge base that integrates nomenclature information with specimens, culture collections and herbaria/fungaria, publications and taxonomists, and represents a summary of the history and recent advances in fungal taxonomy. Published fungal names are categorized based on well-accepted nomenclature rules and can be readily searched with different keywords and strategies. In combination with a standardized name checking tool and a sequence alignment-based identification package, FN makes the registration and typification of nomenclatural novelties of fungi convenient and accurate.

Space Performance Assessment of a Relocatable Health Facility: Mosul Hospital as a Case Study

Relocatable buildings are commonly spread around as an alternative method of construction. To consider it a successful practice, it should perform its function similarly to a traditional way. Assessing a building after its operation determines the rate of its success and decides the possibility of repeating its type. This study aimed to provide a comprehensive knowledge base related to space evaluation of the building through spatial assessment. This study investigated the functional efficiency and dimensional requirements of a relocatable hospital in Mosul, in the south of Iraq. This study compared the dimensional requirements of eight hospital departments to the standard, followed by functional efficacy analysis based on space syntax theory and compared the results to examples used in standards books. The results showed that departments in the relocatable buildings have good plan integration. We concluded that hospitals constructed with containers could achieve functional efficiency.

Knowledgebase of potential multifaceted solutions to antimicrobial resistance

Antimicrobial resistance (AMR), a top threat to global health, challenges preventive and treatment strategies of infections. AMR strains of microbial pathogens arise through multiple mechanisms. The underlying “antibiotic resistance genes” (ARGs) spread through various species by lateral gene transfer thereby causing global dissemination. Human methods also augment this process through inappropriate use, non-compliance to treatment schedule, and environmental waste. Worldwide significant efforts are being invested to discover novel therapeutic solutions for tackling resistant pathogens. Diverse therapeutic strategies have evolved over recent years. In this work we have developed a comprehensive knowledgebase by collecting alternative antimicrobial therapeutic strategies from literature data. Therapeutic strategies against bacteria, virus, fungus and parasites were extracted from PubMed literature using text mining. We have used a subjective (sentimental) approach for data mining new strategies, resulting in broad coverage of novel entities and subsequently add objective data like entity name (including IUPAC), potency, and safety information. The extracted data was organized in a freely accessible web platform, KOMBAT. The KOMBAT comprises 1104 Chemical compounds, 220 of newly identified antimicrobial peptides, 42 bacteriophages, 242 phytochemicals, 106 nanocomposites, and 94 novel entities for phototherapy. Entities tested and evaluated on AMR pathogens are included. We envision that this database will be useful for developing future therapeutics against AMR pathogens. The database can be accessed through http://kombat.igib.res.in/.

The Forgotten Coast: A Synthesis of Current Knowledge of Southern Chukchi Sea Lagoon Ecosystems

In the Southern Chukchi Sea Region (SCSR) of the Alaskan Arctic, approximately 40% of the coastline consists of freshwater-brackish lagoons and the gravel spits that separate them from the ocean. These lagoons are important rearing, feeding, and spawning habitats for diverse fish and invertebrate assemblages composed of freshwater, diadromous, and marine taxa. Many of these species are prey for a suite of marine mammals and avian predators in addition to being important to the food security of subsistence users from the surrounding region. Despite recognition of the ecological and cultural importance of these habitats from as far back as the 1950s, the body of knowledge surrounding lagoons of the SCSR contains many knowledge gaps and fails to comprehensively capture the dynamic nature of both biotic and abiotic factors that define the functional ecology of these habitats. This report synthesizes the available knowledge of SCSR lagoons, including geomorphology, hydrology, food web structure, and local knowledge. We also recommend avenues of future study, such as characterizing the basal trophic levels of lagoon food webs. Only by constructing a more detailed and comprehensive knowledge base of SCSR lagoon ecology will management and conservation efforts in the region be able to address and mitigate potential threats resulting from expanding infrastructure and global climate change, while simultaneously supporting the diverse portfolio of lagoon habitats that have a vital role in regional subsistence practices and food security.

Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project.

The stimulating peripheral activity to relieve conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system (ANS) in support of bioelectronic medicine. As part of this effort, the SPARC project is generating multi-species, multimodal data, models, simulations, and anatomical maps supported by a comprehensive knowledge base of autonomic circuitry. To facilitate the organization of and integration across multi-faceted SPARC data and models, SPARC is implementing the findable, accessible, interoperable, and reusable (FAIR) data principles to ensure that all SPARC products are findable, accessible, interoperable, and reusable. We are therefore annotating and describing all products with a common FAIR vocabulary. The SPARC Vocabulary is built from a set of community ontologies covering major domains relevant to SPARC, including anatomy, physiology, experimental techniques, and molecules. The SPARC Vocabulary is incorporated into tools researchers use to segment and annotate their data, facilitating the application of these ontologies for annotation of research data. However, since investigators perform deep annotations on experimental data, not all terms and relationships are available in community ontologies. We therefore implemented a term management and vocabulary extension pipeline where SPARC researchers may extend the SPARC Vocabulary using InterLex, an online vocabulary management system. To ensure the quality of contributed terms, we have set up a curated term request and review pipeline specifically for anatomical terms involving expert review. Accepted terms are added to the SPARC Vocabulary and, when appropriate, contributed back to community ontologies to enhance ANS coverage. Here, we provide an overview of the SPARC Vocabulary, the infrastructure and process for implementing the term management and review pipeline. In an analysis of >300 anatomical contributed terms, the majority represented composite terms that necessitated combining terms within and across existing ontologies. Although these terms are not good candidates for community ontologies, they can be linked to structures contained within these ontologies. We conclude that the term request pipeline serves as a useful adjunct to community ontologies for annotating experimental data and increases the FAIRness of SPARC data.

A knowledge graph and service for regional geologic time standards

Geologic time is an important dimension in geological research. Geologic time data are commonly collected from multiple sources in data-intensive studies of Earth’s history and raise an issue of data cleansing and integration. A knowledge graph of the international geological time scale has been established to harmonize heterogeneous data to facilitate effective and efficient data-driven discovery. Although many regional geologic time standards are also used in various databases and literature, there is limited discussion or development of knowledge graph for them. In this research, we construct a knowledge graph for the geologic time standards in 17 regions at the Epoch and Age levels. This regional geologic time knowledge graph is integrated with the international geologic time knowledge graph as a comprehensive deep-time knowledge base. A SPARQL endpoint has been established to provide open and free online service to the knowledge base. Several use cases are presented here to demonstrate the functionality of the knowledge graph we built as well as its application in open data exploration. Our work addresses the shortage of machine-readable knowledge graphs for regional geologic time standards and will help accelerate geologic data integration from multiple sources in data-intensive studies. All data and code in this paper are made open source and are accessible on GitHub and Zenodo.

CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations

Congenital heart disease (CHD) is one of themost common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies have reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice. We therefore developed CHDbase, an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications, linking 1124susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes. Metadata such as the information of each publication and the selected population and samples, the strategy of studies, and the major findings of studies were integrated with each item of the research record. We also integrated functional annotations through parsing ∼ 50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity. We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes. The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin. Overall, CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities, supporting a wide range of users in the scientific and medical communities. CHDbase is accessible at http://chddb.fwgenetics.org.

Teachers’ cognitive beliefs about their assessment and use of tools when evaluating students’ learning of technological systems: a questionnaire study

In technology education, assessment is challenging and underdeveloped as it is a nascent practice and teachers do not have a well-defined subject tradition to lean on when assessing students. The aim of this study is to explore Swedish secondary technology teachers’ cognitive beliefs about assessing students’ learning of technological systems, in relation to the assessment tools they use. Data for the study were collected through a questionnaire which was completed by 511 Swedish technology teachers in lower secondary education (grades 7–9). The data were analysed statistically in three main steps. Exploratory factor analysis revealed underlying dimensions in teachers’ cognitive beliefs, which was followed by correlation analysis to discern associations between dimensions of cognitive beliefs. Finally, comparisons were made between groups of teachers to discern how teachers’ cognitive beliefs are influenced by their experience and educational background. The results show that additional education in the technology and engineering fields relates to more positive cognitive beliefs concerning teachers’ ability to assess students’ learning of technological systems. Teachers’ cognitive beliefs about assessment therefore did not primarily relate to the content of technological systems per se but to increased engineering and technology competence more broadly, which may indicate the importance of a comprehensive technological knowledge base in order to be confident in assessment. Furthermore, strong cognitive beliefs about assessment were connected specifically to local, regional and national technological systems, which are generally well-known and visible types of systems, and to the human, socio-technical dimensions of the systems. Cognitive beliefs about knowledge for assessment were also associated with positive attitudes to assessment tools that followed the formative tradition, which may be explained by the prevalence of procedural epistemic practices and modelling in the design and understanding of technological systems. Technology teachers would need additional in-service courses in engineering to broaden their knowledge and increase their cognitive beliefs about assessment. Formative assessment should also be preferred, and it might be appropriate to begin teaching and assessment with well-known local and regional infrastructural systems with a clear socio-technical dimension.

The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer.

Our understanding of prostate cancer (PCa) has shifted from solely caused by a few genetic aberrations to a combination of complex biochemical dysregulations with the prostate metabolome at its core. The role of metabolomics in analyzing the pathophysiology of PCa is indispensable. However, to fully elucidate real-time complex dysregulation in prostate cells, an integrated approach based on metabolomics and other omics is warranted. Individually, genomics, transcriptomics, and proteomics are robust, but they are not enough to achieve a holistic view of PCa tumorigenesis. This review is the first of its kind to focus solely on the integration of metabolomics with multi-omic platforms in PCa research, including a detailed emphasis on the metabolomic profile of PCa. The authors intend to provide researchers in the field with a comprehensive knowledge base in PCa metabolomics and offer perspectives on overcoming limitations of the tool to guide future point-of-care applications.

The LOTUS initiative for open knowledge management in natural products research.

Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.

SecureOnt: A Security Ontology for Establishing Data Provenance in Semantic Web

Security becomes a primary concern during sharing of information over the web. To overcome this problem, many security ontologies have been developed so far. The available security ontologies help to track data provenance and contain different aspects of data security like confidentiality, integrity, data availability, and access control. This paper provides a security ontology for establishing data provenance in the semantic web. The proposed ontology contains a comprehensive knowledge base of data security by consolidating all the available security ontologies and derives data provenance with annotations at the extensional level and thus lower maintenance cost. By this paper, analysts and researchers find a road map, an overview of what exists in terms of security ontologies.

The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.

The Sickle Cell Disease (SCD) Ontology (SCDO, https://scdontology.h3abionet.org/) provides a comprehensive knowledge base of SCD management, systems and standardized human and machine-readable resources that unambiguously describe terminology and concepts about SCD for researchers, patients and clinicians. The SCDO was launched in 2016 and is continuously updated in quantity, as well as in quality, to effectively support the curation of SCD research, patient databasing and clinical informatics applications. SCD knowledge from the scientific literature is used to update existing SCDO terms and create new terms where necessary. Here, we report major updates to the SCDO, from December 2019 until April 2021, for promoting interoperability and facilitating SCD data harmonization, sharing and integration across different studies and for retrospective multi-site research collaborations. SCDO developers continue to collaborate with the SCD community, clinicians and researchers to improve specific ontology areas and expand standardized descriptions to conditions influencing SCD phenotypic expressions and clinical manifestations of the sickling process, e.g. thalassemias. Database URL: https://scdontology.h3abionet.org/

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021update).

DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms, which increased the taxonomy coverage from 17 399 to 55 464. All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared with the last version, the number of gene-term records for most annotation types within the updated Knowledgebase have significantly increased. Moreover, we have incorporated new annotations in the Knowledgebase including small molecule-gene interactions from PubChem, drug-gene interactions from DrugBank, tissue expression information from the Human Protein Atlas, disease information from DisGeNET, and pathways from WikiPathways and PathBank. Eight of ten subgroups split from Uniprot Keyword annotation were assigned to specific types. Finally, we added a species parameter for uploading a list of gene symbols to minimize the ambiguity between species, which increases the efficiency of the list upload and eliminates confusion for users. These current updates have significantly expanded the Knowledgebase and enhanced the discovery power of DAVID.

Insight into real-world complexities is required to enable effective response from the aquaculture sector to climate change

This study demonstrates how a comprehensive knowledge base can be used by the aquaculture industry, researchers, and policymakers as a foundation for more targeted and detailed climate change impact analysis, risk assessments and adaptation planning. Atlantic salmon (Salmo salar) production in Norway was used as a case study and to illustrate the need to consider impacts from multiple stressors across different production stages and the wider supply chain. Based on literature searches and industry news, a total of 45 impacts and 101 adaptation responses were identified. Almost all impacts were linked to multiple climate stressors, and many adaptation responses can be used for a range of impacts. Based on the research, a move towards more targeted and detailed assessments is recommended. This can be facilitated through a strong knowledge base, further research to address complexities, and better communication between all stakeholders. The results also demonstrate the need for more climate change research that reflects the challenges that the aquaculture sector faces, where multiple stressors and the range of impacts across production stages and the wider supply chain are included. Highlighting the wide range of stressors, impacts and adaptation responses provides a more holistic understanding of the real-world complexities that aquaculture producers face. This again could facilitate adoption of more effective responses to climate change needed to maintain or increase production sustainably.

Multi-tissue scRNA-seq reveals immune cell landscape of turbot (Scophthalmus maximus)

In vertebrates, bony fishes possess not only innate immune cells but also T and B cells that are equivalent to those in mammals. However, the precise sub-cluster of immune cells in teleost fish remains largely unknown. Herein, we developed a dynamic bacterial infection model in turbot (Scophthalmus maximus) and created a fish immune cell landscape (FICL) for a primary lymphoid organ (head kidney), a secondary lymphoid organ (spleen), and barrier tissues (gills and posterior intestine). Moreover, through comprehensive characterization of the expression profiles of 16 clusters, including dendritic cells-like (DCs-like), macrophages (MΦs), neutrophils, NK cells, as well as 12 sub-clusters of T and B cells, we found that CD8+ CTLs, CD4−CD8− T, Th17 and ILC3-2 like cells possess a bifunctional role associated with cytotoxicity and immunoregulation during bacterial infection. To our knowledge, these results could provide a useful resource for a better understanding of immune cells in teleost fish and could act as a comprehensive knowledge base for assessing the evolutionary mechanism of adaptive immunity in vertebrates.

VR-enabled engineering consultation chatbot for integrated and intelligent manufacturing services

Industrial equipment manufacturing, such as electric power transformers, require highly customized design, assembly, installation and maintenance services for customers. Engineering consultation is an essential manufacturing service which requires deep domain knowledge. This research develops and implements the framework and the prototype of a Virtual Reality (VR) enabled intelligent engineering consultation chatbot system with natural language communication capabilities. The consultation chatbot case focuses on the power transformer knowledge domain. The system is constructed using a comprehensive knowledge base of Frequently Asked Questions (FAQs) and answers from a power transformer manufacturer. A total of 490,000 technical articles (with more than 1.1 billion words) from Wikipedia and a comprehensive domain-specific document set are used to train a word embedding model for retrieving questions and answers (QA) from the FAQ knowledge base. Immersive VR technology provides a highly interactive QA chatbot with realistic graphical views for informative engineering counselling. The case example demonstrates the accuracy of the proposed VR-enabled chatbot for transformer QAs exceeds 91%.

P128: ITHANET: AN INFORMATION AND DATABASE COMMUNITY PORTAL FOR HAEMOGLOBINOPATHIES

Background: The ITHANET Portal (www.ithanet.eu) is an expanding, publicly available biomedical resource dedicated to haemoglobinopathies. It provides a manually curated, literature-derived collection of published genetic and epidemiological data, also integrating the latest updates on news, events, publications, clinical trials, funding opportunities, and many more. Methods: A team of expert biocurators is involved in the collection, validation and annotation of information with weekly updates on scientific literature collected from PubMed, while the curation strategy also involves the incorporation of new and updated information from existing public databases. ITHANET also accepts contributions to its content with acknowledgement of unpublished data in a specifically designed section. Results: The ITHANET Portal offers a wide range of curated databases, as follows: IthaGenes is a database that organises genes and variations affecting haemoglobinopathies and integrates the NCBI sequence viewer for detailed graphical representation of each variation. IthaMaps is a database that stores epidemiological information as documented in published literature and illustrates this information on a dynamic global to regional map for a total of over 196 countries. IthaChrom provides digitised reports of standard diagnostic high-performance liquid chromatography analyses as a reference tool for haemoglobinopathy diagnosis, allowing database searches of key data. IthaPhen is a database that demonstrates the correlations between genotype and phenotype and is a unique and powerful tool for clinicians and molecular geneticists Conclusions: The ITHANET Portal has a high-profile international governance structure and is already the most comprehensive knowledgebase on haemoglobinopathies. As an official partner of the Human Variome Project’s Global Globin Network, ITHANET has been selected for data storing, curation and sharing within and between countries, as well as for the development of a thalassaemia-specific genotype-phenotype database. In addition, ITHANET is coordinating an Hemoglobinopathy Variant Curation Expert Panel for haemoglobinopathy-specific variant classification under the Clinical Genome Resource.