Issues Associated With the Use of Semantic Web Technology in Knowledge Acquisition for Clinical Decision Support Systems: Systematic Review of the Literature.
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ABSTRACT:
SUBMITTER: Zolhavarieh S
PROVIDER: S-EPMC5517823 | biostudies-other | 2017 Jul
REPOSITORIES: biostudies-other
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Project description:The Protein Ontology (PRO) provides an ontological representation of protein-related entities, ranging from protein families to proteoforms to complexes. Protein Ontology Linked Open Data (LOD) exposes, shares, and connects knowledge about protein-related entities on the Semantic Web using Resource Description Framework (RDF), thus enabling integration with other Linked Open Data for biological knowledge discovery. For example, proteins (or variants thereof) can be retrieved on the basis of specific disease associations. As a community resource, we strive to follow the Findability, Accessibility, Interoperability, and Reusability (FAIR) principles, disseminate regular updates of our data, support multiple methods for accessing, querying and downloading data in various formats, and provide documentation both for scientists and programmers. PRO Linked Open Data can be browsed via faceted browser interface and queried using SPARQL via YASGUI. RDF data dumps are also available for download. Additionally, we developed RESTful APIs to support programmatic data access. We also provide W3C HCLS specification compliant metadata description for our data. The PRO Linked Open Data is available at https://lod.proconsortium.org/ .
| S-EPMC7550340 | biostudies-literature
Project description:With the ever-increasing societal dependence on electricity, one of the critical tasks in power supply is maintaining the power line infrastructure. In the process of making informed, cost-effective, and timely decisions, maintenance engineers must rely on human-created, heterogeneous, structured, and also largely unstructured information. The maturing research on vision-based power line inspection driven by advancements in deep learning offers first possibilities to move towards more holistic, automated, and safe decision-making. However, (current) research focuses solely on the extraction of information rather than its implementation in decision-making processes. The paper addresses this shortcoming by designing, instantiating, and evaluating a holistic deep-learning-enabled image-based decision support system artifact for power line maintenance at a German distribution system operator in southern Germany. Following the design science research paradigm, two main components of the artifact are designed: A deep-learning-based model component responsible for automatic fault detection of power line parts as well as a user-oriented interface responsible for presenting the captured information in a way that enables more informed decisions. As a basis for both components, preliminary design requirements are derived from literature and the application field. Drawing on justificatory knowledge from deep learning as well as decision support systems, tentative design principles are derived. Based on these design principles, a prototype of the artifact is implemented that allows for rigorous evaluation of the design knowledge in multiple evaluation episodes, covering different angles. Through a technical experiment the technical novelty of the artifact’s capability to capture selected faults (regarding insulators and safety pins) in unmanned aerial vehicle (UAV)-captured image data (model component) is validated. Subsequent interviews, surveys, and workshops in a natural environment confirm the usefulness of the model as well as the user interface component. The evaluation provides evidence that (1) the image processing approach manages to address the gap of power line component inspection and (2) that the proposed holistic design knowledge for image-based decision support systems enables more informed decision-making. The paper therefore contributes to research and practice in three ways. First, the technical feasibility to detect certain maintenance-intensive parts of power lines with the help of unique UAV image data is shown. Second, the distribution system operators’ specific problem is solved by supporting decisions in maintenance with the proposed image-based decision support system. Third, precise design knowledge for image-based decision support systems is formulated that can inform future system designs of a similar nature. Supplementary Information The online version contains supplementary material available at 10.1007/s12599-022-00745-z.
| S-EPMC8973684 | biostudies-literature
Project description:ObjectiveClinical Knowledge Authoring Tools (CKATs) are integral to the computerized Clinical Decision Support (CDS) development life cycle. CKATs enable authors to generate accurate, complete, and reliable digital knowledge artifacts in a relatively efficient and affordable manner. This scoping review aims to compare knowledge authoring tools and derive the common features of CKATs.Materials and methodsWe performed a keyword-based literature search, followed by a snowball search, to identify peer-reviewed publications describing the development or use of CKATs. We used PubMed and Embase search engines to perform the initial search (n = 1579). After removing duplicate articles, nonrelevant manuscripts, and not peer-reviewed publication, we identified 47 eligible studies describing 33 unique CKATs. The reviewed CKATs were further assessed, and salient characteristics were extracted and grouped as common CKAT features.ResultsAmong the identified CKATs, 55% use an open source platform, 70% provide an application programming interface for CDS system integration, and 79% provide features to validate/test the knowledge. The majority of the reviewed CKATs describe the flow of information, offer a graphical user interface for knowledge authors, and provide intellisense coding features (94%, 97%, and 97%, respectively). The composed list of criteria for CKAT included topics such as simulating the clinical setting, validating the knowledge, standardized clinical models and vocabulary, and domain independence. None of the reviewed CKATs met all common criteria.ConclusionOur scoping review highlights the key specifications for a CKAT. The CKAT specification proposed in this review can guide CDS authors in developing more targeted CKATs.
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Project description:Driven by internet technology, online has become the main way of news dissemination, but redundant information such as navigation bars and advertisements affects people's access to news content. The research aims to enable users to obtain pure news content from redundant web information. Firstly, based on the narrative characteristics of literary news, the Term Frequency-Inverse Document Frequency (TF-IDF) algorithm is employed to extract pure news content from the analyzed web pages. The algorithm uses keyword matching, text analysis, and semantic processing to determine news content's boundaries and key information. Secondly, the news text classification algorithm (support vector machine, K-nearest neighbor, AdaBoost algorithm) is selected through comparative experiments. The news extraction system based on keyword feature and extended Document Object Model (DOM) tree is constructed. DOM technology analyzes web page structure and extracts key elements and information. Finally, the research can get their narrative characteristics by studying the narrative sequence and structure of 15 American literary news reports. The results reveal that the most used narrative sequence in American literary news is sequence and flashback. The narrative duration is dominated by the victory rate and outline, supplemented by scenes and pauses. In addition, 53.3% of the narrative structures used in literary news are time-connected. This narrative structure can help reporters have a clear conceptual structure when writing, help readers quickly grasp and understand the context of the event and the life course of the protagonists in the report, and increase the report's readability. This research on the narrative characteristics of American literature news can provide media practitioners with a reference on news narrative techniques and strategies.
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Project description:Gene Wiki Plus (GeneWiki+) and the Online Mendelian Inheritance in Man (OMIM) are publicly available resources for sharing information about disease-gene and gene-SNP associations in humans. While immensely useful to the scientific community, both resources are manually curated, thereby making the data entry and publication process time-consuming, and to some degree, error-prone. To this end, this study investigates Semantic Web technologies to validate existing and potentially discover new genotype-phenotype associations in GWP and OMIM. In particular, we demonstrate the applicability of SPARQL queries for identifying associations not explicitly stated for commonly occurring chronic diseases in GWP and OMIM, and report our preliminary findings for coverage, completeness, and validity of the associations. Our results highlight the benefits of Semantic Web querying technology to validate existing disease-gene associations as well as identify novel associations although further evaluation and analysis is required before such information can be applied and used effectively.
| S-EPMC3845769 | biostudies-literature
Project description:BACKGROUND:Chronic wounds such as diabetic foot ulcers, venous leg ulcers, and pressure ulcers are a massive burden to health care facilities. Many randomized controlled trials on different wound care elements have been conducted and published in the Cochrane Library, all of which have only a low evidential basis. Thus, health care professionals are forced to rely on their own experience when making decisions regarding wound care. To progress from experience-based practice to evidence-based wound care practice, clinical decision support systems (CDSS) that help health care providers with decision-making in a clinical workflow have been developed. These systems have proven useful in many areas of the health care sector, partly because they have increased the quality of care, and partially because they have generated a solid basis for evidence-based practice. However, no systematic reviews focus on CDSS within the field of wound care to chronic wounds. OBJECTIVE:The aims of this systematic literature review are (1) to identify models used in CDSS that support health care professionals treating chronic wounds, and (2) to classify each clinical decision support model according to selected variables and to create an overview. METHODS:A systematic review was conducted using 6 databases. This systematic literature review follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement for systematic reviews. The search strategy consisted of three facets, respectively: Facet 1 (Algorithm), Facet 2 (Wound care) and Facet 3 (Clinical decision support system). Studies based on acute wounds or trauma were excluded. Similarly, studies that presented guidelines, protocols and instructions were excluded, since they do not require progression along an active chain of reasoning from the clinicians, just their focus. Finally, studies were excluded if they had not undergone a peer review process. The following aspects were extracted from each article: authors, year, country, the sample size of data and variables describing the type of clinical decision support models. The decision support models were classified in 2 ways: quantitative decision support models, and qualitative decision support models. RESULTS:The final number of studies included in the systematic literature review was 10. These clinical decision support models included 4/10 (40%) quantitative decision support models and 6/10 (60%) qualitative decision support models. The earliest article was published in 2007, and the most recent was from 2015. CONCLUSIONS:The clinical decision support models were targeted at a variety of different types of chronic wounds. The degree of accessibility of the inference engines varied. Quantitative models served as the engine and were invisible to the health care professionals, while qualitative models required interaction with the user.
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Project description:In parallel to the growth in bioscience databases, biomedical publications have increased exponentially in the past decade. However, the extraction of high-quality information from the corpus of scientific literature has been hampered by the lack of machine-interpretable content, despite text-mining advances. To address this, we propose creating a structured digital table as part of an overall effort in developing machine-readable, structured digital literature. In particular, we envision transforming publication tables into standardized triples using Semantic Web approaches. We identify three canonical types of tables (conveying information about properties, networks, and concept hierarchies) and show how more complex tables can be built from these basic types. We envision that authors would create tables initially using the structured triples for canonical types and then have them visually rendered for publication, and we present examples for converting representative tables into triples. Finally, we discuss how 'stub' versions of structured digital tables could be a useful bridge for connecting together the literature with databases, allowing the former to more precisely document the later.
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Project description:BackgroundDispleasure with the functionality of clinical decision support systems (CDSSs) is considered the primary challenge in CDSS development. A major difficulty in CDSS design is matching the functionality to the desired and actual clinical workflow. Computer-interpretable guidelines (CIGs) are used to formalize medical knowledge in clinical practice guidelines (CPGs) in a computable language. However, existing CIG frameworks require a specific interpreter for each CIG language, hindering the ease of implementation and interoperability.ObjectiveThis paper aims to describe a different approach to the representation of clinical knowledge and data. We intended to change the clinician's perception of a CDSS with sufficient expressivity of the representation while maintaining a small communication and software footprint for both a web application and a mobile app. This approach was originally intended to create a readable and minimal syntax for a web CDSS and future mobile app for antenatal care guidelines with improved human-computer interaction and enhanced usability by aligning the system behavior with clinical workflow.MethodsWe designed and implemented an architecture design for our CDSS, which uses the model-view-controller (MVC) architecture and a knowledge engine in the MVC architecture based on XML. The knowledge engine design also integrated the requirement of matching clinical care workflow that was desired in the CDSS. For this component of the design task, we used a work ontology analysis of the CPGs for antenatal care in our particular target clinical settings.ResultsIn comparison to other common CIGs used for CDSSs, our XML approach can be used to take advantage of the flexible format of XML to facilitate the electronic sharing of structured data. More importantly, we can take advantage of its flexibility to standardize CIG structure design in a low-level specification language that is ubiquitous, universal, computationally efficient, integrable with web technologies, and human readable.ConclusionsOur knowledge representation framework incorporates fundamental elements of other CIGs used in CDSSs in medicine and proved adequate to encode a number of antenatal health care CPGs and their associated clinical workflows. The framework appears general enough to be used with other CPGs in medicine. XML proved to be a language expressive enough to describe planning problems in a computable form and restrictive and expressive enough to implement in a clinical system. It can also be effective for mobile apps, where intermittent communication requires a small footprint and an autonomous app. This approach can be used to incorporate overlapping capabilities of more specialized CIGs in medicine.
| S-EPMC7600017 | biostudies-literature
Project description:SummaryThe global response to the COVID-19 pandemic has led to a rapid increase of scientific literature on this deadly disease. Extracting knowledge from biomedical literature and integrating it with relevant information from curated biological databases is essential to gain insight into COVID-19 etiology, diagnosis, and treatment. We used Semantic Web technology RDF to integrate COVID-19 knowledge mined from literature by iTextMine, PubTator, and SemRep with relevant biological databases and formalized the knowledge in a standardized and computable COVID-19 Knowledge Graph (KG). We published the COVID-19 KG via a SPARQL endpoint to support federated queries on the Semantic Web and developed a knowledge portal with browsing and searching interfaces. We also developed a RESTful API to support programmatic access and provided RDF dumps for download.Availability and implementationThe COVID-19 Knowledge Graph is publicly available under CC-BY 4.0 license at https://research.bioinformatics.udel.edu/covid19kg/.
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