An ontology-based approach to the analysis of the acid-base state of patients at operative measures.
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ABSTRACT:
SUBMITTER: Tianxing M
PROVIDER: S-EPMC8670394 | biostudies-literature | 2021
REPOSITORIES: biostudies-literature
Publications
An ontology-based approach to the analysis of the acid-base state of patients at operative measures.
Tianxing Man M Lushnov Mikhail M Ignatov Dmitry I DI Shichkina Yulia Alexandrovna YA Zhukova Natalia Alexandrovna NA Vodyaho Alexander Ivanovich AI
PeerJ. Computer science 20211209
Researchers working in various domains are focusing on extracting information from data sets by data mining techniques. However, data mining is a complicated task, including multiple complex processes, so that it is unfriendly to non-computer researchers. Due to the lack of experience, they cannot design suitable workflows that lead to satisfactory results. This article proposes an ontology-based approach to help users choose appropriate data mining techniques for analyzing domain data. By mergi ...[more]
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Project description:BackgroundOntologies are key enabling technologies for the Semantic Web. The Web Ontology Language (OWL) is a semantic markup language for publishing and sharing ontologies.ObjectiveThe supply of customizable, computable, and formally represented molecular genetics information and health information, via electronic health record (EHR) interfaces, can play a critical role in achieving precision medicine. In this study, we used cystic fibrosis as an example to build an Ontology-based Knowledge Base prototype on Cystic Fibrobis (OntoKBCF) to supply such information via an EHR prototype. In addition, we elaborate on the construction and representation principles, approaches, applications, and representation challenges that we faced in the construction of OntoKBCF. The principles and approaches can be referenced and applied in constructing other ontology-based domain knowledge bases.MethodsFirst, we defined the scope of OntoKBCF according to possible clinical information needs about cystic fibrosis on both a molecular level and a clinical phenotype level. We then selected the knowledge sources to be represented in OntoKBCF. We utilized top-to-bottom content analysis and bottom-up construction to build OntoKBCF. Protégé-OWL was used to construct OntoKBCF. The construction principles included (1) to use existing basic terms as much as possible; (2) to use intersection and combination in representations; (3) to represent as many different types of facts as possible; and (4) to provide 2-5 examples for each type. HermiT 1.3.8.413 within Protégé-5.1.0 was used to check the consistency of OntoKBCF.ResultsOntoKBCF was constructed successfully, with the inclusion of 408 classes, 35 properties, and 113 equivalent classes. OntoKBCF includes both atomic concepts (such as amino acid) and complex concepts (such as "adolescent female cystic fibrosis patient") and their descriptions. We demonstrated that OntoKBCF could make customizable molecular and health information available automatically and usable via an EHR prototype. The main challenges include the provision of a more comprehensive account of different patient groups as well as the representation of uncertain knowledge, ambiguous concepts, and negative statements and more complicated and detailed molecular mechanisms or pathway information about cystic fibrosis.ConclusionsAlthough cystic fibrosis is just one example, based on the current structure of OntoKBCF, it should be relatively straightforward to extend the prototype to cover different topics. Moreover, the principles underpinning its development could be reused for building alternative human monogenetic diseases knowledge bases.
| S-EPMC6320437 | biostudies-literature
Project description:MotivationA typical approach for the interpretation of high-throughput experiments, such as gene expression microarrays, is to produce groups of genes based on certain criteria (e.g. genes that are differentially expressed). To gain more mechanistic insights into the underlying biology, overrepresentation analysis (ORA) is often conducted to investigate whether gene sets associated with particular biological functions, for example, as represented by Gene Ontology (GO) annotations, are statistically overrepresented in the identified gene groups. However, the standard ORA, which is based on the hypergeometric test, analyzes each GO term in isolation and does not take into account the dependence structure of the GO-term hierarchy.ResultsWe have developed a Bayesian approach (GO-Bayes) to measure overrepresentation of GO terms that incorporates the GO dependence structure by taking into account evidence not only from individual GO terms, but also from their related terms (i.e. parents, children, siblings, etc.). The Bayesian framework borrows information across related GO terms to strengthen the detection of overrepresentation signals. As a result, this method tends to identify sets of closely related GO terms rather than individual isolated GO terms. The advantage of the GO-Bayes approach is demonstrated with a simulation study and an application example.
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Project description:BackgroundThe use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses. There is a need for a unified tool that provides the scientific community with the opportunity to explore these different GO similarity measure approaches and their biological applications.ResultsWe have developed DaGO-Fun, an online tool available at http://web.cbio.uct.ac.za/ITGOM, which incorporates many different GO similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. It uses GO data and UniProt proteins with their GO annotations as provided by the Gene Ontology Annotation (GOA) project to precompute GO term information content (IC), enabling rapid response to user queries.ConclusionsThe DaGO-Fun online tool presents the advantage of integrating all the relevant IC-based GO similarity measures, including topology- and annotation-based approaches to facilitate effective exploration of these measures, thus enabling users to choose the most relevant approach for their application. Furthermore, this tool includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis.
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Project description:Fracture to fifth metatarsal's base is one the most common injury experienced at the foot. Studies have for long debated the use of operative and non-operative interventions for the management of the fracture, especially owing to its peculiar vasculature. However, to date, no attempt has been made to synthesize the evidence comparing the efficacy of operative and non-operative interventions for managing the fifth metatarsal's base fracture. To meta-statistically compare the effects of operative and non-operative management of fifth metatarsal base fracture. A systematic identification of literature was performed according to PRISMA guidelines on four academic databases: MEDLINE, Scopus, EMBASE, and CENTRAL. A meta-analysis evaluated the influence of operative and non-operative interventions on rate of non-union, mean duration of union, duration of return to activity, duration of return to sport, visual analog scale, and the American orthopedic foot & ankle scale. Out of 1,170 records, 11 articles including 404 participants (mean age: 29.8 ± 7.4 years) were included in this review. This systematic review presents a 1b level of evidence supporting the use of operative interventions for enhancing fracture union as compared to non-operative interventions. The meta-analysis reveals beneficial effects for operative interventions by demonstrating medium to large effect reduction of rate of non-union (Hedge's g: -0.66), duration of union (-1.7), duration of return to activity (-2.07), visual analog scale (-0.86), and enhancement of the American orthopedic foot & ankle scale score (0.73) as compared to non-operative intervention. The current systematic review and meta-analysis recommend the use of operative interventions for managing the fifth metatarsal's base fracture. The review reports beneficial effects of operative interventions as compared to non-operative interventions for reducing the rate of non-union, duration of union, duration of return to activity, duration of return to sport, visual analog scale, and increasing the American orthopedic foot & ankle scale score.
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Project description:BackgroundSocial networking services (SNSs) contain abundant information about the feelings, thoughts, interests, and patterns of behavior of adolescents that can be obtained by analyzing SNS postings. An ontology that expresses the shared concepts and their relationships in a specific field could be used as a semantic framework for social media data analytics.ObjectiveThe aim of this study was to refine an adolescent depression ontology and terminology as a framework for analyzing social media data and to evaluate description logics between classes and the applicability of this ontology to sentiment analysis.MethodsThe domain and scope of the ontology were defined using competency questions. The concepts constituting the ontology and terminology were collected from clinical practice guidelines, the literature, and social media postings on adolescent depression. Class concepts, their hierarchy, and the relationships among class concepts were defined. An internal structure of the ontology was designed using the entity-attribute-value (EAV) triplet data model, and superclasses of the ontology were aligned with the upper ontology. Description logics between classes were evaluated by mapping concepts extracted from the answers to frequently asked questions (FAQs) onto the ontology concepts derived from description logic queries. The applicability of the ontology was validated by examining the representability of 1358 sentiment phrases using the ontology EAV model and conducting sentiment analyses of social media data using ontology class concepts.ResultsWe developed an adolescent depression ontology that comprised 443 classes and 60 relationships among the classes; the terminology comprised 1682 synonyms of the 443 classes. In the description logics test, no error in relationships between classes was found, and about 89% (55/62) of the concepts cited in the answers to FAQs mapped onto the ontology class. Regarding applicability, the EAV triplet models of the ontology class represented about 91.4% of the sentiment phrases included in the sentiment dictionary. In the sentiment analyses, "academic stresses" and "suicide" contributed negatively to the sentiment of adolescent depression.ConclusionsThe ontology and terminology developed in this study provide a semantic foundation for analyzing social media data on adolescent depression. To be useful in social media data analysis, the ontology, especially the terminology, needs to be updated constantly to reflect rapidly changing terms used by adolescents in social media postings. In addition, more attributes and value sets reflecting depression-related sentiments should be added to the ontology.
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Project description:Physiologic signals such as the electroencephalogram (EEG) demonstrate irregular behaviors due to the interaction of multiple control processes operating over different time scales. The complexity of this behavior can be quantified using multi-scale entropy (MSE). High physiologic complexity denotes health, and a loss of complexity can predict adverse outcomes. Since postoperative delirium is particularly hard to predict, we investigated whether the complexity of preoperative and intraoperative frontal EEG signals could predict postoperative delirium and its endophenotype, inattention. To calculate MSE, the sample entropy of EEG recordings was computed at different time scales, then plotted against scale; complexity is the total area under the curve. MSE of frontal EEG recordings was computed in 50 patients ≥ age 60 before and during surgery. Average MSE was higher intra-operatively than pre-operatively (p = 0.0003). However, intraoperative EEG MSE was lower than preoperative MSE at smaller scales, but higher at larger scales (interaction p < 0.001), creating a crossover point where, by definition, preoperative, and intraoperative MSE curves met. Overall, EEG complexity was not associated with delirium or attention. In 42/50 patients with single crossover points, the scale at which the intraoperative and preoperative entropy curves crossed showed an inverse relationship with delirium-severity score change (Spearman ρ = -0.31, p = 0.054). Thus, average EEG complexity increases intra-operatively in older adults, but is scale dependent. The scale at which preoperative and intraoperative complexity is equal (i.e., the crossover point) may predict delirium. Future studies should assess whether the crossover point represents changes in neural control mechanisms that predispose patients to postoperative delirium.
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Project description:Tuberculosis (TB) is the world's leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes. The network, enriched with molecular function ontology, was analyzed using Network Based Inference (NBI). The association scores computed from NBI are used to identify novel drug-target interactions. These interactions are further evaluated based on a combined evidence approach for identification of potential drug repurposing candidates. In this approach, targets which have no known variation in clinical isolates, no human homologs, and are essential for Mtb's survival and or virulence are prioritized. We analyzed predicted DTIs to identify target pairs whose predicted drugs may have synergistic bactericidal effect. From the list of predicted DTIs from RepTB, four TB targets, namely, FolP1 (Dihydropteroate synthase), Tmk (Thymidylate kinase), Dut (Deoxyuridine 5'-triphosphate nucleotidohydrolase) and MenB (1,4-dihydroxy-2-naphthoyl-CoA synthase) may be selected for further validation. In addition, we observed that in some cases there is significant chemical structure similarity between predicted and reported drugs of prioritized targets, lending credence to our approach. We also report new chemical space for prioritized targets that may be tested further. We believe that with increasing drug-target interaction dataset RepTB will be able to offer better predictive value and is amenable for identification of drug-repurposing candidates for other disease indications too.
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Project description:MotivationProbability distributions play a central role in mathematical and statistical modelling. The encoding, annotation and exchange of such models could be greatly simplified by a resource providing a common reference for the definition of probability distributions. Although some resources exist, no suitably detailed and complex ontology exists nor any database allowing programmatic access.ResultsProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 80 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for model annotation and facilitates the encoding of distribution-based models, related functions and quantities.Availability and implementationhttp://probonto.orgContactmjswat@ebi.ac.ukSupplementary informationSupplementary data are available at Bioinformatics online.
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