Search Results (11)

More than 7000 rare diseases affect over 400 million people, posing significant challenges for medical research and healthcare. The integration of precision medicine with artificial intelligence offers promising solutions. This work introduces a classifier developed to discern whether research and news articles pertain to rare or non-rare diseases. Our methodology involves extracting 709 rare disease MeSH terms from Mondo and MeSH to improve rare disease categorization. We evaluate our classifier on abstracts from PubMed/MEDLINE and an expert-annotated news dataset, which includes news articles on four selected rare neurodevelopmental disorders (NDDs)—considered the largest category of rare diseases—from a total of 16 analyzed. We achieved F1 scores of 85% for abstracts and 71% for news articles, demonstrating robustness across both datasets and highlighting the potential of integrating artificial intelligence and ontologies to improve disease classification. Although the results are promising, they also indicate the need for further refinement in managing data heterogeneity. Our classifier improves the identification and categorization of medical information, essential for advancing research, enhancing information access, influencing policy, and supporting personalized treatments. Future work will focus on expanding disease classification to distinguish between attributes such as infectious and hereditary diseases, addressing data heterogeneity, and incorporating multilingual capabilities. Full article

In his 1843–1844 Upbuilding Discourses on patience, Søren Kierkegaard makes the claim that one gains one’s soul in patience. Philosophically speaking, this claim seems to be a meshing together of two unrelated topics: the virtue of patience, which usually falls under moral philosophy, and the topic of the soul, which belongs to metaphysics or religious discourse. Rather than interpreting Kierkegaard’s talk about the soul as merely poetic or religious rather than properly philosophical, in this essay I attempt to take his connection between the virtue of patience and the constitution of the person seriously. I do so by arguing that the constitutive elements of the Kierkegaardian self can be understood hermeneutically as a proto-fundamental ontology. I then identify how Kierkegaard describes the virtue of patience in distinctly hermeneutical terms not as qualities or traits that adhere to the person but as a particular way of inhabiting space and time in relation to God. In patience, the self remains rooted in the present, bearing the weight of the loss and lack therein, while maintaining an anticipatory openness toward the future—a future that ultimately only God can provide. Patience, I conclude, is a way of being in time that is necessary at the constitutive level of the hermeneutical self. Full article

Three-dimensional models represent the shape and appearance of real-world objects in a virtual manner, enabling users to obtain a comprehensive and accurate understanding by observing their appearance from multiple perspectives. The semantic retrieval of 3D models is closer to human understanding, but semantic annotation for describing 3D models is difficult to automate, and it is still difficult to construct an easy-to-use 3D model knowledge base. This paper proposes a method for building a 3D model knowledge base to enhance the ability to intelligently manage and reuse 3D models. The sources of 3D model knowledge are obtained from two aspects: on the one hand, constructing mapping rules between the 3D model features and semantics, and on the other hand, extraction from a common sense database. Firstly, the viewpoint orientation is established, the semantic transformation rules of different feature values are established, and the representation degree of different features is divided to describe the degree of the contour approximating the regular shape under different perspectives through classification. An automatic output model semantic description of the contour is combined with spatial orientation. Then, a 3D model visual knowledge ontology is designed from top to bottom based on the upper ontology of the machine-readable comprehensive knowledge base and the relational structure of the ConceptNet ontology. Finally, using a weighted directed graph representation method with a sparse-matrix-integrated semantic dictionary as a carrier, an entity dictionary and a relational dictionary are established, covering attribute names and attribute value data. The sparse matrix is used to record the index information of knowledge triplets to form a three-dimensional model knowledge base. The feasibility of this method is demonstrated by semantic retrieval and reasoning on the label meshes dataset and the cultural relics dataset. Full article

Cervical cancer is the leading cause of cancer-related death among women in developing countries. However, no comprehensive molecular mechanism for cervical cancer has been established, as many studies were small-cohort studies conducted with small sample sizes. A thorough literature search was performed using the PubMed, Scopus, EBSCOhost, and Science Direct databases. Medical Subject Heading (MeSH) terms such as “Uterine Cervical Neoplasms” and “gene expression” were used as the keywords in all fields. A total of 4027 studies were retrieved, and only clinical studies, which used the microarray method to identify differentially expressed genes (DEGs) in the cervical tissue of cervical cancer patients, were selected. Following the screening, 6 studies were selected and 1128 DEGs were extracted from the data. Sixty-two differentially expressed genes from at least two studies were selected for further analysis by DAVID, STRING, and Cytoscape software. In cervical cancer pathogenesis, three significant clusters with high intermolecular interactions from the Protein–Protein Interaction (PPI) network complex revealed three major molecular mechanisms, including cell signaling, cell cycle, and cell differentiation. Subsequently, eight genes were chosen as the candidate genes based on their involvement in the relevant gene ontology (GO) and their interaction with other genes in the PPI network through undirected first neighbor nodes. The present systematic review improves our understanding of the molecular mechanism of cervical cancer and the proposed genes that can be used to expand the biomarker panel in the screening for cervical cancer. The targeted genes may be beneficial for the development of better treatment strategies. Full article

For the mechanical analysis work in the structural design phase, data conversion and information transfer between BIM model and finite element model have become the main factors limiting its efficiency and quality, with the development of BIM (building information modeling) technology application in the whole life cycle. The combined application of BIM and ontology technology has promoted the automation of compliance checking, cost management, green building evaluation, and many other fields. Based on OpenBIM, this study combines IFC (Industry Foundation Classes) and the ontology system and proposes an automatic generation method for converting BIM to the finite element model. Firstly, the elements contained in the finite element model are generalized and the information set requirement, to be extracted or inferred from BIM for the generation of the finite element model, is obtained accordingly. Secondly, the information extraction technical route is constructed to satisfy the acquisition of the information set, including three main aspects, i.e., IFC-based material information, spatial information, and other basic information; ontology-based finite element cell selection method; and APDL statement generation methods based on JAVA, C#, etc. Finally, a complete technical route and a software architecture, designed for converting BIM to the finite element model, are derived. To assess the feasibility of the method, a simple structure is tested in this paper, and the result indicates that the automatic decision-making reasoning mechanism of constructing element type and meshing method can be explored by ontology and IFC. This study contributes to the body of knowledge by providing an efficient method for automatic generation of the BIM structure model and a reference for future applications using BIM in structural analysis. Full article

Preeclampsia is a pregnancy-specific disorder characterized by the presence of hypertension with the onset of either proteinuria, maternal organ or uteroplacental dysfunction. Preeclampsia is one of the leading causes of maternal and fetal mortality and morbidity worldwide. However, the etiopathologies of preeclampsia are not fully understood. Many studies have indicated that genes are differentially expressed between normal and in the disease state. Hence, this study systematically searched the literature on human gene expression that was differentially expressed in preeclampsia. An electronic search was performed through 2019 through PubMed, Scopus, Ovid-Medline, and Gene Expression Omnibus where the following MeSH (Medical Subject Heading) terms were used and they had been specified as the primary focus of the articles: Gene, placenta, preeclampsia, and pregnancy in the title or abstract. We also found additional MeSH terms through Cochrane Library: Transcript, sequencing, and profiling. From 687 studies retrieved from the search, only original publications that had performed high throughput sequencing of human placental tissues that reported on differentially expressed genes in pregnancies with preeclampsia were included. Two reviewers independently scrutinized the titles and abstracts before examining the eligibility of studies that met the inclusion criteria. For each study, study design, sample size, sampling type, and method for gene analysis and gene were identified. The genes listed were further analyzed with the DAVID, STRING and Cytoscape MCODE. Three original research articles involving preeclampsia comprising the datasets in gene expression were included. By combining three studies together, 250 differentially expressed genes were produced at a significance setting of p < 0.05. We identified candidate genes: LEP, NRIP1, SASH1, and ZADHHC8P1. Through GO analysis, we found extracellular matrix organization as the highly significant enriched ontology in a group of upregulated genes and immune process in downregulated genes. Studies on a genetic level have the potential to provide new insights into the regulation and to widen the basis for identification of changes in the mechanism of preeclampsia. Integrated bioinformatics could identify differentially expressed genes which could be candidate genes and potential pathways in preeclampsia that may improve our understanding of the cause and underlying molecular mechanisms that could be used as potential biomarkers for risk stratification and treatment. Full article

Built heritage has been documented by reality-based modeling for geometric description and by ontology for knowledge management. The current challenge still involves the extraction of geometric primitives and the establishment of their connection to heterogeneous knowledge. As a recently developed 3D information modeling environment, building information modeling (BIM) entails both graphical and non-graphical aspects of the entire building, which has been increasingly applied to heritage documentation and generates a new issue of heritage/historic BIM (HBIM). However, HBIM needs to additionally deal with the heterogeneity of geometric shape and semantic knowledge of the heritage object. This paper developed a new mesh-to-HBIM modeling workflow and an integrated BIM management system to connect HBIM elements and historical knowledge. Using the St-Pierre-le-Jeune Church, Strasbourg, France as a case study, this project employs Autodesk Revit as a BIM environment and Dynamo, a built-in visual programming tool of Revit, to extend the new HBIM functions. The mesh-to-HBIM process segments the surface mesh, thickens the triangle mesh to 3D volume, and transfers the primitives to BIM elements. The obtained HBIM is then converted to the ontology model to enrich the heterogeneous knowledge. Finally, HBIM geometric elements and ontology semantic knowledge is joined in a unified BIM environment. By extending the capability of the BIM platform, the HBIM modeling process can be conducted in a time-saving way, and the obtained HBIM is a semantic model with object-oriented knowledge. Full article

The appropriate categorisation of written information by health professionals is very important to guarantee its accessibility. Unfortunately, the information technology tools that support professionals on that task imply a heavy workload, so that the responsibility for categorising the written content is often delegated to administrative staff. Well-known health ontologies such as SNOMED-CT or MeSH provide a representation of the clinical contents to be used by the information systems. This research proposes a computer based method to automatically extract and code the diagnostics, procedures and treatments according to health ontologies. A Knowledge Management System based on an extended version of Drupal is used to implement and evaluate this proposal. Results provide a positive evidence on the application of the method to support medical professionals. Full article

Biomedicine is a pillar of the collective, scientific effort of human self-discovery, as well as a major source of humanistic data codified primarily in biomedical documents. Despite their rigid structure, maintaining and updating a considerably-sized collection of such documents is a task of overwhelming complexity mandating efficient information retrieval for the purpose of the integration of clustering schemes. The latter should work natively with inherently multidimensional data and higher order interdependencies. Additionally, past experience indicates that clustering should be semantically enhanced. Tensor algebra is the key to extending the current term-document model to more dimensions. In this article, an alternative keyword-term-document strategy, based on scientometric observations that keywords typically possess more expressive power than ordinary text terms, whose algorithmic cornerstones are third order tensors and MeSH ontological functions, is proposed. This strategy has been compared against a baseline using two different biomedical datasets, the TREC (Text REtrieval Conference) genomics benchmark and a large custom set of cognitive science articles from PubMed. Full article

In order to facilitate cooperation between underwater robots, it is a must for robots to exchange information with unambiguous meaning. However, heterogeneity, existing in information pertaining to different robots, is a major obstruction. Therefore, this paper presents a networked ontology, named the Smart and Networking Underwater Robots in Cooperation Meshes (SWARMs) ontology, to address information heterogeneity and enable robots to have the same understanding of exchanged information. The SWARMs ontology uses a core ontology to interrelate a set of domain-specific ontologies, including the mission and planning, the robotic vehicle, the communication and networking, and the environment recognition and sensing ontology. In addition, the SWARMs ontology utilizes ontology constructs defined in the PR-OWL ontology to annotate context uncertainty based on the Multi-Entity Bayesian Network (MEBN) theory. Thus, the SWARMs ontology can provide both a formal specification for information that is necessarily exchanged between robots and a command and control entity, and also support for uncertainty reasoning. A scenario on chemical pollution monitoring is described and used to showcase how the SWARMs ontology can be instantiated, be extended, represent context uncertainty, and support uncertainty reasoning. Full article

Ontologies have been widely used to facilitate semantic interoperability and serve as a common information model in many applications or domains. The Smart and Networking Underwater Robots in Cooperation Meshes (SWARMs) project, aiming to facilitate coordination and cooperation between heterogeneous underwater vehicles, also adopts ontologies to formalize information that is necessarily exchanged between vehicles. However, how to derive more useful contexts based on ontologies still remains a challenge. In particular, the extreme nature of the underwater environment introduces uncertainties in context data, thus imposing more difficulties in context reasoning. None of the existing context reasoning methods could individually deal with all intricacies in the underwater robot field. To this end, this paper presents the first proposal applying a hybrid context reasoning mechanism that includes ontological, rule-based, and Multi-Entity Bayesian Network (MEBN) reasoning methods to reason about contexts and their uncertainties in the underwater robot field. The theoretical foundation of applying this reasoning mechanism in underwater robots is given by a case study on the oil spill monitoring. The simulated reasoning results are useful for further decision-making by operators or robots and they show that the consolidation of different reasoning methods is a promising approach for context reasoning in underwater robots. Full article