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The collaborations of the diseases might be the key to understand the mechanism of the diseases since it is difficult to detect the role of complex genes and micro RNA in diseases. With the rapid development of technology, several metabolites of many kinds of diseases could be obtained by the advanced machines. Some diseases are related to several metabolites, and some metabolites have strong relationship...
With the increasing number of ontologies being designed to represent and manage knowledge in all sorts of sectors, ontology alignment and integration become more and more important in aggregating intelligent efforts on homogenous and heterogeneous data. From the computational perspective, it is challenging due to the ubiquitous existence of diverse classifications of same data. In this paper, we propose...
In recent years, there has been explosive growth in the amount of biomedical publications. In this paper, we propose a semantic framework that aims to automatically generate an ontology by extracting assertions and topics from multiple free-text scientific publications in PubMed. The pipeline approach for knowledge discovery and ontology generation in the proposed framework has been implemented on...
Discovering similar diseases is very helpful for revealing the pathogenesis of diseases and making direction in drug use. And related diseases are often triggered by disease-related genes. Therefore, function interaction networks structured by disease-related genes are suitable for measurement of disease similarity, and some methods have utilized the advantage of function interaction of disease-related...
The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors...
This paper presents a system architecture that designs a querying refinement method. The method employs the general principles of facet analysis in a particular paradigm, as well as the notion of ‘focus’, which is a sort of context for a user query. The method provides the user with contextual information about the query, which is computed by using the user documents provided that the documents are...
Prioritizing genes according to their association with a disease allows researchers to explore genes in more informed ways. Although some useful algorithms have been developed, they are based on single gene importance, gene interaction networks, or gene modules with little consideration of relative gene importance in the context of modules. In this paper, we propose to prioritize genes considering...
Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype similarity. We proposed a network-based method PhenoNet to calculate the similarity between...
This research proposed a TCM FS Ontology using FS-associated information retrieved from ancient Chinese medical texts. To standardize the process, we rigorously followed the 7-steps-approach proposed by Standard University. Besides, the establishing of axioms constraining the relationships between concepts may provide reference for the construction of knowledge base in future studies.
Document clustering is a text mining technique used to provide better document search and browsing in digital libraries or online corpora. In this research, a vector representation of concepts of diseases and similarity measurement between concepts are proposed. They identify the closest concepts of diseases in the context of a corpus. Each document is represented by using the vector space model....
Psoriasis is a chronic, recurrent, inflammatory skin disease, with varied incidence rates for various populations in different regions of the world. According to statistics, the prevalence of psoriasis in European countries is about 1% ∼ 3%, and 0.47% for China in 2008, which appears on the rise year by year. [1,2] Evidence suggests that genetic and environmental factors play important roles in the...
According to the World Health Organization, there are about 15% of universe population have some forms of disability. One of these disabilities is Cerebral Palsy CP which is a permanent motor disorder that appears in early age causing mental and physical disabilities. Based on WHO, between 1.5 to 2.8 cases per 1000 birth have CP Disability in the world. In Gaza Strip, 2.6% of population has some forms...
The current drug development pipelines are characterised by long processes with high attrition rates and elevated costs. More than 80% of new compounds fail in the later stages of testing due to severe side-effects caused by unknown biomolecular targets of the compounds. In this work, we present a measure that can predict shared targets for drugs in DrugBank through large scale analysis of the biomedical...
Twitter and social media as a whole has great potential as a source of disease surveillance data however the general messiness of tweets presents several challenges for standard information extraction methods. Current methods for disease surveillance on twitter rely on inflexible keyword based approaches that require messages to be pre-filtered on the basis of a disease name which is supplied a priori...
A variety of knowledge discovery applications on healthcare big data require effective medical ontologies of diseases that can abstract the healthcare record data in order to support formal reasoning. Domain specific ontologies are often created by teams of clinicians manually, partitioning the conditions present in that domain on pre-defined boundaries. However, it is often hard to determine the...
Clinical notes contain information that is crucial for the diagnosis process. However, it is usually not properly manually analyzed due to the tremendous efforts and time it takes. Hence, an automated approach is eagerly needed to maximize clinical knowledge management and reduce cost. In this paper, we propose a framework SESARF: a Semantic Extractor to identify hidden risk factors in clinical notes...
Blood is the life in our vessels. It makes up the 8% of our body weight. Loss of blood from 750 ml to 2000 ml is enough to enter us to shock condition due to loss of circulating volume. In situations like these, urgent blood transfusion needs to be handled with extensive care. Not all emergency services may have haematology experts, a good helper application with blood transfusion rules that also...
Crowdsourcing data is an essential part of information collection in healthcare. Patient data serves as the foundation for creating healthcare policy, creating new pharmaceuticals, and determining treatment. In this paper, we propose a novel conceptual method of standardizing and classifying the crowdsourcing of healthcare data using modular ontologies, authoritative medical ontologies (AMOs) and...
Gene-phenotype association prediction can be applied to reveal the inherited basis of human diseases and help drug development. Gene-phenotype associations are related to complex biological process and influenced by various factors, such as relationship between phenotypes and that among genes. While due to sparseness of curated gene-phenotype associations, existing approaches are limited to prediction...
The work of this p aper is done within the context of European Project E! 8949 PrEmISES 1. One of the central pieces of PrEmISES[16] is the use of automatic tool generation algorithms for the creation of ontologies. The objective of this work is to extend the work from PrEmISES for raising the medical literacy of empowered patients by creating a digital library that contains relevant articles from...
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