Biomedical ontologies
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Mappings between ontologies enable reuse and interoperability of biomedical knowledge. The Radiology Gamuts Ontology (RGO)—an ontology of 16 918 diseases, interventions, and imaging observations—provides a resource for differential diagnosis and automated textual report understanding in radiology.
6p visteverogers 24-06-2023 4 2 Download
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The Unified Medical Language System (UMLS) integrates various source terminologies to support interoperability between biomedical information systems. In this article, we introduce a novel transformationbased auditing method that leverages the UMLS knowledge to systematically identify missing hierarchical IS-A relations in the source terminologies.
8p vighostrider 25-05-2023 5 3 Download
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Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and Human Phenotype Ontology (HPO). Because of the advantage of identifying novel relationships between terms, calculating similarity between ontology terms is one of the major tasks in this research area.
10p vilarryellison 29-10-2021 6 0 Download
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More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible.
9p viwyoming2711 16-12-2020 9 1 Download
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Semantic similarity measures estimate the similarity between concepts, and play an important role in many text processing tasks. Approaches to semantic similarity in the biomedical domain can be roughly divided into knowledge based and distributional based methods.
13p viwyoming2711 16-12-2020 6 1 Download
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Biomarkers and target-specific phenotypes are important to targeted drug design and individualized medicine, thus constituting an important aspect of modern pharmaceutical research and development. More and more, the discovery of relevant biomarkers is aided by in silico techniques based on applying data mining and computational chemistry on large molecular databases.
17p viwyoming2711 16-12-2020 15 1 Download
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Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed in text. There are many recognizers for specific ontologies, but a general approach for concept recognition is an open problem.
29p vikentucky2711 26-11-2020 11 1 Download
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Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies.
15p vikentucky2711 26-11-2020 9 1 Download
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This article provides an overview of the first BIOASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BIOASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies.
28p vikentucky2711 24-11-2020 15 1 Download
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Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new entities need to be frequently annotated to enrich the corpus.
10p vikentucky2711 24-11-2020 16 1 Download
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The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources.
21p vikentucky2711 24-11-2020 18 1 Download
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MicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs in human have been discovered and registered, but still lack of information or algorithms to reveal the relations among miRNAs, environmental chemicals and human health.
10p vioklahoma2711 19-11-2020 12 1 Download
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Biomedical information and knowledge, structural and non-structural, stored in different repositories can be semantically connected to form a hybrid knowledge network. How to compute relatedness between concepts and discover valuable but implicit information or knowledge from it effectively and efficiently is of paramount importance for precision medicine, and a major challenge facing the biomedical research community.
14p vioklahoma2711 19-11-2020 17 2 Download
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Functional annotation of genes and gene products is a major challenge in the post-genomic era. Nowadays, gene function curation is largely based on manual assignment of Gene Ontology (GO) annotations to genes by using published literature.
13p vioklahoma2711 19-11-2020 9 1 Download
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Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature.
14p viflorida2711 30-10-2020 9 2 Download
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Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling technologies in bioinformatics, providing resources for improved natural language processing tasks.
12p viflorida2711 30-10-2020 17 2 Download
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Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages. The rise of bioinformatics and high-throughput technologies has led us to the requirement of ontology representation of cell types and cell lines.
5p viconnecticut2711 29-10-2020 11 2 Download
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An improved approach to infer protein-protein interaction based on a hierarchical vector space model
Comparing and classifying functions of gene products are important in today’s biomedical research. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most widely used indicators for protein interaction.
14p viconnecticut2711 28-10-2020 15 1 Download
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Biomedical knowledge grows in complexity, and becomes encoded in network-based repositories, which include focused, expert-drawn diagrams, networks of evidence-based associations and established ontologies.
15p viconnecticut2711 28-10-2020 10 1 Download
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This paper has presented LOD-ABOG framework which shows that current LOD sources and technologies are a promising solution to automate the process of biomedical ontology generation and extract relations to a greater extent. In addition, unlike existing frameworks which require domain experts in ontology development process, the proposed approach requires involvement of them only for improvement purpose at the end of ontology life cycle.
13p viconnecticut2711 28-10-2020 14 0 Download