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- research-articleNovember 2020
Multi-Ontology Refined Embeddings (MORE): A hybrid multi-ontology and corpus-based semantic representation model for biomedical concepts
Journal of Biomedical Informatics (JOBI), Volume 111, Issue CNov 2020https://doi.org/10.1016/j.jbi.2020.103581Graphical abstractDisplay Omitted
Highlights- MORE is a novel word embedding model for biomedical concepts.
- This model ...
Currently, a major limitation for natural language processing (NLP) analyses in clinical applications is that concepts are not effectively referenced in various forms across different texts. This paper introduces ...
- research-articleJuly 2019
Building a Biomedical Ontology for Respiratory Tract Infection
ICCCM '19: Proceedings of the 7th International Conference on Computer and Communications ManagementJuly 2019, Pages 8–12https://doi.org/10.1145/3348445.3348461Respiratory tract infections are most common disease which can affect any human during any part of their age. According to sources almost 60% of all antibiotic prescription is due to Respiratory tract infection. The concepts and their relations related ...
- research-articleJanuary 2019
COMPETENCY QUESTIONS FOR BIOMEDICAL ONTOLOGY REUSE
Procedia Computer Science (PROCS), Volume 160, Issue C2019, Pages 362–368https://doi.org/10.1016/j.procs.2019.11.079AbstractReusing ontologies has been recognized as a good practice that most ontology building methodologies encourage. Indeed, reuse supports the semantic interoperability among different datasets and applications, increases accuracy, and reduces ...
- ArticleJune 2015
A New Ontology-Based Method for Functional Composed Comparison of MicroRNAs
CBMS '15: Proceedings of the 2015 IEEE 28th International Symposium on Computer-Based Medical SystemsJune 2015, Pages 258–263https://doi.org/10.1109/CBMS.2015.55MicroRNAs (miRNAs) are small non-coding RNA molecules that negatively regulate gene expression, playing critical roles in many relevant biological processes. Since there are no terms of miRNAs annotation in Gene Ontology (GO) nor a database with miRNA ...
- ArticleOctober 2014
Conference v2.0: An Uncertain Version of the OAEI Conference Benchmark
AbstractThe Ontology Alignment Evaluation Initiative is a set of benchmarks for evaluating the performance of ontology alignment systems. In this paper we re-examine the Conference track of the OAEI, with a focus on the degree of agreement between the ...
- ArticleOctober 2014
Towards Annotating Potential Incoherences in BioPortal Mappings
AbstractBioPortal is a repository for biomedical ontologies that also includes mappings between them from various sources. Considered as a whole, these mappings may cause logical errors, due to incompatibilities between the ontologies or even erroneous ...
- articleFebruary 2011
Using an ECG reference ontology for semantic interoperability of ECG data
Journal of Biomedical Informatics (JOBI), Volume 44, Issue 1February, 2011, Pages 126–136https://doi.org/10.1016/j.jbi.2010.08.007In this paper we test the hypothesis that a domain reference ontology of the electrocardiogram (ECG) can be employed in an effective manner to achieve semantic integration between ECG data standards. Several standardization initiatives, namely AHA/MIT-...
- articleOctober 2008
GFO-Bio: A biological core ontology
Applied Ontology (APPONT), Volume 3, Issue 4October 2008, Pages 219–227The rapid increase in the number and use of biological ontologies necessitates developing systems for their integration. In this paper we present a core ontology for biology, and outline its application for integrating biological domain ontologies. Our ...
- ArticleMay 2008
NutriGeneOntology: A Biomedical Ontology for Nutrigenomics Research
BMEI '08: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01May 2008, Pages 915–919https://doi.org/10.1109/BMEI.2008.315Currently, in Nutritional Genomics it is crucial to have computing models and solutions and technological platforms in order to support acquisition, storage, management and presentation of all the information generated. Our aim is to build a biomedical ...
- ArticleMarch 2023
A Method for Recommending Ontology Alignment Strategies
AbstractIn different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between ...
- articleJanuary 2007
Entities and relations in medical imaging: An analysis of computed tomography reporting
Applied Ontology (APPONT), Volume 2, Issue 1January 2007, Pages 67–79Biomedical ontologies define entities and relations in order to represent knowledge in the biomedical domain. In addition, many ontologies further represent supplementary knowledge by linking terms from an external controlled vocabulary to the entities ...
- ArticleJune 2006
A Query-Based Medical Information Summarization System Using Ontology Knowledge
CBMS '06: Proceedings of the 19th IEEE Symposium on Computer-Based Medical SystemsJune 2006, Pages 37–42https://doi.org/10.1109/CBMS.2006.25As huge amounts of knowledge are created rapidly, effective information access becomes an important issue. Especially for critical domains, such as medical and financial areas, efficient retrieval of concise and relevant information is highly desired. ...
- ArticleMay 2006
The Image as Spatial Region: Location and Adjacency within the Radiological Image
Proceedings of the 2006 conference on Formal Ontology in Information Systems: Proceedings of the Fourth International Conference (FOIS 2006)May 2006, Pages 89–100Biomedical ontologies define entities and relations in order to represent knowledge in the biomedical domain. In this paper we concentrate on the domain of medical imaging. In previous work, we analyzed a representative sample of computed tomography ...