3,268 research outputs found
Infectious Disease Ontology
Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain
Representing and coding the knowledge embedded in texts of Health Science Web published articles
Despite the fact that electronic publishing is a common activity to scholars electronic journals are still based in the print model and do not take full advantage of the facilities offered by the Semantic Web environment. This is a report of the results of a research project with the aim of investigating the possibilities of electronic publishing journal articles both as text for human reading and in machine readable format recording the new knowledge contained in the article. This knowledge is identified with the scientific methodology elements such as problem, methodology, hypothesis, results, and conclusions. A model integrating all those elements is proposed which makes explicit and records the knowledge embedded in the text of scientific articles as an ontology. Knowledge thus represented enables its processing by intelligent software agents The proposed model aims to take advantage of these facilities enabling semantic retrieval and validation of the knowledge contained in articles. To validate and enhance the model a set of electronic journal articles were analyzed
Graph-Sparse LDA: A Topic Model with Structured Sparsity
Originally designed to model text, topic modeling has become a powerful tool
for uncovering latent structure in domains including medicine, finance, and
vision. The goals for the model vary depending on the application: in some
cases, the discovered topics may be used for prediction or some other
downstream task. In other cases, the content of the topic itself may be of
intrinsic scientific interest.
Unfortunately, even using modern sparse techniques, the discovered topics are
often difficult to interpret due to the high dimensionality of the underlying
space. To improve topic interpretability, we introduce Graph-Sparse LDA, a
hierarchical topic model that leverages knowledge of relationships between
words (e.g., as encoded by an ontology). In our model, topics are summarized by
a few latent concept-words from the underlying graph that explain the observed
words. Graph-Sparse LDA recovers sparse, interpretable summaries on two
real-world biomedical datasets while matching state-of-the-art prediction
performance
CREATING A BIOMEDICAL ONTOLOGY INDEXED SEARCH ENGINE TO IMPROVE THE SEMANTIC RELEVANCE OF RETREIVED MEDICAL TEXT
Medical Subject Headings (MeSH) is a controlled vocabulary used by the National Library of Medicine to index medical articles, abstracts, and journals contained within the MEDLINE database. Although MeSH imposes uniformity and consistency in the indexing process, it has been proven that using MeSH indices only result in a small increase in precision over free-text indexing. Moreover, studies have shown that the use of controlled vocabularies in the indexing process is not an effective method to increase semantic relevance in information retrieval. To address the need for semantic relevance, we present an ontology-based information retrieval system for the MEDLINE collection that result in a 37.5% increase in precision when compared to free-text indexing systems. The presented system focuses on the ontology to: provide an alternative to text-representation for medical articles, finding relationships among co-occurring terms in abstracts, and to index terms that appear in text as well as discovered relationships. The presented system is then compared to existing MeSH and Free-Text information retrieval systems. This dissertation provides a proof-of-concept for an online retrieval system capable of providing increased semantic relevance when searching through medical abstracts in MEDLINE
Information Retrieval Systems Adapted to the Biomedical Domain
The terminology used in Biomedicine shows lexical peculiarities that have
required the elaboration of terminological resources and information retrieval
systems with specific functionalities. The main characteristics are the high
rates of synonymy and homonymy, due to phenomena such as the proliferation of
polysemic acronyms and their interaction with common language. Information
retrieval systems in the biomedical domain use techniques oriented to the
treatment of these lexical peculiarities. In this paper we review some of the
techniques used in this domain, such as the application of Natural Language
Processing (BioNLP), the incorporation of lexical-semantic resources, and the
application of Named Entity Recognition (BioNER). Finally, we present the
evaluation methods adopted to assess the suitability of these techniques for
retrieving biomedical resources.Comment: 6 pages, 4 table
NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation
Biomedical researchers use ontologies to annotate their data with ontology
terms, enabling better data integration and interoperability. However, the
number, variety and complexity of current biomedical ontologies make it
cumbersome for researchers to determine which ones to reuse for their specific
needs. To overcome this problem, in 2010 the National Center for Biomedical
Ontology (NCBO) released the Ontology Recommender, which is a service that
receives a biomedical text corpus or a list of keywords and suggests ontologies
appropriate for referencing the indicated terms. We developed a new version of
the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new
recommendation approach that evaluates the relevance of an ontology to
biomedical text data according to four criteria: (1) the extent to which the
ontology covers the input data; (2) the acceptance of the ontology in the
biomedical community; (3) the level of detail of the ontology classes that
cover the input data; and (4) the specialization of the ontology to the domain
of the input data. Our evaluation shows that the enhanced recommender provides
higher quality suggestions than the original approach, providing better
coverage of the input data, more detailed information about their concepts,
increased specialization for the domain of the input data, and greater
acceptance and use in the community. In addition, it provides users with more
explanatory information, along with suggestions of not only individual
ontologies but also groups of ontologies. It also can be customized to fit the
needs of different scenarios. Ontology Recommender 2.0 combines the strengths
of its predecessor with a range of adjustments and new features that improve
its reliability and usefulness. Ontology Recommender 2.0 recommends over 500
biomedical ontologies from the NCBO BioPortal platform, where it is openly
available.Comment: 29 pages, 8 figures, 11 table
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