Evaluation of research in biomedical ontologies

Hoehndorf, Robert; Dumontier, Michel; Gkoutos, Georgios V.

doi:10.1093/bib/bbs053

Cited by 64 publications

(48 citation statements)

References 107 publications

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“…Following today’s practice [32], we listed five parameters to evaluate the result of the application of ontological analysis, namely: generality , openess , flexibility , coherence and consistency .

Generality.

…”

Section: Resultsmentioning

confidence: 99%

Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases

et al. 2016

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BackgroundOntologies are widely used both in the life sciences and in the management of public and private companies. Typically, the different offices in an organization develop their own models and related ontologies to capture specific tasks and goals. Although there might be an overall coordination, the use of distinct ontologies can jeopardize the integration of data across the organization since data sharing and reusability are sensitive to modeling choices.ResultsThe paper provides a study of the entities that are typically found at the reception, analysis and report phases in public institutes in the life science domain. Ontological considerations and techniques are introduced and their implementation exemplified by studying the Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), a public veterinarian institute with different geographical locations and several laboratories. Different modeling issues are discussed like the identification and characterization of the main entities in these phases; the classification of the (types of) data; the clarification of the contexts and the roles of the involved entities. The study is based on a foundational ontology and shows how it can be extended to a comprehensive and coherent framework comprising the different institute’s roles, processes and data. In particular, it shows how to use notions lying at the borderline between ontology and applications, like that of knowledge object. The paper aims to help the modeler to understand the core viewpoint of the organization and to improve data transparency.ConclusionsThe study shows that the entities at play can be analyzed within a single ontological perspective allowing us to isolate a single ontological framework for the whole organization. This facilitates the development of coherent representations of the entities and related data, and fosters the use of integrated software for data management and reasoning across the company.

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Generality.

…”

Section: Resultsmentioning

confidence: 99%

Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases

et al. 2016

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“…In [31], the authors state that “good ontologies are the ones that serve their purpose” and in [32] it is stated that evaluation of (‘applied’) ontology will “depend on the desired application”. As the current primary purpose of HuPSON is to aid in text-mining, its evaluation was focused mainly on how it performed with regard to literature-based mining of simulation knowledge.…”

Section: Methodsmentioning

confidence: 99%

HuPSON: the human physiology simulation ontology

et al. 2013

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BackgroundLarge biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain.ResultsWe propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles; the constructed ontology has been evaluated via structural features, competency questions and use case scenarios.The ontology is freely available at: http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html (owl files) and http://bishop.scai.fraunhofer.de/scaiview/ (browser).ConclusionsHuPSON provides a framework for a) annotating simulation experiments, b) retrieving relevant information that are required for modelling, c) enabling interoperability of algorithmic approaches used in biomedical simulation, d) comparing simulation results and e) linking knowledge-based approaches to simulation-based approaches. It is meant to foster a more rapid uptake of semantic technologies in the modelling and simulation domain, with particular focus on the VPH domain.

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“…Enriching the content of a single dataset has been heavily researched, especially in the medical field. This is due to having mature and well maintained biomedical ontologies [7].…”

Section: Background and Related Workmentioning

confidence: 99%

Applying NoSQL Databases for Integrating Web Educational Stores - An Ontology-Based Approach

Fayez

Joy

2015

Data Science

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Original citation:Al Fayez, Reem Qadan and Joy, Mike (2015) Applying NoSQL databases for integrating web educational stores -an ontology-based approach. In: Maneth, Sebastian, (ed. Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way.)Publisher's statement: "The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-20424-6_4 " A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. Abstract. Educational content available on the web is playing an important role in the teaching and learning process. Learners search for different types of learning objects such as videos, pictures, and blog articles and use them to understand concepts they are studying in books and articles. The current search platforms provided can be frustrating to use. Either they are not specified for educational purposes or they are provided as a service by a library or a repository for searching a limited dataset of educational content. This paper presents a novel system for automatic harvesting and connecting of medical educational objects based on biomedical ontologies. The challenge in this work is to transform disjoint heterogeneous web databases entries into one coherent linked dataset. First, harvesting APIs were developed for collecting content from various web sources such as YouTube, blogging platforms, and PubMed library. Then, the system maps its entries into one data model and annotates its content using biomedical ontologies to enable its linkage. The resulted dataset is organized in a proposed NoSQL RDF Triple Store which consists of 2720 entries of articles, videos, and blogs. We tested the system using different ontologies for enriching its content such as MeSH and SNOMED CT and compared the results obtained. Using SNOMED CT doubled the number of linkages built between the dataset entries. Experiments of querying the dataset is conducted and the results are promising compared with simple text-based search.

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Evaluation of research in biomedical ontologies

Cited by 64 publications

References 107 publications

Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases

Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases

HuPSON: the human physiology simulation ontology

Applying NoSQL Databases for Integrating Web Educational Stores - An Ontology-Based Approach

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