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doi:10.1093/nar/gkq331 The Ontology Lookup Service: bigger and better
, 2010
"... The Ontology Lookup Service (OLS; ..."
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Optimize first, buy later: Analyzing metrics to ramp-up very large knowledge bases
- In Proc. of ISWC 2010, volume 6496 of LNCS
, 2010
"... Abstract. As knowledge bases move into the landscape of larger ontologies having terabytes of related data, we must work on optimizing the performance of our tools. We are easily tempted to buy bigger machines or to fill rooms with armies of little ones to address the scalability problem. Yet, caref ..."
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Cited by 12 (4 self)
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Abstract. As knowledge bases move into the landscape of larger ontologies having terabytes of related data, we must work on optimizing the performance of our tools. We are easily tempted to buy bigger machines or to fill rooms with armies of little ones to address the scalability problem. Yet, careful analysis and evaluation of the characteristics of our data—using metrics—often leads to dramatic improvements in performance. Firstly, are current scalable systems scalable enough? It is hard to say: we found that current benchmarks obscure the load-time costs for large or deep ontologies (some as large as 500,000 classes). Therefore, we have synthesized a set of representative ontologies which helps to expose those costs. Secondly, in designing for scalability, how do we squeeze-out more performance? We found that optimizing for data distribution and ontology evolution significantly improves load time (including materialization of the transitive closure) for the NCBO Resource Index—a database of 16.4 billion annotations linking 2.4 million ontology terms to 3.5 million data elements—from one week to less than one hour on the same machine for one of our larger datasets. 1
PD: Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res 2013, 41(Database issue):D865–D870
- Bhattacharyya B, Karpinka JB, Fortriede J, Bowes JB, Zorn AM, Vize
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Will semantic web technologies work for the development of ICD-11
- The Semantic Web – ISWC 2010 – 9th International Semantic Web Conference, ISWC 2010
"... Abstract. The World Health Organization is beginning to use Semantic Web technologies in the development of the 11th revision of the International Classification of Diseases (ICD-11). Health officials use ICD in all United Nations member countries to compile basic health statistics, to monitor healt ..."
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Abstract. The World Health Organization is beginning to use Semantic Web technologies in the development of the 11th revision of the International Classification of Diseases (ICD-11). Health officials use ICD in all United Nations member countries to compile basic health statistics, to monitor health-related spending, and to inform policy makers. While previous revisions of ICD encoded minimal information about a disease, and were mainly published as books and tabulation lists, the creators of ICD-11 envision that it will become a multi-purpose and coherent classification ready for electronic health records. Most important, they plan to have ICD-11 applied for a much broader variety of uses than previous revisions. The new requirements entail significant changes in the way we represent disease information, as well as in the technologies and processes that we use to acquire the new content. In this paper, we describe the previous processes and technologies used for developing ICD. We then describe the requirements for the new development process and present the Semantic Web technologies that we use for ICD-11. We outline the experiences of the domain experts using the software system that we implemented using Semantic Web technologies. We then discuss the benefits and challenges in following this approach and conclude with lessons learned from this experience.
A corpus of OWL DL ontologies
- Proc. DL’13
, 2013
"... Abstract. Tool development for and empirical experimentation in OWL ontology engineering require a wide variety of suitable ontologies as input for testing and evaluation purposes. Empirical activities often resort to (somewhat arbitrarily) hand curated corpora available on the web, such as the NCBO ..."
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Cited by 8 (1 self)
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Abstract. Tool development for and empirical experimentation in OWL ontology engineering require a wide variety of suitable ontologies as input for testing and evaluation purposes. Empirical activities often resort to (somewhat arbitrarily) hand curated corpora available on the web, such as the NCBO BioPortal and the TONES Repository, or manually select a set of well-known ontologies. Results may be biased, even heavily, towards these datasets. Sampling from a large corpus of ontologies, on the other hand, may lead to more representative results. Current large scale repositories/web crawls are mostly uncurated, suffer from duplication and contain large numbers of ontology versions, variants, and facets, and therefore do not lend themselves to random sampling. In this paper, we describe the creation of a corpus of OWL DL ontologies using strategies such as web crawling, various forms of de-duplications and manual cleaning, which allows random sampling of ontologies for a variety of empirical applications.
The national center for biomedical ontology
- Journal of American Medical Informatics Association
, 2012
"... The National Center for Biomedical Ontology (NCBO) is now in its seventh year. The goals of this National Center for Biomedical Computing are to create and maintain a repository of biomedical ontologies and terminologies; to build tools and Web services to enable the use of ontologies and terminolog ..."
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Cited by 8 (1 self)
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The National Center for Biomedical Ontology (NCBO) is now in its seventh year. The goals of this National Center for Biomedical Computing are to create and maintain a repository of biomedical ontologies and terminologies; to build tools and Web services to enable the use of ontologies and terminologies in clinical and translational research; to educate our trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and to collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the NCBO is a Web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world’s biomedical ontologies and terminologies, and supports a wide range of Web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. MISSION
A common layer of interoperability for biomedical ontologies based on
- OWL EL. Bioinformatics
, 2011
"... Motivation: Ontologies are essential in biomedical research due to their ability to semantically integrate content from different scienti-c databases and resources. Their application improves capabilities for querying and mining biological knowledge. An increasing number of ontologies is being devel ..."
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Cited by 8 (5 self)
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Motivation: Ontologies are essential in biomedical research due to their ability to semantically integrate content from different scienti-c databases and resources. Their application improves capabilities for querying and mining biological knowledge. An increasing number of ontologies is being developed for this purpose, and considerable effort is invested into formally dening them in order to represent their semantics explicitly. However, current biomedical ontologies do not facilitate data integration and interoperability yet, since reasoning over these ontologies is very complex and cannot be performed efciently or is even impossible. We propose the use of less expressive subsets of ontology representation languages to enable efcient reasoning and achieve the goal of genuine interoperability between ontologies. Results: We present and evaluate EL Vira, a framework that trans-forms OWL ontologies into the OWL EL subset thereby enabling the use of tractable reasoning. We illustrate which OWL constructs and inferences are kept and lost following the conversion and demon-strate the performance gain of reasoning indicated by the signicant reduction of processing time. We applied EL Vira to the Open Bio-medical Ontologies and provide a repository of ontologies resulting from this conversion. EL Vira creates a common layer of ontological interoperability that, for the rst time, enables the creation of software solutions that can employ biomedical ontologies to perform inferences and answer complex queries to support scientic analyses. Availability and implementation: The EL Vira software is availa-ble from
Indented Tree or Graph? A Usability Study of Ontology Visualization Techniques in the Context of Class Mapping Evaluation
"... Abstract. Research effort in ontology visualization has largely focused on developing new visualization techniques. At the same time, researchers have paid less attention to investigating the usability of common visualization techniques that many practitioners regularly use to visualize ontological ..."
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Abstract. Research effort in ontology visualization has largely focused on developing new visualization techniques. At the same time, researchers have paid less attention to investigating the usability of common visualization techniques that many practitioners regularly use to visualize ontological data. In this paper, we focus on two popular ontology visualization techniques: indented tree and graph. We conduct a controlled usability study with an emphasis on the effectiveness, efficiency, workload and satisfaction of these visualization techniques in the context of assisting users during evaluation of ontology mappings. Findings from this study have revealed both strengths and weaknesses of each visualization technique. In particular, while the indented tree visualization is more organized and familiar to novice users, subjects found the graph visualization to be more controllable and intuitive without visual redundancy, particularly for ontologies with multiple inheritance.
Linked Open Ontology Services
"... Abstract. Ontology repository systems are used for publishing and sharing ontologies and vocabularies for content indexing, information retrieval, content integration, and other purposes. However, interlinking these distributed repositories to provide global search and browsing over the repositories ..."
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Cited by 6 (6 self)
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Abstract. Ontology repository systems are used for publishing and sharing ontologies and vocabularies for content indexing, information retrieval, content integration, and other purposes. However, interlinking these distributed repositories to provide global search and browsing over the repositories has not been made. In the spirit of Linked Open Data, we propose creating a network of Linked Open Ontology Services (LOOS) consisting of ontology repositories that publish their content using a shared API. To test the approach, we have defined an HTTP API and present a proof-of-concept implementation consisting of three client applications that are used for accessing a LOOS network of over 50 ontology servers, part of the Ontology Library Service ONKI. 1
