@conference {W04-05, title = {W04-05: OntONeo: The Obstetric and Neonatal Ontology}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

OntONeo is an ontology for the obstetric and neonatal domain, which has been created to provide a consensus representation of salient electronic health record (EHR) data and in order to serve interoperability of the associated data and information systems. Regardless of medical specialty, in general, every EHR deal with data about the entities involved in a health care appointment. We observed the existence at least three actors: health care facility, the physician, and the patient. Besides dealing with the social entities that participating in a health care appointment, we must also deal with the characteristics that define them and the events that are involved. Here, we demonstrate the utility of ontologies of social entities in the obstetric and neonatal domain. We present how OntONeo is dealing with the material entities who perform or participates in a health care encounter. The definition of these actors plus their related characteristics and events will also contribute to turning on the interoperability of information among EHR from different specialties. OntONeo is being developed with an approach based on ontological realism and the principles of OBO Foundry, including reuse of reference ontologies. Among our reusable ontologies, we can mention for instance the OMRSE, d-acts, PATO and OBI.

}, url = {http://ceur-ws.org/Vol-1747/IT403_ICBO2016.pdf}, author = {F. Farinelli and M.B. Almeida} } @conference {IT505, title = {IT505: Towards a Standard Ontology Metadata Model}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

Bio-ontologies are becoming increasingly important in semantic alignment for data integration, information exchange, and semantic interoperability. Due to the large number of emerging bio-ontologies, it is challenging for ontology for their applications. Therefore, it is important to have a consistent terminology metadata model and a resource for discovering appropriate ontologies or other resource for use in annotating data. This paper aims to seek a common, shareable, and comprehensive method to create, disseminate, and consume metadata about terminology resources.

}, url = {http://ceur-ws.org/Vol-1747/IT505_ICBO2016.pdf}, author = {Hua Min and Stuart Turner and Sherri de Coronado and Brian Davis and Trish Whetzel and Robert R. Freimuth and Harold R. Solbrig and Richard Kiefer and Michael Riben and Grace A. Stafford and Lawrence Wright and Riki Ohira} } @conference {IT403, title = {IT403: OntONeo: The Obstetric and Neonatal Ontology}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child. As a strategy to advance such interoperability we use an approach based on ontological realism and on the ontology development principles of the Open Biomedical Ontologies Foundry, including reuse of reference ontologies wherever possible. We describe the structure and coverage domain of OntONeo and the process of creating and maintaining the ontology.

}, url = {http://ceur-ws.org/Vol-1747/IT403_ICBO2016.pdf}, author = {Fernanda Farinelli and Mauricio Almeida and Peter Elkin and Barry Smith} } @conference {IT402, title = {IT402: Enhancing the Human Phenotype Ontology for Use by the Layperson}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

In rare or undiagnosed diseases, physicians rely upon genotype and phenotype information in order to compare abnormalities to other known cases and to inform diagnoses. Patients are often the best sources of information about their symptoms and phenotypes. The Human Phenotype Ontology (HPO) contains over 12,000 terms describing abnormal human phenotypes. However, the labels and synonyms in the HPO primarily use medical terminology, which can be difficult for patients and their families to understand. In order to make the HPO more accessible to non-medical experts, we systematically added new synonyms using non-expert terminology (i.e., layperson terms) to the existing HPO classes or tagged existing synonyms as layperson. As a result, the HPO contains over 6,000 classes with layperson synonyms.

}, url = {http://ceur-ws.org/Vol-1747/IT402_ICBO2016.pdf}, author = {Nicole Vasilevsky and Mark Engelstad and Erin Foster and Chris Mungall and Peter Robinson and Sebastian K{\"o}hler and Melissa Haendel} } @conference {IP27, title = {IP27: Dealing with elements of medical encounters: an approach based on ontological realism}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies.

}, url = {http://ceur-ws.org/Vol-1747/IP27_ICBO2016.pdf}, author = {Fernanda Farinelli and Mauricio Almeida and Peter Elkin and Barry Smith} } @conference {IP26, title = {IP26: Performance Evaluation Clinical Task Ontology(PECTO)}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

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}, url = {http://ceur-ws.org/Vol-1747/IP26_ICBO2016.pdf}, author = {Jose F Florez-Arango and Santiago Pati{\~n}o-Giraldo and Jack W Smith and Sriram Iyengar} } @conference {IP05, title = {IP05: An Ontological Representation for the Transtheoretical Theory}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

Ontologies are widely used in computer science and medicine. Ontologies may be useful in health promotion and disease prevention for intervention development. Interventionists usually use theory to guide intervention design and evaluation, but there is no standard vocabulary for health behavior theory. A formal mechanism for converting theory to a computer-based representation may provide a tool that can assist in the development of computer-based interventions. This paper demonstrates how ontology can be used to represent a health behavior theory using the Transtheoretical Model (TTM) of behavior change as an example.

}, url = {http://ceur-ws.org/Vol-1747/IP05_ICBO2016.pdf}, author = {Hua Min and Robert H. Friedman and Julie Wright} } @conference {D201, title = {D101: Plant Image Segmentation and Annotation with Ontologies in BisQue}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

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}, url = {http://ceur-ws.org/Vol-1747/D101_ICBO2016.pdf}, author = {Justin Preece and Justin Elser and Pankaj Jaiswal and Kris Kvilekval and Dmitry Fedorov and B.S. Manjunath and Ryan Kitchen and Xu Xu and Dmitrios Trigkakis and Sinisa Todorovic and Seth Carbon} } @conference {BP03, title = {BP03: Label Embedding Approach for Transfer Learning}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, abstract = {

Automatically tagging textual mentions with the concepts, types and entities that they represent are important tasks for which supervised learning has been found to be very effective. In this paper, we consider the problem of exploiting multiple sources of training data with variant ontologies. We present a new transfer learning approach based on embedding multiple label sets in a shared space, and using it to augment the training data.

}, url = {http://ceur-ws.org/Vol-1747/BP03_ICBO2016.pdf}, author = {Rasha Obeidat and Xiaoli Fern and Prasad Tadepalli} }