@conference {IT406, title = {IT406-IP35: The Planteome Project}, 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 = {

The Planteome project is a centralized online plant informatics portal which provides semantic integration of widely diverse datasets with the goal of plant improvement. Traditional plant breeding methods for crop improvement may be combined with next-generation analysis methods and automated scoring of traits and phenotypes to develop improved varieties. The Planteome project (www.planteome.org) develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data. Data annotations linking phenotypes and germplasm to genomics resources are achieved by data transformation and mapping species-specific controlled vocabularies to the reference ontologies. Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression and genetic diversity data across a wide range of plant species. The project database and the online resources provide researchers tools to search and browse and access remotely via APIs for semantic integration in annotation tools and data repositories providing resources for plant biology, breeding, genomics and genetics.

}, url = {http://ceur-ws.org/Vol-1747/IT406-IP35_ICBO2016.pdf}, author = {Laurel Cooper and Austin Meier and Justin Elser and Justin Preece and Xu Xu and Ryan Kitchen and Botong Qu and Eugene Zhang and Sinisa Todorovic and Pankaj Jaiswal and Marie-Ang{\'e}lique Laporte and Elizabeth Arnaud and Seth Carbon and Chris Mungall and Barry Smith and Georgios Gkoutos and John Doonan} } @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 {IT206, title = {IT206: The UNEP Ontologies and the OBO Foundry}, 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/IT206_ICBO2016.pdf}, author = {Barry Smith and Mark Jensen} } @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 {IP18, title = {IP18: The ImmPort Antibody 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 = {

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}, url = {http://ceur-ws.org/Vol-1747/IP18_ICBO2016.pdf}, author = {William Duncan and Travis Allen and Jonathan Bona and Olivia Helfer and Barry Smith and Alan Ruttenberg and Alexander D. Diehl} } @conference {D202, title = {D201: Ontobull and BFOConvert: Web-based programs to support automatic ontology conversion}, 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 = {

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull (http://ontobull.hegroup.org) has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is pro- vided to demonstrate the features of Ontobull and BFOConvert.

}, url = {http://ceur-ws.org/Vol-1747/D201_ICBO2016.pdf}, author = {Edison Ong and Zuoshuang Xiang and Jie Zheng and Barry Smith and Yongqun He} }