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Adapting Disease Vocabularies for Curation at the Rat Genome Database

Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Elizabeth Bolton, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Mary Shimoyama, Melinda R. Dwinell
2018 International Conference on Biomedical Ontology  
The changes were necessitated because no single vocabulary or ontology was freely accessible and complete enough to cover all of the disease states described in the biomedical literature.  ...  During that time the controlled vocabulary used for disease curation has changed a few times.  ...  Osteoarthritis with Mild Chondrodysplasia Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 2 Proceedings of the 9th International Conference on  ... 
dblp:conf/icbo/LaulederkindHWB18 fatcat:xxszfjfo5zawlmdzs7jm74fzpa

eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools

Edison Ong, Yongqun He, Jie Zheng
2018 International Conference on Biomedical Ontology  
., Ontofox, Ontodog, Ontorat, and Ontokiwi) can be used to support the implementation of these XOD principles. The development of the Cell Line Ontology (CLO) is used for the demonstration.  ...  The eXtensible ontology development (XOD) strategy proposes four principles to support interoperable and robust ontology development.  ...  ACKNOWLEDGMENT The development of Ontoanimal tools was primarily supported by a NIH R01 grant (1R01AI081062).  ... 
dblp:conf/icbo/OngH018 fatcat:cptx7yrcezcm5hijfjhimlkj24

Protégé 5.5 - Improvements for Editing Biomedical Ontologies

Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen
2018 International Conference on Biomedical Ontology  
ACKNOWLEDGEMENTS We are heavily indebted to the Biomedical Ontology Community for suggestions and feedback on the new features that we have presented in this paper.  ...  This work was funded by Grant GM121724 from the National Institute of General Medical Sciences at the United States National Institutes of Health.  ...  Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 1 ICBO 2018 August 7-10, 2018 1 Horridge et al Fig. 3 : Breadcrumb and Term Header.  ... 
dblp:conf/icbo/HorridgeGNTM18 fatcat:jbgnudlzzbeenmfyohsyuti2z4

Ontological Framework for Representation of Tractable Flavor: Food Phenotype, Sensation, Perception

Tarini Naravane, Matthew Lange
2018 International Conference on Biomedical Ontology  
While the biological basis for food consumption is primarily to nourish bodily functions, it fulfills a greater second function of sensory pleasure.  ...  Together these three matrices represent an initial ontological model for the flavor and sensory experience portion of the emerging semantic web of food. I.  ...  International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA August 7-10, 2018  ... 
dblp:conf/icbo/NaravaneL18 fatcat:qzoreaegijgrte75dp4bwl4cvm

A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate Plants

Lorena Endara, J. Gordon Burleigh, Laurel Cooper, Pankaj Jaiswal, Marie-Angélique Laporte, Hong Cui
2018 International Conference on Biomedical Ontology  
, like the Plant Ontology (PO) and the Plant Trait Ontology (TO).  ...  missing from the existing ontologies.  ...  ACKNOWLEDGMENT Nathalie Nagalingum (California Academy of Sciences) and Eric Schuettpeltz (Smithsonian Institution) provided taxonomic descriptions and guided the sampling strategy, Annika Smith (Florida  ... 
dblp:conf/icbo/EndaraBCJLC18 fatcat:7xto7a3yezgu3dnepwenwdqudu

Domain Informational Vocabulary Extraction Experiences with Publication Pipeline Integration and Ontology Curation

Amit Gupta, Weijia Xu, Pankaj Jaiswal, Crispin Taylor, Jennifer Regala
2018 International Conference on Biomedical Ontology  
DIVE implements an ensemble of text mining methods for biological entity extraction from article text.  ...  Furthermore, DIVE tracks expert user curation actions on its web interface for future training and improvement of the entity detection algorithm.  ...  DIVE Search Interface Proceedings of the 9th International Conference on Biological Ontology(ICBO 2018), Corvallis, Oregon, USA August 7-10, 2018  ... 
dblp:conf/icbo/GuptaXJTR18 fatcat:4ctwu7meefgkxjkx3coztavbui

Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks

Dimitrios Trigkakis, Justin Preece, Austin Meier, Justin Elser, Kristian Kvilekval, Dmitry Fedorov, B. S. Manjunath, Pankaj Jaiswal, Sinisa Todorovic
2018 International Conference on Biomedical Ontology  
Joyce for their assistance and dedication in hosting the Planteome BisQue module on their infrastructure, via the CyVerse Extended Collaborative Support program.  ...  ACKNOWLEDGMENTS We acknowledge and thank the following curators for testing and using the desktop leaf annotation tool to generate annotated image data for model training purposes: Laurel Cooper, Noor  ...  Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA August 7-10, 2018  ... 
dblp:conf/icbo/TrigkakisPMEKFM18 fatcat:5k4vtzlqaffsdch35cknt6x5aa

OOPS: The Ontology of Plant Stress, A Semi-Automated Standardization Methodology

Austin Meier, Marie-Angélique Laporte, Justin Elser, Laurel Cooper, Justin Preece, Pankaj Jaiswal, Jorrit H. Poelen
2018 International Conference on Biomedical Ontology  
One such standard is the use of a standardized vocabulary, or ontology.  ...  Standardizing the definitions and linking plant stress with established hierarchies leverages previous work of developed knowledge bases such as taxonomic classifications and other ontologies.  ...  ACKNOWLEDGMENT This work was supported by IOS:1340112 from the National Science Foundation.  ... 
dblp:conf/icbo/MeierLECPJP18 fatcat:7mfulpxtkrc7fhznlwwu3hevoe

Synthetic immunology: modulating the human immune system

Barbara Geering, Martin Fussenegger
2015 Trends in Biotechnology  
We are reporting here on this scheme, our ongoing attempts to map the terms used to existing ontologies, and the challenges encountered.  ...  of the immune exposures themselves is not well standardized.  ...  ACKNOWLEDGEMENTS This work was supported by the National Institute of Allergy And Infectious Diseases of the National Institutes of Health under Award Number NIH U19 AI118610 and U19AI089992.  ... 
doi:10.1016/j.tibtech.2014.10.006 pmid:25466879 fatcat:lmnww7jhdfefjl354isbiu7k64

KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration

Yongqun He, Becky Steck, Edison Ong, Laura Mariani, Chrysta Lienczewski, Ulysses J. Balis, Matthias Kretzler, Jonathan Himmelfarb, John F. Bertram, Evren U. Azeloglu, Ravi Iyengar, Deborah Hoshizaki (+1 others)
2018 International Conference on Biomedical Ontology  
Toward this goal, we developed a Kidney Tissue Atlas Ontology (KTAO). KTAO reuses and aligns with existing ontologies such as the Cell Ontology, UBERON, and Human Phenotype Ontology.  ...  KTAO also generates new semantic axioms to logically link terms of entities in different domains.  ...  ACKNOWLEDGMENT This KPMP project is supported by the NIH National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) U2C Project #: 1U2CDK114886-01.  ... 
dblp:conf/icbo/HeSOMLBKHBAIHM18 fatcat:ve3ohq67cng2nfuto2o727l2b4

Does the Foundational Model of Anatomy Ontology Provide a Knowledgebase for Learning and Assessment in Anatomy Education?

Melissa D. Clarkson, Mark E. Whipple
2018 International Conference on Biomedical Ontology  
Throughout the development of the Foundational Model of Anatomy (FMA) ontology, one of the use cases put forth has been anatomy education.  ...  Each of the 33 patterns was evaluated for whether this type of knowledge is compatible with the modeling and scope of the FMA.  ...  ACKNOWLEDGMENT Many thanks to James Brinkley and José (Onard) Mejino of the Structural Informatics Group at the University of Washington for supporting M.D.C.'s earlier work with the FMA.  ... 
dblp:conf/icbo/ClarksonW18 fatcat:vra35673ifd2nh2dnt5hkvijkq

TOCSOC: A Temporal Ontology for Comparing the Survival Outcomes of Clinical Trials in Oncology

Deendayal Dinakarpandian, Michaela Liedtke, Mark A. Musen, Bhavish Dinakar
2018 International Conference on Biomedical Ontology  
The approach has been illustrated by examples from the oncology literature. The temporal ontology and the accompanying reasoner are freely available on Github (https://github.com/pdddinakar/TOCSOC).  ...  We propose a temporal ontology of survival outcome measures that a) helps to standardize the vocabulary for reporting survival outcomes and b) makes it possible to automatically rank the relative efficacy  ...  ACKNOWLEDGMENTS This work was conducted using the Protégé resource, which is supported by grant GM10331601 from the National Institute of General Medical Sciences of the United States National Institutes  ... 
dblp:conf/icbo/DinakarpandianL18 fatcat:qogzsal5vngzhofa3hxpzuavlq

Transforming and Unifying Research with Biomedical Ontologies: The Penn TURBO Project

Christian J. Stoeckert Jr., David L. Birtwell, Hayden Freedman, Mark A. Miller, Heather Williams
2018 International Conference on Biomedical Ontology  
There is also the need to track the provenance of information used when making decisions on what is the actual phenotype of a person.  ...  We take a realism-based ontology approach to address these problems through transformation and instantiation of clinical data with an OBO-Foundry based application ontology in a semantic graph database  ...  We thank Werner Ceusters and William Hogan for their advice and feedback on implementation of referent tracking.  ... 
dblp:conf/icbo/StoeckertBFMW18 fatcat:n7ioutzvvfe7rfade64kvykydq

The New SNOMED CT International Medicinal Product Model

Olivier Bodenreider, Julie James
2018 International Conference on Biomedical Ontology  
We present the status of implementation as of July 2018 and illustrate differences between the original and new models through an example. Conclusions.  ...  We present the main elements of the model, with focus on types of entities and their interrelations, definitional attributes for clinical drugs, and categories of groupers. Results.  ...  ACKNOWLEDGMENT This work was supported in part by the Intramural Research Program of the NIH, National Library of Medicine.  ... 
dblp:conf/icbo/BodenreiderJ18 fatcat:humrqtbporaqvaukwpyik7lpn4

Quality Assurance of Ontology Content Reuse

Michael Halper, Christopher Ochs, Yehoshua Perl, Sivaram Arabandi, Mark A. Musen
2018 International Conference on Biomedical Ontology  
An analysis is carried out on a sample of the large collection of BioPortal-hosted ontologies, many of which employ reuse.  ...  The findings indicate that curators and authors, particularly those new to the reuse process, should be on the alert when developing an ontology with reused content to avoid introducing problems into their  ...  The content is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.  ... 
dblp:conf/icbo/HalperOPAM18 fatcat:dhydd7ygobfknnhes5klnbzttm
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