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Ontodog: a web-based ontology community view generation tool

J. Zheng, Z. Xiang, C. J. Stoeckert, Y. He
2014 Bioinformatics  
Ontodog is a web-based system to support generation of ontology community views.  ...  Currently over 100 ontologies including all OBO Foundry ontologies are available in Ontodog to generate views for a specific application or community.  ...  We developed Ontodog, a web-based tool, to address these needs and generate ontology community views automatically without need for programming skills and requiring minimal ontology knowledge.  ... 
doi:10.1093/bioinformatics/btu008 pmid:24413522 pmcid:PMC3998133 fatcat:3e2tk26wvzb5hkpi5yjb7beqdq

Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms

Yongqun He, Jie Zheng, Yu Lin
2015 International Conference on Biomedical Ontology  
Each tool has specific functions; together, these tools support the extraction of a single or subset of terms and community views from existing ontologies, generation and editing of ontology terms, query  ...  Ontoanimal tools are a suite of web-based ontology tools developed to support efficient and integrated ontology development and applications.  ...  ACKNOWLEDGEMENTS This research was supported by a NIH R01 grant (1R01AI081062).  ... 
dblp:conf/icbo/HeZL15 fatcat:nsrtkwddqrbeba2spefpm4tejq

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

Edison Ong, Yongqun He, Jie Zheng
2018 International Conference on Biomedical Ontology  
In this software demo, we show how Ontoanimal tools (e.g., Ontofox, Ontodog, Ontorat, and Ontokiwi) can be used to support the implementation of these XOD principles.  ...  These principles include ontology term reuse, semantic alignment, design pattern usage, and community extensibility.  ...  ACKNOWLEDGMENT The development of Ontoanimal tools was primarily supported by a NIH R01 grant (1R01AI081062).  ... 
dblp:conf/icbo/OngH018 fatcat:cptx7yrcezcm5hijfjhimlkj24

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong
2018 Journal of Biomedical Semantics  
The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development.  ...  These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new  ...  Acknowledgements We acknowledge the OBO Foundry consortium and OBO ontology developers for their support and collaborations.  ... 
doi:10.1186/s13326-017-0169-2 pmid:29329592 pmcid:PMC5765662 fatcat:5w3acqcqd5hnxphdq76ruqlrja

Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations

Jie Zheng, Elisabetta Manduchi, Christian J. Stoeckert Jr.
2013 International Conference on Biomedical Ontology  
This process should be generally applicable and consists of integration of a subset of reference ontologies.  ...  The ontology is validated in three aspects based on our needs including data annotation, queries and automated classification.  ...  Brush, for discussion and consistent implementation of high level cell terms in three ontologies. This research is supported by NIH grant 1R01GM093132-01 and by 5 U01 DK 072473.  ... 
dblp:conf/icbo/ZhengMS13 fatcat:axxrwq7phndlvlddzg2k2n3lrq

A Survey Of Semantic Integration Approaches In Bioinformatics

Chaimaa Messaoudi, Rachida Fissoune, Hassan Badir
2016 Zenodo  
We provide a survey of some approaches and techniques for integrating biological data, we focus on those developed in the ontology community.  ...  Technological advances of computer science and data analysis are helping to provide continuously huge volumes of biological data, which are available on the web.  ...  system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified  ... 
doi:10.5281/zenodo.1128003 fatcat:hqgxuhfqwrgori2u7ox2c3c2ce

Taking a view on bio-ontologies

Simon Jupp, Andrew Gibson, James Malone, Robert Stevens
2012 International Conference on Biomedical Ontology  
Each of these views serves a special purpose to different user communities; however, it does ensure the underlying ontology can remain for the annotation and integration of biological data.  ...  We use this technique to encode a number of views inside the Experimental Factor Ontology.  ...  ACKNOWLEDGEMENTS AG is supported by the BioRange programme of The Netherlands Bioinformatics Centre (NBIC; http://www.nbic.nl), supported by a BSIK grant through The Netherlands Genomics Initiative (NGI  ... 
dblp:conf/icbo/JuppGMS12 fatcat:hu4zzc24tvanjd67syr754ymue

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
2016 Nucleic Acids Research  
Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term.  ...  In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies.  ...  ACKNOWLEDGEMENTS The authors thank James A.  ... 
doi:10.1093/nar/gkw918 pmid:27733503 pmcid:PMC5210626 fatcat:pbsi2gstdjalbdcfkye3sq2mlq

Design insights for the next wave ontology authoring tools

Markel Vigo, Caroline Jay, Robert Stevens
2014 Proceedings of the 32nd annual ACM conference on Human factors in computing systems - CHI '14  
up to a new generation of users.  ...  We map the data to a set of design recommendations, which describe how tools of the future can support ontology authoring.  ...  ACKNOWLEDGMENTS Research funded by the EPSRC project: WhatIf: Answering "What if. . . " Questions for Ontology Authoring. EPSRC reference EP/J014176/1.  ... 
doi:10.1145/2556288.2557284 dblp:conf/chi/VigoJS14 fatcat:5iv45juiz5d7pcujrmkoz5sceu

Ontology-supported research on vaccine efficacy, safety and integrative biological networks

Yongqun He
2014 Expert Review of Vaccines  
Several community-based ontologies (including the Vaccine Ontology, Ontology of Adverse Events, and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation  ...  of Life, and ontology-based approaches to study and apply the OneNet theory.  ...  The tool Ontodog generates ontology community views from a large ontology [119] .  ... 
doi:10.1586/14760584.2014.923762 pmid:24909153 pmcid:PMC4815432 fatcat:t3xq23efsrgyrn5zp3xo2v2dji

OBIB-a novel ontology for biobanking

Mathias Brochhausen, Jie Zheng, David Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis, Christian J. Stoeckert
2016 Journal of Biomedical Semantics  
Results: Based on the two previous ontologies the Ontology for Biobanking (http://purl.obolibrary.org/obo/obib.owl) was created.  ...  Methods: Based in the principles laid out by the Open Biological and Biomedical Ontologies Foundry two biobanking ontologies have been developed.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.  ... 
doi:10.1186/s13326-016-0068-y pmid:27148435 pmcid:PMC4855778 fatcat:wdzfjd5njbalbpynojkdlk6tli

IMIA LaMB WG related event: Proceedings of 3rd International Conference on Biomedical Ontology, 2012, Graz

Ronald Cornet, Robert Stevens, Melanie Courtot, Trish Whetzel, Janna Hastings, Stefan Schulz, Ludger Jansen
2019 Zenodo  
It brings together representatives of all major communities involved in the development and application of ontologies in biomedical research ...  ...  This conference carried on the tradition of discussing medical ontologies, increasingly used in biology and medicine, and their use in annotation of both clinical and experimental data is now a common  ...  information to a Gene Ontology annotation.  ... 
doi:10.5281/zenodo.3381830 fatcat:pnndilxgzzbujnoqz7pytggtdi

Ontology-Based Vaccine and Drug Adverse Event Representation and Theory-Guided Systematic Causal Network Analysis Toward Integrative Pharmacovigilance Research

Yongqun He
2016 Current Pharmacology Reports  
., MedDRA, CTCAE, and WHO-ART), the community-based Ontology of Adverse Events (OAEs) has many advantages in AE classifications.  ...  The OAE-derived Ontology of Vaccine AEs (OVAE) and Ontology of Drug Neuropathy AEs (ODNAE) serve as AE knowledge bases and support data integration and analysis.  ...  Each tool has specific functions; together, these tools are able to extract ontology subsets, provide ontology community views, generate and edit ontology terms, query and visualize ontology terms, provide  ... 
doi:10.1007/s40495-016-0055-0 pmid:27458549 pmcid:PMC4957564 fatcat:kgyrslkfb5huzir75mm5cv22my