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Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns

Zuoshuang Xiang, Jie Zheng, Yu Lin, Yongqun He
2015 Journal of Biomedical Semantics  
Results: Inspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s).  ...  Conclusions: With ever increasing ontology development and applications, Ontorat provides a timely platform for generating and annotating a large number of ontology terms by following design patterns.  ...  The content of this paper is solely the responsibility of the author and does not necessarily represent the official views of the NIAID and the NIH or other funding organizations.  ... 
doi:10.1186/2041-1480-6-4 pmid:25785185 pmcid:PMC4362828 fatcat:nqnxmvxsmvbizdabzczxppvdri

Ontorat: Automatic generation and editing of ontology terms

Yongqun He, Jie Zheng, Yu Lin
2015 International Conference on Biomedical Ontology  
As a demonstration, Ontorat is applied to automatically generate assay terms with axioms and annotations added into the Ontology for Biomedical Investigations (OBI).  ...  The web-based Ontorat ( program has been developed to automatically generate and edit ontology terms from a spreadsheet format input (Excel or tab-delimited file) based on an  ...  ONTORAT NEW TERM GENERATION One major function of Ontorat is to generate multiple new ontology terms based on an ODP for a specific ontology.  ... 
dblp:conf/icbo/HeZL15a fatcat:xjot2j3lpbfcni2jix2u3mtyki

Ontorat web server for automatic generation and annotations of new ontology terms

Zuoshuang Xiang, Yu Lin, Yongqun He
2012 International Conference on Biomedical Ontology  
Ontorat is developed based on the Ontology Design Patterns (OCPs) in the field of ontology engineering.  ...  One frequently observed phenomenon during ontology development is that often we need to create a large number of new ontology terms that follow the same design patterns of logical definitions and axioms  ... 
dblp:conf/icbo/XiangLH12 fatcat:z2abjm2i5radhppziydlhho5he

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

Edison Ong, Yongqun He, Jie Zheng
2018 International Conference on Biomedical Ontology  
These principles include ontology term reuse, semantic alignment, design pattern usage, and community extensibility.  ...  ., 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 CLO and LINCS work were supported by an external data science research award of the grant U54HL127624 (BD2K LINCS Data Coordination and Integration Center, DCIC).  ... 
dblp:conf/icbo/OngH018 fatcat:cptx7yrcezcm5hijfjhimlkj24

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  ...  Based on the Web Ontology Language (OWL) and Semantics Web technologies, these tools have widely been used by thousands of ontology developers in over 20 communities.  ...  Ontorat: Adding new terms and new axioms to an ontology based on design pattern The Ontorat program ( automatically generates and edits ontology terms and axioms and provides  ... 
dblp:conf/icbo/HeZL15 fatcat:nsrtkwddqrbeba2spefpm4tejq

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  
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  ...  The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development.  ...  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

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson, James Malone
2016 Journal of Biomedical Semantics  
Building ontologies by design patterns and providing simple mechanisms for the addition of new content helps reduce the overall cost and effort required to develop an ontology.  ...  As requests for new terms are made, the need for expert ontologists represents a bottleneck in the development process.  ...  Acknowledgements We acknowledge core funds from EMBL-EBI, this work is also funded in part by the National Center for Biomedical Ontology, one of the National Centers for Biomedical Computing funded by  ... 
doi:10.1186/s13326-016-0055-3 pmid:27042287 pmcid:PMC4818523 fatcat:5id6btkb5zc7bo4kgvk2phfoae

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  
KTAO also generates new semantic axioms to logically link terms of entities in different domains.  ...  Such a representation supports kidney knowledge base generation, query, and data integration.  ...  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

Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs

Mei U Wong, Rebecca Racz, Edison Ong, Yongqun He
2018 AMIA Annual Symposium Proceedings  
The Ontology of Adverse Events (OAE) is a community-based ontology in the domain of AEs. In this study, OAE was first updated by including AE severity grading and OAE-CTCAE mapping.  ...  An OAE subset containing CTCAE-related terms and their associated OAE terms was generated to facilitate term usage.  ...  Darrell Abernethy's insightful edits and comments on this manuscript. We also appreciate Dr. Sirarat Sarntivijai's discussion and comments.  ... 
pmid:29854250 pmcid:PMC5977606 fatcat:uxzaqxq4fvgtzgb25yi5pm5aeq

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events

Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu, Yongqun He
2016 Journal of Biomedical Semantics  
ODNAE includes 139 drug mechanisms of action from NDF-RT and 186 biological processes represented in the Gene Ontology (GO). In total ODNAE contains 1579 terms.  ...  The ODNAE-based methods used in this study can also be extended to the representation and study of other categories of adverse events.  ...  Jane Bai's help in discussion and data interpretation in the domain of neuropathy adverse events.  ... 
doi:10.1186/s13326-016-0069-x pmid:27213033 pmcid:PMC4875649 fatcat:pvg7ocuntffmhfpvk54nltdgqq

TermGenie – a web-application for pattern-based ontology class generation

Heiko Dietze, Tanya Z Berardini, Rebecca E Foulger, David P Hill, Jane Lomax, David Osumi-Sutherland, Paola Roncaglia, Christopher J Mungall
2014 Journal of Biomedical Semantics  
Results: TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates.  ...  In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created.  ...  Acknowledgements We thank all the GO curators who have provided feedback on the GO TermGenie instance. Thanks to Jen Hammock from the Encyclopaedia of Life for testing the OBA TermGenie instance.  ... 
doi:10.1186/2041-1480-5-48 pmid:25937883 pmcid:PMC4417543 fatcat:xvxr32qbbzgk5jnff5nqmsf5ce

ROBOT: A Tool for Automating Ontology Workflows

Rebecca C. Jackson, James P. Balhoff, Eric Douglass, Nomi L. Harris, Christopher J. Mungall, James A. Overton
2019 BMC Bioinformatics  
ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions.  ...  , extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats.  ...  Overton is president and owner of Knocean, Inc. Jackson is a contractor for Knocean, Inc.  ... 
doi:10.1186/s12859-019-3002-3 pmid:31357927 pmcid:PMC6664714 fatcat:6ic6qtpusffz7h6slgfkkrztmu

Discovery of emerging design patterns in ontologies using tree mining

Agnieszka Ławrynowicz, Jedrzej Potoniec, Michał Robaczyk, Tania Tudorache, Rinke Hoekstra
2018 Semantic Web Journal  
To the best of our knowledge, this is the first method for automatic discovery of emerging design patterns in ontologies.  ...  We conduct an experimental study on a set of 331 ontologies from the BioPortal repository.  ...  This work is also supported in part by grants GM086587 and GM103316 from the US National Institutes of Health.  ... 
doi:10.3233/sw-170280 pmid:30505251 pmcid:PMC6261490 fatcat:fayk77sxmbdobbiere7i42ke34

CLO: The cell line ontology

Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F Meehan, Alexander D Diehl, Uma D Vempati, Stephan C Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki (+13 others)
2014 Journal of Biomedical Semantics  
The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species  ...  The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines.  ...  Acknowledgements The work described is funded in part by the National Institutes of Health (NIH) grants 1R01AI081062 (YH) from the National Institute of Allergy and  ... 
doi:10.1186/2041-1480-5-37 pmid:25852852 pmcid:PMC4387853 fatcat:ojqttwnoxjeedid4n7jzjsi3du

ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions

Hong Yu, Solomiya Nysak, Noemi Garg, Edison Ong, Xianwei Ye, Xiangyan Zhang, Yongqun He
2019 BMC Bioinformatics  
To logically represent the complex relations among drug, drug ingredient and mechanism of action, AE, age, disease, and other related factors, an ontology design pattern was developed and applied to generate  ...  Built on a generalizable ODAE design pattern and extending the OAE and NDF-RT ontology, ODAE has represented various AEs associated with the over 200 neuropathy-inducing drugs given different age and disease  ...  Based on the general design pattern (Fig. 3a) , we can generate axioms for Linezolid as follows: LINEZOLID: ('drug associated with AE' some ('rash AE' and ('occurs in' some Adult and ('has disease' some  ... 
doi:10.1186/s12859-019-2729-1 fatcat:omdyll52e5e5xapauyirmax55q
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