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Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

David P Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Z Berardini, Heiko Dietze, Harold J Drabkin, Marcus Ennis, Rebecca E Foulger, Midori A Harris, Janna Hastings, Namrata S Kale (+7 others)
2013 BMC Genomics  
The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes.  ...  We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally  ...  This ontology imports ChEBI and contains special rules that allow acids and their conjugate bases to be treated as equivalent within the context of in-vivo biological processes.  ... 
doi:10.1186/1471-2164-14-513 pmid:23895341 pmcid:PMC3733925 fatcat:ts753ihc5fdrjjz4akrcmaejga

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Mark Williams, Christoph Steinbeck
2012 Nucleic Acids Research  
ChEBI ( is a database and ontology of chemical entities of biological interest.  ...  All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy.  ...  ACKNOWLEDGEMENTS The authors are extremely grateful for the continuing contributions from many members of the scientific community to the success of ChEBI.  ... 
doi:10.1093/nar/gks1146 pmid:23180789 pmcid:PMC3531142 fatcat:7btmvq3i3zgtrcukjm7pkb35ii

Primer on Ontologies [chapter]

Janna Hastings
2016 Msphere  
As molecular biology has increasingly become a data-intensive discipline, ontologies have emerged as an essential computational tool to assist in the organisation, description and analysis of data.  ...  The technology that underlies ontologies has its roots in logic-based artifi cial intelligence, allowing for sophisticated automated inference and error detection.  ...  Open Access charges were funded by the University College London Library, the Swiss Institute of Bioinformatics, the Agassiz Foundation, and the Foundation for the University of Lausanne.  ... 
doi:10.1007/978-1-4939-3743-1_1 pmid:27812931 fatcat:43zdghetxfdgvmklv3lme4q6tu

OnE: An Ontology Evaluation Framework

Dipankana Banerjee, Shiv Shakti Ghosh, Tarun Kumar Mondal
2020 Knowledge organization  
Also, for this purpose, an ontology on the domain of agricultural chemicals has been constructed by following the human-centric faceted approach for ontology construction (HCFOC) and has been evaluated  ...  A comprehensive set of evaluation criteria, named OnE, for evaluating ontologies has been proposed in this paper.  ...  Also, main functional groups accountable for biological activities could be specified. Degtyarenko (2007) has compared established commercial chemistry resources and CHEBI.  ... 
doi:10.5771/0943-7444-2020-4-283 fatcat:yg6fbvx4end27akrhs3mfke6tu

A Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled Concepts

Hao Liu, Ling Chen, Ling Zheng, Yehoshua Perl, James Geller
2018 International Conference on Biomedical Ontology  
The Chemical Entities of Biological Interest (ChEBI) ontology is an important knowledge source of chemical entities in a biological context.  ...  An Abstraction Network, which provides a compact summarization of an ontology, supports the methodology.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
dblp:conf/icbo/LiuCZPG18 fatcat:tytdend77jhlpkpdeplv3l67t4

Structure-based classification and ontology in chemistry

Janna Hastings, Despoina Magka, Colin Batchelor, Lian Duan, Robert Stevens, Marcus Ennis, Christoph Steinbeck
2012 Journal of Cheminformatics  
Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI.  ...  Recent years have seen an explosion in the availability of data in the chemistry domain.  ...  This project was partially supported by the BBSRC, grant agreement number BB/G022747/1 within the 'Bioinformatics and biological resources' fund.  ... 
doi:10.1186/1758-2946-4-8 pmid:22480202 pmcid:PMC3361486 fatcat:54c73jnc6jgmjlbdob2vzyupi4

Desiderata for domain reference ontologies in biomedicine

Anita Burgun
2006 Journal of Biomedical Informatics  
The purpose of this paper is to explore how two domain reference ontologies-the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (  ...  An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entire range of macroscopic, microscopic, and subcellular anatomy  ...  Acknowledgment The author thanks Olivier Bodenreider and Olivier Dameron for providing valuable insight.  ... 
doi:10.1016/j.jbi.2005.09.002 pmid:16266830 fatcat:rs266b2rh5bo5dvyccqzrgkcrq

A Quality-Assurance Study of ChEBI

Hasan Yumak, Ling Chen, Michael Halper, Ling Zheng, Yehoshua Perl, Gai Elhanan
2016 International Conference on Biomedical Ontology  
The Chemical Entities of Biological Interest (ChEBI) ontology has become a standard reference for chemicals appearing in biological contexts.  ...  A study of the correctness of a random sample of ChEBI concepts is carried out. The results show that quite a large number of ChEBI concepts suffer from some kind of problematic modeling.  ...  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/YumakCHZPE16 fatcat:m7eadoyxo5dcrbliu3ibp3yl44

Wanting what we don't want to want: Representing addiction in interoperable bio-ontologies

Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan, Barry Smith
2012 International Conference on Biomedical Ontology  
We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology,  ...  Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research  ...  JH is partially supported by the EU under the OpenScreen project, work package 'Standardization'. Smith's work was supported by NIH Roadmap Grant U54 HG004028 National Center for Biomedical Ontology.  ... 
dblp:conf/icbo/HastingsNCMS12 fatcat:akafkietrfdrbondibz6arg2be

OBO Foundry Food Ontology Interconnectivity

Damion M. Dooley, Liliana Andrés-Hernández, Georgeta Bordea, Leigh Carmody, Duccio Cavalieri, Lauren E. Chan, Pol Castellano-Escuder, Carl Lachat, Fleur Mougin, Francesco Vitali, Chen Yang, Magalie Weber (+1 others)
2021 Joint Ontology Workshops  
Since its creation in 2016, the FoodOn ontology has become an interconnected partner in various academic and government inter-agency ontology work spanning agricultural and public health domains.  ...  This paper examines existing and potential data interoperability capabilities arising from FoodOn and partner food-related ontologies belonging to the encyclopedic Open Biological and Biomedical Ontology  ...  Acknowledgements This work is primarily supported by the USDA Non-Assistance Cooperative Agreement 58-8040-8-014-F and Genome Canada Grant 286GET to W. Hsiao.  ... 
dblp:conf/jowo/DooleyABCCCCLMV21 fatcat:kjfis6qujbf65o4bsatah36k6y

Ontologies in Medicinal Chemistry: Current Status and Future Challenges

Asuncion Gomez-Perez, Marcos Martinez-Romero, Alejandro Rodriguez-Gonzalez, Guillermo Vazquez, Jose M. Vazquez-Naya
2013 Current Topics in Medicinal Chemistry  
Ontologies have emerged in AI as a key tool to formally represent and semantically organize aspects of the real world.  ...  Recent years have seen a dramatic increase in the amount and availability of data in the diverse areas of medicinal chemistry, making it possible to achieve significant advances in fields such as the design  ...  , which classifies entities on the basis of their role within an application, biological or 6 chemical context (e.g. pesticide, placebo, antioxidant, etc.); and (4) Subatomic Particle, which classifies  ... 
doi:10.2174/1568026611313050003 pmid:23548021 fatcat:6hyje3smivfldn2svxvnhtsw6i

Self-organizing ontology of biochemically relevant small molecules

Leonid L Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck, Michel Dumontier
2012 BMC Bioinformatics  
Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest.  ...  We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes.  ...  Acknowledgements We thank Marcus Ennis from the European Bioinformatics Institute Chemical Entities of Biological Interest Team for help with identifying errors in our automatically generated chemical  ... 
doi:10.1186/1471-2105-13-3 pmid:22221313 pmcid:PMC3267649 fatcat:puntuu4sufgxliesimufxeeefa

Better living through ontologies at the Immune Epitope Database

Randi Vita, James A. Overton, Alessandro Sette, Bjoern Peters
2017 Database: The Journal of Biological Databases and Curation  
We describe how we use ontologies in the IEDB, providing a concrete example of the benefits of ontologies in practice. Database URL: V C The Author(s)  ...  While the use of independently developed ontologies has long been recommended as a best practice, there continues to be a significant number of projects that develop their own vocabularies instead, or  ...  For example, the IEDB contains data stating that benzylpenicillin is an epitope recognized in the context of an allergic reaction.  ... 
doi:10.1093/database/bax014 pmid:28365732 pmcid:PMC5467561 fatcat:jitj52pmpfdndoxa3ngmz4j4aq

Toxicology ontology perspectives

Barry Hardy
2012 ALTEX: Alternatives to Animal Experimentation  
Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated  ...  A significant set of resources is already available to provide a foundation for an ontological framework for 21 st century mechanistic-based toxicology research.  ...  Acknowledgements Opentox -An Open Source Predictive toxicology Framework,, was funded under the eU Seventh Framework Program: HeAltH-2007-1.3-3 Promotion, development, validation, acceptance  ... 
doi:10.14573/altex.2012.2.139 pmid:22562487 fatcat:ixzxgpvnbvd2peamgwe2loy5ge

Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification

Janna Hastings, Martin Glauer, Adel Memariani, Fabian Neuhaus, Till Mossakowski
2021 Journal of Cheminformatics  
ChEBI is a prominent example of a chemical ontology, widely used in life science contexts.  ...  There is a need for tools that are able to automatically classify chemical data into chemical ontologies, which can be framed as a hierarchical multi-class classification problem.  ...  Machine learning has a long history of applications in computational chemistry. For example, it is used for the prediction of various chemical and biological properties from chemical structures (e.g.  ... 
doi:10.1186/s13321-021-00500-8 pmid:33726837 fatcat:3xlvsmlwnfbkfjwi2igyajrela
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