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Recent Developments in the ChEBI Ontology

Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Kenneth Haug, Zara Josephs, Gareth Owen, Steve Turner, Christoph Steinbeck
2011 International Conference on Biomedical Ontology  
dblp:conf/icbo/HastingsMDEHJOTS11 fatcat:fk7op5qtivbolezvkxhxueq4lu

Modular Extensions to the ChEBI Ontology

Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Venkatesh Muthukrishnan, Steve Turner, Gareth Owen, Christoph Steinbeck
2012 International Conference on Biomedical Ontology  
This poster showcases recent developments and forthcoming enhancements to the ontology, focusing on modular extensions of the content.  ...  These extensions are being developed in support of error detection and consistency checking and to improve the capability for automated reasoning about the biological context of chemicals.  ...  ACKNOWLEDGEMENTS ChEBI is funded by the BBSRC, grant agreement BB/G022747/1 within the 'Bioinformatics and biological resources' fund.  ... 
dblp:conf/icbo/HastingsMDEMTOS12 fatcat:5rscubypezarrigeazu57irwxe

GO faster ChEBI with Reasonable Biochemistry

Duncan Hull
2008 Nature Precedings  
Recent changes to the ontology have created new opportunities for automated reasoning with description logic, that have not previously been fully exploited in Chemistry.  ...  Chemical Entities of Biological Interest (ChEBI) is a database and ontology that represents biochemical knowledge about small molecules.  ...  Introduction Many new ontologies have been developed in recent years [46] , inspired by the success of the Gene Ontology (GO) [3] and with the aim of facilitating data integration in both the chemical  ... 
doi:10.1038/npre.2008.2329.1 fatcat:y4fynojmhvetvocdvnpldpsbza

Identifying Chemical Entities based on ChEBI

Tiago Grego, Francisco R. Pinto, Francisco M. Couto
2012 International Conference on Biomedical Ontology  
entities in the entity recognition and resolution process.  ...  This software demonstration paper presents Identifying Chemical Entities (ICE), a platform composed by algorithms for chemical entity recognition, entity resolution to a reference database, namely ChEBI  ...  ACKNOWLEDGEMENTS The authors want to thank the Portuguese Fundação para a Ciência e Tecnologia through the financial support of the SPNet project (PTDC/EIA-EIA/119119/2010), the SOMER project (PTDC/EIA-EIA  ... 
dblp:conf/icbo/GregoPC12 fatcat:dyuf5c5r75eafm6alejposcpm4

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  
processes in GO are now defined in terms of the ChEBI entities that participate in them.  ...  Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features.  ...  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

OntoQuery: easy-to-use web-based OWL querying

I. Tudose, J. Hastings, V. Muthukrishnan, G. Owen, S. Turner, A. Dekker, N. Kale, M. Ennis, C. Steinbeck
2013 Bioinformatics  
The Web Ontology Language (OWL) provides a sophisticated language for building complex domain ontologies and is widely used in bio-ontologies such as the Gene Ontology.  ...  OntoQuery software is fully compatible with all OWL-based ontologies and is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at  ...  Although the tool was initially developed for ChEBI, it is applicable to any ontology.  ... 
doi:10.1093/bioinformatics/btt514 pmid:24008420 pmcid:PMC3810857 fatcat:7pfztu2bevg4vpmpsmy3gr7tqa

Chemical Entities of Biological Interest: an update

Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck
2009 Nucleic Acids Research  
a 30-fold increase in the number of chemical structures stored in ChEBI.  ...  ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge the contribution of the following people to the success of the project: Michael  ... 
doi:10.1093/nar/gkp886 pmid:19854951 pmcid:PMC2808869 fatcat:phtdfvxygrhczfberkbzgmyvyy

Prediction of Drugs Target Groups Based on ChEBI Ontology

Yu-Fei Gao, Lei Chen, Guo-Hua Huang, Tao Zhang, Kai-Yan Feng, Hai-Peng Li, Yang Jiang
2013 BioMed Research International  
of this sort and bridge the gap between ChEBI ontology and drugs target groups.  ...  In the study, we proposed a novel prediction method based on drug/compound ontology information extracted from ChEBI to identify drugs target groups from which the kind of functions of a drug may be deduced  ...  Conflict of Interests The authors declare that there is no conflict of interests regarding the publication of this paper. Acknowledgments  ... 
doi:10.1155/2013/132724 pmid:24350241 pmcid:PMC3853244 fatcat:mojjpp624nawxlfpmwlyuvmxny

Efforts toward a More Consistent and Interoperable Sequence Ontology

Michael Bada, Karen Eilbeck
2012 International Conference on Biomedical Ontology  
Here we present our recent developmen-tal approaches to address three issues of import for the SO: (1) repre-sentation of molecular sequences versus abstract sequences; (2) inte-gration with the ChEBI  ...  The Sequence Ontology (SO), a member of the Open Biomedical On-tologies (OBOs) library, was developed with the goals of standardizing the vocabulary and semantics of biological--sequence annotation with  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of this work by NIH/NHGRI R01HG004341. We also thank Colin Batchelor for his participation in helpful discussions.  ... 
dblp:conf/icbo/BadaE12 fatcat:73sedbgb7radhozxsfqi7u6nde

DNAmod: the DNA modification database

Ankur Jai Sood, Coby Viner, Michael M. Hoffman
2019 Journal of Cheminformatics  
To address this need, we have developed DNAmod: the DNA modification database.  ...  DNAmod enables researchers to rapidly review previous work, select mapping techniques, and track recent developments concerning modified bases of interest.  ...  We thank the creators of ChEBI [13] , and all those who have worked to improve it [21, 22, 48] .  ... 
doi:10.1186/s13321-019-0349-4 pmid:31016417 pmcid:PMC6478773 fatcat:6elkrxo4nbes7j36obuinhidpm

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  
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  ...  consistent and in alignment with the chemical expertise captured in ChEBI.  ...  The GO and ChEBI have been constructed largely for different purposes and, until recently, have only been loosely connected.  ... 
doi:10.1186/1471-2164-14-513 pmid:23895341 pmcid:PMC3733925 fatcat:ts753ihc5fdrjjz4akrcmaejga

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.  ...  However, ChEBI is manually maintained and as such cannot easily scale to the full scope of public chemical data.  ...  from the CHEBI ontology as described in the Methods.  ... 
doi:10.1186/s13321-021-00500-8 pmid:33726837 fatcat:3xlvsmlwnfbkfjwi2igyajrela

Building a drug ontology based on RxNorm and other sources

Josh Hanna, Eric Joseph, Mathias Brochhausen, William R Hogan
2013 Journal of Biomedical Semantics  
We built DrOn in a modular fashion to facilitate simpler extension and development of the ontology and to allow reasoning and construction to scale.  ...  However, one of the obstacles we faced when creating the Drug Ontology (DrOn) was the difficulty in reusing drug information from existing sources.  ...  , and the Arkansas Biosciences Institute, the major research component of the Arkansas Tobacco Settlement Proceeds Act of 2000.  ... 
doi:10.1186/2041-1480-4-44 pmid:24345026 pmcid:PMC3931349 fatcat:6rxzj42oczeknafi3oiuolozju

Using Wikipedia categories for compact representations of chemical documents

Benjamin Köhncke, Wolf-Tilo Balke
2010 Proceedings of the 19th ACM international conference on Information and knowledge management - CIKM '10  
from the ChEBI ontology.  ...  We compare the results to the domain-specific ChEBI ontology and the results show that Wikipedia categories indeed allow useful descriptions for chemical documents that are even better than descriptions  ...  the ChEBI ontology.  ... 
doi:10.1145/1871437.1871735 dblp:conf/cikm/KohnckeB10 fatcat:tidhqgl2zzb37nqgoqeyhdzuv4

MetaboLights: a resource evolving in response to the needs of its scientific community

2019 Nucleic Acids Research  
In this article, we describe the significant updates that we have made over the last two years to the resource to respond to the increasing amount and diversity of data being submitted by the metabolomics  ...  MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information.  ...  A successful example of this is the recent development of a bespoke submission pipeline for metabolon (https://www.metabolon.com).  ... 
doi:10.1093/nar/gkz1019 pmid:31691833 pmcid:PMC7145518 fatcat:5rsskhax7fcb5hi46huaududya
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