Paula de Matos, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Steve Turner, Christoph Steinbeck,
... access databases were initiated by the bioinformatics community, ChEBI [1] and PubChem. PubChem serves as automated repository on the biological activities of small molecules and ChEBI (Chemical Entities of Biological Interest) as a manually ... molecular entities focused on 'small' chemical compounds. Although ChEBI is reasonably compact containing just over 18,000 ... chemical nomenclature, an ontology and chemical structures. The ChEBI database has a strong focus on quality with ... and best IUPAC practices when drawing chemical structures. ChEBI is currently undergoing a period of restructuring which ...
Tópico(s): Semantic Web and Ontologies
2010 - BioMed Central | Journal of Cheminformatics
Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John W. May, Christoph Steinbeck, Pedro Mendes,
ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as ... entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over ... structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non- ... collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic ...
Tópico(s): Bioinformatics and Genomic Networks
2016 - BioMed Central | Journal of Cheminformatics
... weights for mMIMO systems, where both Chebyshev iteration (ChebI) and Newton iteration (NI) are investigated separately to ... and SOR. Firstly, joint Chebyshev and NS method (ChebI-NS) is proposed not only to accelerate the ... improved SOR-AMI methods, NI-SOR-AMI and ChebI-SOR-AMI, are investigated for further convergence acceleration, where NI and ChebI approaches are combined with the SOR-AMI, respectively. ... channel conditions. Simulation results verify that the proposed ChebI-NS has the highest convergence rate compared to ...
Tópico(s): Energy Harvesting in Wireless Networks
2020 - Springer Nature | EURASIP Journal on Wireless Communications and Networking
Eva Meixner, Ulrich Goldmann, Vitaly Sedlyarov, Stefania Scorzoni, Manuele Rebsamen, Enrico Girardi, Giulio Superti‐Furga,
... organized in a convenient ontological structure, based on ChEBI (Chemical Entities of Biological Interest). Substrate-based ontology ... and organization. The Chemical Entities of Biological Interest (ChEBI) ontology contains more than 46,000 manually curated ... By mapping the substrates from manual annotation to ChEBI ontology terms (Table EV2), a controlled, hierarchical vocabulary ... different transporters. 2,266 ontology terms from the ChEBI ontology were connected to annotated SLC substrates (Fig ... to the ontology graph (Fig 2A): In the ChEBI ontology, chemical tautomers and conjugate bases/acids (protonated ...
Tópico(s): 3D Printing in Biomedical Research
2020 - Springer Nature | Molecular Systems Biology
Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck,
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either natural ... cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between ... and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac. ...
Tópico(s): Bioinformatics and Genomic Networks
2009 - Oxford University Press | Nucleic Acids Research
Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Magali Zbinden, Andrew McNaught, Rafael Alcántara, M. Darsow, Mickaël Guedj, Michael Ashburner,
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either natural ... cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between ... and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac. ...
Tópico(s): Genomics and Phylogenetic Studies
2007 - Oxford University Press | Nucleic Acids Research
David P. Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Berardini, Heiko Dietze, Harold Drabkin, Marcus Ennis, Rebecca E. Foulger, Midori A. Harris, Janna Hastings, Namrata Kale, Paula de Matos, Chris Mungall, Gareth Owen, Paola Roncaglia, Christoph Steinbeck, Steve Turner, Jane Lomax,
... GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of ... in alignment with the chemical expertise captured in ChEBI. We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of ... defined semantic relationships to corresponding chemical terms in ChEBI. The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of ...
Tópico(s): Semantic Web and Ontologies
2013 - BioMed Central | BMC Genomics
Paula de Matos, Nico Adams, Janna Hastings, Pablo Moreno, Christoph Steinbeck,
... the field. The Chemical Entities of Biological Interest (ChEBI) database is one such database. The scope of ChEBI includes any constitutionally or isotopically distinct atom, molecule, ... in the processes of living organisms. In addition, ChEBI contains a chemical ontology which relates the small ... that the small molecules are active in. The ChEBI database also provides a central reference point in ...
Tópico(s): Bioinformatics and Genomic Networks
2011 - Springer Science+Business Media | Methods in molecular biology
Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Mark Williams, Christoph Steinbeck,
ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and ... GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated ...
Tópico(s): Computational Drug Discovery Methods
2012 - Oxford University Press | Nucleic Acids Research
Despoina Magka, Markus Krötzsch, Ian Horrocks,
... most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that ... and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential ... subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to ... contribute to a more rapid development of the ChEBI ontology and to the efforts of the ChEBI team to make annotated chemical datasets available to ...
Tópico(s): Computational Drug Discovery Methods
2014 - BioMed Central | Journal of Biomedical Semantics
Pablo Moreno, Stephan Beisken, Bhavana Harsha, Venkatesh Muthukrishnan, Ilinca Tudose, Adriano Dekker, Stefanie Dornfeldt, Franziska Taruttis, Ivo Große, Janna Hastings, Steffen Neumann, Christoph Steinbeck,
... analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can ... weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of ... interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a ...
Tópico(s): Computational Drug Discovery Methods
2015 - BioMed Central | BMC Bioinformatics
Elisabeth Coudert, Sébastien Géhant, Edouard de Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian Sigrist, Nicole Redaschi, Alan Bridge, Alan Bridge, Lucila Aimo, Ghislaine Argoud‐Puy, Andrea Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M Batista Neto, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals‐Casas, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Sébastien Géhant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz, Chantal Hulo, Nevila Hyka‐Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian Sigrist, Karin Sonesson, Shyamala Sundaram, Alex Bateman, María Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily Bowler-Barnett, Ramona Britto, Hema Bye- A-Jee, Austra Cukura, Paul Denny, Tunca Doğan, ThankGod E. Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasaamy, Antonia Lock, Aurélien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel L Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James Stephenson, Prabhat Totoo, E. B. Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy Wu, Cecilia Arighi, Leslie Arminski, Chuming Chen, Chuming Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C R Vinayaka, Qinghua Wang, Yuqi Wang,
... cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support ... ligand binding sites using stable unique identifiers from ChEBI, which we now use as the reference vocabulary ... the chemical structure data, nomenclature and classification that ChEBI provides. Availability and implementation Binding site annotations for cognate ligands described using ChEBI are available for UniProtKB protein sequence records in ...
Tópico(s): Bioinformatics and Genomic Networks
2022 - Oxford University Press | Bioinformatics
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck,
ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes ... accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of ...
Tópico(s): Microbial Metabolic Engineering and Bioproduction
2015 - Oxford University Press | Nucleic Acids Research
... a collaboration with Chemical Entities of Biological Interest (ChEBI), resulting in the first re-source that brings ... published immunological data with the expertise of the ChEBI database. This procedure took advantage of the distinct expertise of the IEDB and ChEBI databases to improve content and enhance interoperability of ...
Tópico(s): Blood groups and transfusion
2011 - OMICS Publishing Group | Immunome Research
Natalie Stanford, Katherine Wolstencroft, Martin Golebiewski, Renate Kania, Nick Juty, Christopher Tomlinson, Stuart Owen, Sarah Butcher, Henning Hermjakob, Nicolas Le Novère, Wolfgang Mueller, Jacky L. Snoep, Carole Goble,
... as a model repository https://www.cellml.org/ ChEBI Chemical Entities of Biological Interest—a dictionary of molecular entities https://www.ebi.ac.uk/chebi/init.do COMBINE Computational Modelling in Biology Network ... GO—47% Ashburner et al, 2000), small molecules (ChEBI—21% Hastings et al, 2013) and model simulations ( ... Turner S, Williams M, Steinbeck C (2013) The ChEBI reference database and ontology for biologically relevant chemistry: ...
Tópico(s): Biomedical Text Mining and Ontologies
2015 - Springer Nature | Molecular Systems Biology
Amin Baghalian, Shervin Tashakori, Volkan Senyurek, Muhammet Ünal, Dwayne McDaniel, İbrahim N. Tansel,
... this study, the Comprehensive Heterodyne Effect Based Inspection (CHEBI) method is proposed to address this issue. The CHEBI method applies ascending and descending broadband frequency sweeps ... shaped aluminum specimen. These results confirm that the CHEBI can be successfully applied for detection of cracks ...
Tópico(s): Structural Health Monitoring Techniques
2018 - Elsevier BV | Measurement
Kirill Degtyarenko, Janna Hastings, Paula de Matos, Marcus Ennis,
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on "small" chemical compounds. This unit provides a detailed guide to browsing, searching, downloading, and programmatic access to the ChEBI database.
Tópico(s): Bioinformatics and Genomic Networks
2009 - Wiley | Current Protocols in Bioinformatics
Michael Bada, Lawrence Hunter,
... function (MF) ontologies, Chemical Entities of Biological Interest (ChEBI) and the Cell Type Ontology (CL). Many of ... CC–CC terms are relatively well-aligned, while ChEBI–MF, BP–ChEBI and CC–MF terms are relatively not aligned ...
Tópico(s): Bioinformatics and Genomic Networks
2008 - Oxford University Press | Bioinformatics
Marvin Schulz, Falko Krause, Nicolas Le Novère, Edda Klipp, Wolfram Liebermeister,
... 2000) and small chemical compounds to entries from ChEBI (Degtyarenko et al, 2008). The MIRIAM initiative (Le ... between similar, but slightly different BCs (e.g., CHEBI:17634 for D-glucose and CHEBI:17925 for α-D-glucose). To capture such ...
Tópico(s): Fractal and DNA sequence analysis
2011 - Springer Nature | Molecular Systems Biology
Ilinca Tudose, Janna Hastings, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Adriano Dekker, Namrata Kale, Marcus Ennis, Christoph Steinbeck,
... is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at http://www.ebi.ac.uk/chebi/tools/ontoquery. Contact: hastings@ebi.ac.uk
Tópico(s): Natural Language Processing Techniques
2013 - Oxford University Press | Bioinformatics
Charles Bettembourg, Christian Diot, Olivier Dameron,
... and to a similarity measure applied to the ChEBI ontology. Thresholds were evaluated over the whole HomoloGene ... We applied this method on the GO and ChEBI ontologies. Qualitative analysis using the thresholds on the ...
Tópico(s): Machine Learning in Bioinformatics
2015 - Public Library of Science | PLoS ONE
Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He,
... TCMDPO for traditional Chinese medicines, NCBITaxon for taxonomy, ChEBI for chemical elements, and OAE for adverse events) ... rheumatism drugs. Using the total of 555 unique ChEBI chemical entities identified from these drugs, our ChEBI-based classification analysis identified 18 anti-inflammatory, 33 ...
Tópico(s): Traditional Chinese Medicine Studies
2017 - Springer Science+Business Media | BMC Systems Biology
Yufei Gao, Lei Chen, Guohua Huang, Tao Zhang, Kai‐Yan Feng, Haipeng Li, Yang Jiang,
... based on drug/compound ontology information extracted from ChEBI to identify drugs target groups from which the ... of this sort and bridge the gap between ChEBI ontology and drugs target groups.
Tópico(s): Microbial Natural Products and Biosynthesis
2013 - Hindawi Publishing Corporation | BioMed Research International
Rahi Navelkar, Gareth Owen, Venkatesh Mutherkrishnan, Paul Thiessen, Tiejun Cheng, Evan Bolton, Nathan Edwards, Michael Tiemeyer, Matthew P. Campbell, María Martin, Jeet Vora, Robel Kahsay, Raja Mazumder,
... and increase glycan data in bioinformatics databases like ChEBI and PubChem, and connecting them to resources at ... have supporting experimental evidence and citations. Databases like ChEBI and PubChem were designed to accommodate complete atomistic ... outlines a workflow developed in collaboration between GlyGen, ChEBI and PubChem to improve the visibility and connectivity ... 10,500 (including ambiguously defined) glycans into the ChEBI database. The integrated glycans were prioritized based on ... be harmonized between different resources. The current PubChem, ChEBI and GlyTouCan mappings can be downloaded from GlyGen ( ...
Tópico(s): Genomics and Phylogenetic Studies
2021 - Oxford University Press | Glycobiology
Janna Hastings, Paula de Matos, Marcus Ennis, Christoph Steinbeck,
... of such data. One such chemical ontology is ChEBI (Chemical Entities of Biological Interest), a candidate member ontology of the OBO Foundry. ChEBI is a publicly available, manually annotated database of ... entities as of the last release (May 2009). ChEBI provides stable unique identifiers for chemical entities; a ... structural and role-based classification within the ontology. ChEBI is widely used for annotation of chemicals within biological databases, text-mining, and data integration. ChEBI can be accessed online at "http://www.ebi. ...
Tópico(s): Semantic Web and Ontologies
2009 - Nature Portfolio | Nature Precedings
Diego E. Chebi, Phillip E. Fanwick, Ian P. Rothwell,
... and rhodium(I) compounds containing pyridylmethyl ligationDiego E. Chebi, Phillip E. Fanwick, and Ian P. RothwellCite this: ...
Tópico(s): Radiopharmaceutical Chemistry and Applications
1990 - American Chemical Society | Organometallics
Sharon M. Beshouri, Diego E. Chebi, Phillip E. Fanwick, Ian P. Rothwell, John C. Huffman,
... 1,2-hydrogen shiftSharon M. Beshouri, Diego E. Chebi, Phillip E. Fanwick, Ian P. Rothwell, and John ...
Tópico(s): Chemical Synthesis and Reactions
1990 - American Chemical Society | Organometallics
Bryan D. Steffey, Linda Chamberlain, Robert W. Chesnut, Diego E. Chebi, Phillip E. Fanwick, Ian P. Rothwell,
... Linda R. Chamberlain, Robert W. Chesnut, Diego E. Chebi, Phillip E. Fanwick, and Ian P. RothwellCite this: ...
Tópico(s): Inorganic and Organometallic Chemistry
1989 - American Chemical Society | Organometallics
Bjoern Peters, The OBI Consortium,
... ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe biological reality. ...
Tópico(s): Research Data Management Practices
2009 - Nature Portfolio | Nature Precedings
Bjoern Peters, Bjoern Peters, The OBI Consortium,
... ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe biological reality. ...
Tópico(s): Scientific Computing and Data Management
2009 - Nature Portfolio | Nature Precedings