Publications

Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology.

Published in Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 2018

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Recommended citation: Tomasz Puzyn, Nina Jeliazkova, Haralambos Sarimveis, Richard Marchese, Vladimir Lobaskin, Robert Rallo, Andrea-N. Richarz, Agnieszka Gajewicz, Manthos Papadopulos, Janna Hastings, Mark Cronin, Emilio Benfenati, Alberto Fernandez, "Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology.." Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 2018.

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans.

Published in Frontiers in molecular biosciences, 2018

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Recommended citation: Michael Witting, Janna Hastings, Nicolas Rodriguez, Chintan Joshi, Jake Hattwell, Paul Ebert, Michel Weeghel, Arwen Gao, Michael Wakelam, Riekelt Houtkooper, Abraham Mains, Nicolas Le, Sean Sadykoff, Frank Schroeder, Nathan Lewis, Horst-Joachim Schirra, Christoph Kaleta, Olivia Casanueva, "Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans.." Frontiers in molecular biosciences, 2018.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

Published in PLoS biology, 2017

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Recommended citation: Julie McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Melanie Courtot, John Deck, Michel Dumontier, Donal Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Heriche, Henning Hermjakob, Jon Ison, Rafael Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le, James Malone, Maria Martin, Johanna McEntyre, Chris Morris, Juha Muilu, Wolfgang Muller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky Snoep, Stian Soiland-Reyes, Natalie Stanford, Neil Swainston, Nicole Washington, Alan Williams, Sarala Wimalaratne, Lilly Winfree, Katherine Wolstencroft, Carole Goble, Christopher Mungall, Melissa Haendel, Helen Parkinson, "Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.." PLoS biology, 2017.

Primer on Ontologies.

Published in Methods in molecular biology (Clifton, N.J.), 2017

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Recommended citation: Janna Hastings, "Primer on Ontologies.." Methods in molecular biology (Clifton, N.J.), 2017.

Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research.

Published in European journal of human genetics : EJHG, 2016

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Recommended citation: Ola Spjuth, Maria Krestyaninova, Janna Hastings, Huei-Yi Shen, Jani Heikkinen, Melanie Waldenberger, Arnulf Langhammer, Claes Ladenvall, Tonu Esko, Mats-Ake Persson, Jon Heggland, Joern Dietrich, Sandra Ose, Christian Gieger, Janina Ried, Annette Peters, Isabel Fortier, Eco Geus, Janis Klovins, Linda Zaharenko, Gonneke Willemsen, Jouke-Jan Hottenga, Jan-Eric Litton, Juha Karvanen, Dorret Boomsma, Leif Groop, Johan Rung, Juni Palmgren, Nancy Pedersen, Mark McCarthy, Cornelia Duijn, Kristian Hveem, Andres Metspalu, Samuli Ripatti, Inga Prokopenko, Jennifer Harris, "Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research.." European journal of human genetics : EJHG, 2016.

libChEBI: an API for accessing the ChEBI database.

Published in Journal of cheminformatics, 2016

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Recommended citation: Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John May, Christoph Steinbeck, Pedro Mendes, "libChEBI: an API for accessing the ChEBI database.." Journal of cheminformatics, 2016.

Data standards can boost metabolomics research, and if there is a will, there is a way.

Published in Metabolomics : Official journal of the Metabolomic Society, 2016

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Recommended citation: Philippe Rocca-Serra, Reza Salek, Masanori Arita, Elon Correa, Saravanan Dayalan, Alejandra Gonzalez-Beltran, Tim Ebbels, Royston Goodacre, Janna Hastings, Kenneth Haug, Albert Koulman, Macha Nikolski, Matej Oresic, Susanna-Assunta Sansone, Daniel Schober, James Smith, Christoph Steinbeck, Mark Viant, Steffen Neumann, "Data standards can boost metabolomics research, and if there is a will, there is a way.." Metabolomics : Official journal of the Metabolomic Society, 2016.

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.

Published in Journal of cheminformatics, 2016

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Recommended citation: Yannick Djoumbou, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David Wishart, "ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.." Journal of cheminformatics, 2016.

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

Published in BMC bioinformatics, 2015

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Recommended citation: Pablo Moreno, Stephan Beisken, Bhavana Harsha, Venkatesh Muthukrishnan, Ilinca Tudose, Adriano Dekker, Stefanie Dornfeldt, Franziska Taruttis, Ivo Grosse, Janna Hastings, Steffen Neumann, Christoph Steinbeck, "BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.." BMC bioinformatics, 2015.

The eNanoMapper database for nanomaterial safety information.

Published in Beilstein journal of nanotechnology, 2015

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Recommended citation: Nina Jeliazkova, Charalampos Chomenidis, Philip Doganis, Bengt Fadeel, Roland Grafstrom, Barry Hardy, Janna Hastings, Markus Hegi, Vedrin Jeliazkov, Nikolay Kochev, Pekka Kohonen, Cristian Munteanu, Haralambos Sarimveis, Bart Smeets, Pantelis Sopasakis, Georgia Tsiliki, David Vorgrimmler, Egon Willighagen, "The eNanoMapper database for nanomaterial safety information.." Beilstein journal of nanotechnology, 2015.

Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.

Published in Frontiers in neuroinformatics, 2014

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Recommended citation: Janna Hastings, Gwen Frishkoff, Barry Smith, Mark Jensen, Russell Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica Turner, Maryann Martone, "Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.." Frontiers in neuroinformatics, 2014.

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

Published in Bioinformatics (Oxford, England), 2013

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Recommended citation: Ilinca Tudose, Janna Hastings, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Adriano Dekker, Namrata Kale, Marcus Ennis, Christoph Steinbeck, "OntoQuery: easy-to-use web-based OWL querying.." Bioinformatics (Oxford, England), 2013.

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

Published in BMC genomics, 2013

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Recommended citation: David Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Berardini, Heiko Dietze, Harold Drabkin, Marcus Ennis, Rebecca Foulger, Midori Harris, Janna Hastings, Namrata Kale, Paula Matos, Christopher Mungall, Gareth Owen, Paola Roncaglia, Christoph Steinbeck, Steve Turner, Jane Lomax, "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.." BMC genomics, 2013.

The ChEMBL database as linked open data.

Published in Journal of cheminformatics, 2013

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Recommended citation: Egon Willighagen, Andra Waagmeester, Ola Spjuth, Peter Ansell, Antony Williams, Valery Tkachenko, Janna Hastings, Bin Chen, David Wild, "The ChEMBL database as linked open data.." Journal of cheminformatics, 2013.

The MetaboLights repository: curation challenges in metabolomics.

Published in Database : the journal of biological databases and curation, 2013

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Recommended citation: Reza Salek, Kenneth Haug, Pablo Conesa, Janna Hastings, Mark Williams, Tejasvi Mahendraker, Eamonn Maguire, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Susanna-Assunta Sansone, Christoph Steinbeck, "The MetaboLights repository: curation challenges in metabolomics.." Database : the journal of biological databases and curation, 2013.

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

Published in Nucleic acids research, 2013

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Recommended citation: Janna Hastings, Paula Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Mark Williams, Christoph Steinbeck, "The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.." Nucleic acids research, 2013.

MetaboLights–an open-access general-purpose repository for metabolomics studies and associated meta-data.

Published in Nucleic acids research, 2013

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Recommended citation: Kenneth Haug, Reza Salek, Pablo Conesa, Janna Hastings, Paula Matos, Mark Rijnbeek, Tejasvi Mahendraker, Mark Williams, Steffen Neumann, Philippe Rocca-Serra, Eamonn Maguire, Alejandra Gonzalez-Beltran, Susanna-Assunta Sansone, Julian Griffin, Christoph Steinbeck, "MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.." Nucleic acids research, 2013.

Structure-based classification and ontology in chemistry.

Published in Journal of cheminformatics, 2012

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Recommended citation: Janna Hastings, Despoina Magka, Colin Batchelor, Lian Duan, Robert Stevens, Marcus Ennis, Christoph Steinbeck, "Structure-based classification and ontology in chemistry.." Journal of cheminformatics, 2012.

Toxicology ontology perspectives.

Published in ALTEX, 2012

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Recommended citation: Barry Hardy, Gordana Apic, Philip Carthew, Dominic Clark, David Cook, Ian Dix, Sylvia Escher, Janna Hastings, David Heard, Nina Jeliazkova, Philip Judson, Sherri Matis-Mitchell, Dragana Mitic, Glenn Myatt, Imran Shah, Ola Spjuth, Olga Tcheremenskaia, Luca Toldo, David Watson, Andrew White, Chihae Yang, "Toxicology ontology perspectives.." ALTEX, 2012.

Requirements for semantic biobanks.

Published in Studies in health technology and informatics, 2012

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Recommended citation: Andre Andrade, Markus Kreuzthaler, Janna Hastings, Maria Krestyaninova, Stefan Schulz, "Requirements for semantic biobanks.." Studies in health technology and informatics, 2012.

Accessing and using chemical property databases.

Published in Methods in molecular biology (Clifton, N.J.), 2012

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Recommended citation: Janna Hastings, Zara Josephs, Christoph Steinbeck, "Accessing and using chemical property databases.." Methods in molecular biology (Clifton, N.J.), 2012.

A toxicology ontology roadmap.

Published in ALTEX, 2012

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Recommended citation: Barry Hardy, Gordana Apic, Philip Carthew, Dominic Clark, David Cook, Ian Dix, Sylvia Escher, Janna Hastings, David Heard, Nina Jeliazkova, Philip Judson, Sherri Matis-Mitchell, Dragana Mitic, Glenn Myatt, Imran Shah, Ola Spjuth, Olga Tcheremenskaia, Luca Toldo, David Watson, Andrew White, Chihae Yang, "A toxicology ontology roadmap.." ALTEX, 2012.

A database for chemical proteomics: ChEBI.

Published in Methods in molecular biology (Clifton, N.J.), 2012

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Recommended citation: Paula Matos, Nico Adams, Janna Hastings, Pablo Moreno, Christoph Steinbeck, "A database for chemical proteomics: ChEBI.." Methods in molecular biology (Clifton, N.J.), 2012.

Controlled vocabularies and semantics in systems biology.

Published in Molecular systems biology, 2011

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Recommended citation: Melanie Courtot, Nick Juty, Christian Knupfer, Dagmar Waltemath, Anna Zhukova, Andreas Drager, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le, "Controlled vocabularies and semantics in systems biology.." Molecular systems biology, 2011.

Chemical Entities of Biological Interest: an update.

Published in Nucleic acids research, 2010

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Recommended citation: Paula Matos, Rafael Alcantara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck, "Chemical Entities of Biological Interest: an update.." Nucleic acids research, 2010.