For the normative version of our publication list see Christoph Steinbeck‘s ORCID profile.
Fritsch, Sebastian; Neumann, Stefan; Schaub, Jonas; Steinbeck, Christoph; Zielesny, Achim
ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK) Journal Article
In: Journal of cheminformatics, vol. 11, no. 1, pp. 37, 2019.
@article{Fritsch:2019dt,
title = {ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK)},
author = {Sebastian Fritsch and Stefan Neumann and Jonas Schaub and Christoph Steinbeck and Achim Zielesny},
url = {https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0361-8},
doi = {10.1186/s13321-019-0361-8},
year = {2019},
date = {2019-01-01},
journal = {Journal of cheminformatics},
volume = {11},
number = {1},
pages = {37},
publisher = {BioMed Central},
abstract = {The Ertl algorithm for automated functional groups (FG) detection and extraction of organic molecules is implemented on the basis of the Chemistry Development Kit (CDK). A distinct impact of the chosen CDK aromaticity model is demonstrated by an FG analysis of the ChEMBL database compounds. The average performance of less than a millisecond for a single-molecule FG extraction allows for fast processing of even large compound databases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Steinbeck, Christoph; Sorokina, Maria; Steinbeck, Christoph
NaPLeS: a natural products likeness scorer—web application and database Journal Article
In: Journal of Cheminformatics, 2019.
@article{Christoph_Steinbeck60376927,
title = {NaPLeS: a natural products likeness scorer—web application and database},
author = {Christoph Steinbeck and Maria Sorokina and Christoph Steinbeck},
url = {http://doi.org/10.1186/s13321-019-0378-z},
doi = {10.1186/s13321-019-0378-z},
year = {2019},
date = {2019-01-01},
journal = {Journal of Cheminformatics},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
S, Herres-Pawlis; O, Koepler; C, Steinbeck
NFDI4Chem: Shaping a Digital and Cultural Change in Chemistry. Journal Article
In: Angewandte Chemie (International ed. in English), 2019.
@article{PMID:31313429b,
title = {NFDI4Chem: Shaping a Digital and Cultural Change in Chemistry.},
author = {Herres-Pawlis S and Koepler O and Steinbeck C},
doi = {10.1002/anie.201907260},
year = {2019},
date = {2019-01-01},
journal = {Angewandte Chemie (International ed. in English)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pupier, Marion; Nuzillard, Jean Marc; Wist, Julien; Schlörer, Nils E; Kuhn, Stefan; Erdelyi, Mate; Steinbeck, Christoph; Williams, Antony J; Butts, Craig; Claridge, Tim D W; Mikhova, Bozhana; Robien, Wolfgang; Dashti, Hesam; Eghbalnia, Hamid R; Far`es, Christophe; Adam, Christian; Pavel, Kessler; Moriaud, Fabrice; Elyashberg, Mikhail; Argyropoulos, Dimitris; Pérez, Manuel; Giraudeau, Patrick; Gil, Roberto R; Trevorrow, Paul; Jeannerat, Damien
NMReDATA, a standard to report the NMR assignment and parameters of organic compounds Journal Article
In: Magnetic Resonance in Chemistry, 2018.
@article{Pupier:2018jo,
title = {NMReDATA, a standard to report the NMR assignment and parameters of organic compounds},
author = {Marion Pupier and Jean Marc Nuzillard and Julien Wist and Nils E Schlörer and Stefan Kuhn and Mate Erdelyi and Christoph Steinbeck and Antony J Williams and Craig Butts and Tim D W Claridge and Bozhana Mikhova and Wolfgang Robien and Hesam Dashti and Hamid R Eghbalnia and Christophe Far{`e}s and Christian Adam and Kessler Pavel and Fabrice Moriaud and Mikhail Elyashberg and Dimitris Argyropoulos and Manuel Pérez and Patrick Giraudeau and Roberto R Gil and Paul Trevorrow and Damien Jeannerat},
url = {https://onlinelibrary.wiley.com/doi/full/10.1002/mrc.4737},
doi = {10.1002/mrc.4737},
year = {2018},
date = {2018-01-01},
journal = {Magnetic Resonance in Chemistry},
publisher = {Wiley-Blackwell},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ritter, Marcel; Neupane, Sandesh; Seidel, Raphael A; Steinbeck, Christoph; Pohnert, Georg
In vivo and in vitro identification of Z-BOX C – a new bilirubin oxidation end product Journal Article
In: Organic & Biomolecular Chemistry, vol. 6, pp. 967, 2018.
@article{Ritter:2018bd,
title = {In vivo and in vitro identification of Z-BOX C – a new bilirubin oxidation end product},
author = {Marcel Ritter and Sandesh Neupane and Raphael A Seidel and Christoph Steinbeck and Georg Pohnert},
url = {http://pubs.rsc.org/en/content/articlehtml/2018/ob/c8ob00164b},
doi = {10.1039/C8OB00164B},
year = {2018},
date = {2018-01-01},
journal = {Organic & Biomolecular Chemistry},
volume = {6},
pages = {967},
publisher = {The Royal Society of Chemistry},
abstract = {A new bilirubin oxidation end product (BOX) was isolated and characterized. The formation of the so-called Z-BOX C proceeds from bilirubin via propentdyopents as intermediates. This BOX was detected in pathological human bile samples using liquid chromatography/mass spectrometry and has potential relevance for liver dysfunction and cerebral vasospasms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Peters, Kristian; Worrich, Anja; Weinhold, Alexander; Alka, Oliver; Balcke, Gerd; Birkemeyer, Claudia; Bruelheide, Helge; Calf, Onno; Dietz, Sophie; Dührkop, Kai; Gaquerel, Emmanuel; Heinig, Uwe; Kücklich, Marlen; Macel, Mirka; Müller, Caroline; Poeschl, Yvonne; Pohnert, Georg; Ristok, Christian; Rodr'iguez, Victor; Ruttkies, Christoph; Schuman, Meredith; Schweiger, Rabea; Shahaf, Nir; Steinbeck, Christoph; Tortosa, Maria; Treutler, Hendrik; Ueberschaar, Nico; Velasco, Pablo; Weiß, Brigitte; Widdig, Anja; Neumann, Steffen; Dam, Nicole
Current Challenges in Plant Eco-Metabolomics Journal Article
In: International Journal of Molecular Sciences, vol. 19, no. 5, pp. 1385, 2018.
@article{Peters:2018cv,
title = {Current Challenges in Plant Eco-Metabolomics},
author = {Kristian Peters and Anja Worrich and Alexander Weinhold and Oliver Alka and Gerd Balcke and Claudia Birkemeyer and Helge Bruelheide and Onno Calf and Sophie Dietz and Kai Dührkop and Emmanuel Gaquerel and Uwe Heinig and Marlen Kücklich and Mirka Macel and Caroline Müller and Yvonne Poeschl and Georg Pohnert and Christian Ristok and Victor Rodr{'i}guez and Christoph Ruttkies and Meredith Schuman and Rabea Schweiger and Nir Shahaf and Christoph Steinbeck and Maria Tortosa and Hendrik Treutler and Nico Ueberschaar and Pablo Velasco and Brigitte Weiß and Anja Widdig and Steffen Neumann and Nicole Dam},
url = {http://www.mdpi.com/1422-0067/19/5/1385/htm},
doi = {10.3390/ijms19051385},
year = {2018},
date = {2018-01-01},
journal = {International Journal of Molecular Sciences},
volume = {19},
number = {5},
pages = {1385},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant-organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Guo, Huijuan; Benndorf, Rene; König, Stefanie; Leichnitz, Daniel; Weigel, Christiane; Peschel, Gundela; Berthel, Patrick; Kaiser, Marcel; Steinbeck, Christoph; Werz, Oliver; Poulsen, Michael; Beemelmanns, Christine
Expanding the Rubterolone Family - Intrinsic Reactivity and Directed Diversification of PKS-derived Pyrans Journal Article
In: Chemistry – A European Journal, 2018.
@article{Guo:2018ge,
title = {Expanding the Rubterolone Family - Intrinsic Reactivity and Directed Diversification of PKS-derived Pyrans},
author = {Huijuan Guo and Rene Benndorf and Stefanie König and Daniel Leichnitz and Christiane Weigel and Gundela Peschel and Patrick Berthel and Marcel Kaiser and Christoph Steinbeck and Oliver Werz and Michael Poulsen and Christine Beemelmanns},
url = {https://onlinelibrary.wiley.com/doi/full/10.1002/chem.201802066},
doi = {10.1002/chem.201802066},
year = {2018},
date = {2018-01-01},
journal = {Chemistry – A European Journal},
publisher = {Wiley-Blackwell},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
McAlpine, James B; Chen, Shao-Nong; Kutateladze, Andrei; MacMillan, John B; Appendino, Giovanni; Barison, Andersson; Beniddir, Mehdi A; Biavatti, Maique W; Bluml, Stefan; Boufridi, Asmaa; Butler, Mark S; Capon, Robert J; Choi, Young H; Coppage, David; Crews, Phillip; Crimmins, Michael T; Csete, Marie; Dewapriya, Pradeep; Egan, Joseph M; Garson, Mary J; Genta-Jouve, Grégory; Gerwick, William H; Gross, Harald; Harper, Mary Kay; Hermanto, Precilia; Hook, James M; Hunter, Luke; Jeannerat, Damien; Ji, Nai-Yun; Johnson, Tyler A; Kingston, David G I; Koshino, Hiroyuki; Lee, Hsiau-Wei; Lewin, Guy; Li, Jie; Linington, Roger G; Liu, Miaomiao; McPhail, Kerry L; Molinski, Tadeusz F; Moore, Bradley S; Nam, Joo-Won; Neupane, Ram P; Niemitz, Matthias; Nuzillard, Jean Marc; Oberlies, Nicholas H; Ocampos, Fernanda M M; Pan, Guohui; Quinn, Ronald J; Reddy, Sai D; Renault, Jean-Hugues; Rivera-Chávez, José; Robien, Wolfgang; Saunders, Carla M; Schmidt, Thomas J; Seger, Christoph; Shen, Ben; Steinbeck, Christoph; Stuppner, Hermann; Sturm, Sonja; Taglialatela-Scafati, Orazio; Tantillo, Dean J; Verpoorte, Robert; Wang, Bin-Gui; Williams, Craig M; Williams, Philip G; Wist, Julien; Yue, Jian-Min; Zhang, Chen; Xu, Zhengren; Simmler, Charlotte; Lankin, David C; Bisson, Jonathan; Pauli, Guido F
The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research Journal Article
In: Natural Product Reports, vol. 33, pp. 1028, 2018.
@article{McAlpine:2018ee,
title = {The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research},
author = {James B McAlpine and Shao-Nong Chen and Andrei Kutateladze and John B MacMillan and Giovanni Appendino and Andersson Barison and Mehdi A Beniddir and Maique W Biavatti and Stefan Bluml and Asmaa Boufridi and Mark S Butler and Robert J Capon and Young H Choi and David Coppage and Phillip Crews and Michael T Crimmins and Marie Csete and Pradeep Dewapriya and Joseph M Egan and Mary J Garson and Grégory Genta-Jouve and William H Gerwick and Harald Gross and Mary Kay Harper and Precilia Hermanto and James M Hook and Luke Hunter and Damien Jeannerat and Nai-Yun Ji and Tyler A Johnson and David G I Kingston and Hiroyuki Koshino and Hsiau-Wei Lee and Guy Lewin and Jie Li and Roger G Linington and Miaomiao Liu and Kerry L McPhail and Tadeusz F Molinski and Bradley S Moore and Joo-Won Nam and Ram P Neupane and Matthias Niemitz and Jean Marc Nuzillard and Nicholas H Oberlies and Fernanda M M Ocampos and Guohui Pan and Ronald J Quinn and Sai D Reddy and Jean-Hugues Renault and José Rivera-Chávez and Wolfgang Robien and Carla M Saunders and Thomas J Schmidt and Christoph Seger and Ben Shen and Christoph Steinbeck and Hermann Stuppner and Sonja Sturm and Orazio Taglialatela-Scafati and Dean J Tantillo and Robert Verpoorte and Bin-Gui Wang and Craig M Williams and Philip G Williams and Julien Wist and Jian-Min Yue and Chen Zhang and Zhengren Xu and Charlotte Simmler and David C Lankin and Jonathan Bisson and Guido F Pauli},
url = {https://pubs.rsc.org/en/content/articlehtml/2018/np/c7np00064b},
doi = {10.1039/C7NP00064B},
year = {2018},
date = {2018-01-01},
journal = {Natural Product Reports},
volume = {33},
pages = {1028},
publisher = {The Royal Society of Chemistry},
abstract = {Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Peters, Kristian; Bradbury, James; Bergmann, Sven; Capuccini, Marco; Cascante, Marta; de Atauri, Pedro; Ebbels, Tim; Foguet, Carles; Glen, Robert; González-Beltrán, Alejandra; Handakas, Evangelos; Hankemeier, Thomas; Herman, Stephanie; Haug, Kenneth; Holub, Petr; Izzo, Massimiliano; Jacob, Daniel; Johnson, David; Jourdan, Fabien; Kale, Namrata; Karaman, Ibrahim; Khalili, Bita; Khoonsari, Payam Emami; Kultima, Kim; Lampa, Samuel; Larsson, Anders; Moreno, Pablo; Neumann, Steffen; Novella, Jon Ander; O'Donovan, Claire; Pearce, Jake TM; Peluso, Alina; Pireddu, Luca; Piras, Marco Enrico; Reed, Michelle AC; Rocca-Serra, Philippe; Roger, Pierrick; Rosato, Antonio; Rueedi, Rico; Ruttkies, Christoph; Sadawi, Noureddin; Salek, Reza; Sansone, Susanna-Assunta; Selivanov, Vitaly; Spjuth, Ola; Schober, Daniel; Thévenot, Etienne A; Tomasoni, Mattia; van Rijswijk, Merlijn; van Vliet, Michael; Viant, Mark; Weber, Ralf; Zanetti, Gianluigi; Steinbeck, Christoph
PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud Journal Article
In: bioRxiv, pp. 409151, 2018.
@article{Peters:2018dt,
title = {PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud},
author = {Kristian Peters and James Bradbury and Sven Bergmann and Marco Capuccini and Marta Cascante and Pedro de Atauri and Tim Ebbels and Carles Foguet and Robert Glen and Alejandra González-Beltrán and Evangelos Handakas and Thomas Hankemeier and Stephanie Herman and Kenneth Haug and Petr Holub and Massimiliano Izzo and Daniel Jacob and David Johnson and Fabien Jourdan and Namrata Kale and Ibrahim Karaman and Bita Khalili and Payam Emami Khoonsari and Kim Kultima and Samuel Lampa and Anders Larsson and Pablo Moreno and Steffen Neumann and Jon Ander Novella and Claire O'Donovan and Jake TM Pearce and Alina Peluso and Luca Pireddu and Marco Enrico Piras and Michelle AC Reed and Philippe Rocca-Serra and Pierrick Roger and Antonio Rosato and Rico Rueedi and Christoph Ruttkies and Noureddin Sadawi and Reza Salek and Susanna-Assunta Sansone and Vitaly Selivanov and Ola Spjuth and Daniel Schober and Etienne A Thévenot and Mattia Tomasoni and Merlijn van Rijswijk and Michael van Vliet and Mark Viant and Ralf Weber and Gianluigi Zanetti and Christoph Steinbeck},
url = {http://biorxiv.org/lookup/doi/10.1101/409151},
doi = {10.1101/409151},
year = {2018},
date = {2018-01-01},
journal = {bioRxiv},
pages = {409151},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<p>Background: Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism9s metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological and many other applied biological domains. Its computationally-intensive nature has driven requirements for open data formats, data repositories and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. Findings: The PhenoMeNal (Phenome and Metabolome aNalysis) e-infrastructure provides a complete, workflow-oriented, interoperable metabolomics data analysis solution for a modern infrastructure-as-a-service (IaaS) cloud platform. PhenoMeNal seamlessly integrates a wide array of existing open source tools which are tested and packaged as Docker containers through the project9s continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi and Pachyderm. Conclusions: PhenoMeNal constitutes a keystone solution in cloud infrastructures available for metabolomics. It provides scientists with a ready-to-use, workflow-driven, reproducible and shareable data analysis platform harmonizing the software installation and configuration through user-friendly web interfaces. The deployed cloud environments can be dynamically scaled to enable large-scale analyses which are interfaced through standard data formats, versioned, and have been tested for reproducibility and interoperability. The flexible implementation of PhenoMeNal allows easy adaptation of the infrastructure to other application areas and 9omics research domains.</p>},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
K, Peters; J, Bradbury; S, Bergmann; M, Capuccini; M, Cascante; de P, Atauri; TMD, Ebbels; C, Foguet; R, Glen; A, Gonzalez-Beltran; UL, Günther; E, Handakas; C, Steinbeck
PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud. Journal Article
In: GigaScience, 2018.
@article{PMID:30535405,
title = {PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.},
author = {Peters K and Bradbury J and Bergmann S and Capuccini M and Cascante M and Atauri de P and Ebbels TMD and Foguet C and Glen R and Gonzalez-Beltran A and Günther UL and Handakas E and Steinbeck C},
doi = {10.1093/gigascience/giy149},
year = {2018},
date = {2018-01-01},
journal = {GigaScience},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Spicer, Rachel A; Salek, Reza; Steinbeck, Christoph
A decade after the metabolomics standards initiative it's time for a revision Journal Article
In: Scientific Data, vol. 4, pp. sdata2017138, 2017.
@article{Spicer:2017cr,
title = {A decade after the metabolomics standards initiative it's time for a revision},
author = {Rachel A Spicer and Reza Salek and Christoph Steinbeck},
url = {http://www.nature.com/articles/sdata2017138},
doi = {10.1038/sdata.2017.138},
year = {2017},
date = {2017-09-01},
journal = {Scientific Data},
volume = {4},
pages = {sdata2017138},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
van Rijswijk, Merlijn; Beirnaert, Charlie; Caron, Christophe; Cascante, Marta; Dominguez, Victoria; Dunn, Warwick B; Ebbels, Timothy M D; Giacomoni, Franck; González-Beltrán, Alejandra; Hankemeier, Thomas; Haug, Kenneth; Izquierdo-Garcia, Jose L; Jiménez, Rafael C; Jourdan, Fabien; Kale, Namrata; Klapa, Maria I; Kohlbacher, Oliver; Koort, Kairi; Kultima, Kim; Corguillé, Gildas Le; Moschonas, Nicholas K; Neumann, Steffen; O'Donovan, Claire; Reczko, Martin; Rocca-Serra, Philippe; Rosato, Antonio; Salek, Reza M; Sansone, Susanna-Assunta; Satagopam, Venkata; Schober, Daniel; Shimmo, Ruth; Spicer, Rachel A; Spjuth, Ola; Thévenot, Etienne A; Viant, Mark R; Weber, Ralf J M; Willighagen, Egon L; Zanetti, Gianluigi; Steinbeck, Christoph
The future of metabolomics in ELIXIR Journal Article
In: F1000Research, vol. 6, pp. 1649, 2017.
@article{vanRijswijk:2017jk,
title = {The future of metabolomics in ELIXIR},
author = {Merlijn van Rijswijk and Charlie Beirnaert and Christophe Caron and Marta Cascante and Victoria Dominguez and Warwick B Dunn and Timothy M D Ebbels and Franck Giacomoni and Alejandra González-Beltrán and Thomas Hankemeier and Kenneth Haug and Jose L Izquierdo-Garcia and Rafael C Jiménez and Fabien Jourdan and Namrata Kale and Maria I Klapa and Oliver Kohlbacher and Kairi Koort and Kim Kultima and Gildas Le Corguillé and Nicholas K Moschonas and Steffen Neumann and Claire O'Donovan and Martin Reczko and Philippe Rocca-Serra and Antonio Rosato and Reza M Salek and Susanna-Assunta Sansone and Venkata Satagopam and Daniel Schober and Ruth Shimmo and Rachel A Spicer and Ola Spjuth and Etienne A Thévenot and Mark R Viant and Ralf J M Weber and Egon L Willighagen and Gianluigi Zanetti and Christoph Steinbeck},
url = {https://f1000research.com/articles/6-1649/v1},
doi = {10.12688/f1000research.12342.1},
year = {2017},
date = {2017-09-01},
journal = {F1000Research},
volume = {6},
pages = {1649},
abstract = {Read the latest article version by Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-Garcia, Rafael C. Jimenez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire OtextquoterightDonovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck, at F1000Research.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Spicer, Rachel; Salek, Reza M; Moreno, Pablo; Cañueto, Daniel; Steinbeck, Christoph
Navigating freely-available software tools for metabolomics analysis Journal Article
In: Metabolomics, vol. 13, no. 9, pp. 106, 2017.
@article{Spicer:2017jc,
title = {Navigating freely-available software tools for metabolomics analysis},
author = {Spicer, Rachel and Salek, Reza M and Moreno, Pablo and Cañueto, Daniel and Steinbeck, Christoph},
url = {https://link.springer.com/article/10.1007/s11306-017-1242-7},
doi = {10.1007/s11306-017-1242-7},
year = {2017},
date = {2017-08-01},
journal = {Metabolomics},
volume = {13},
number = {9},
pages = {106},
publisher = {Springer US},
abstract = {The field of metabolomics has expanded greatly over the past two decades, both as an experimental science with applications in many areas, as well as in regards to data standards and bioinformatics so},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pèrez-Riverol, Yasset; Bai, Mingze; da Veiga Leprevost, Felipe; Squizzato, Silvano; Park, Young Mi; Haug, Kenneth; Carroll, Adam J; Spalding, Dylan; Paschall, Justin; Wang, Mingxun; Del-Toro, Noemi; Ternent, Tobias; Zhang, Peng; Buso, Nicola; Bandeira, Nuno; Deutsch, Eric W; Campbell, David S; Beavis, Ronald C; Salek, Reza M; Sarkans, Ugis; Petryszak, Robert; Keays, Maria; Fahy, Eoin; Sud, Manish; Subramaniam, Shankar; Barbera, Ariana; Jim'enez, Rafael C; Nesvizhskii, Alexey I; Sansone, Susanna-Assunta; Steinbeck, Christoph; Lopez, Rodrigo; Vizca'ino, Juan A; Ping, Peipei; Hermjakob, Henning
Discovering and linking public omics data sets using the Omics Discovery Index Journal Article
In: Nature Biotechnology, vol. 35, no. 5, pp. 406–409, 2017.
@article{PerezRiverol:2017ek,
title = {Discovering and linking public omics data sets using the Omics Discovery Index},
author = {Pèrez-Riverol, Yasset and Bai, Mingze and da Veiga Leprevost, Felipe and Squizzato, Silvano and Park, Young Mi and Haug, Kenneth and Carroll, Adam J and Spalding, Dylan and Paschall, Justin and Wang, Mingxun and Del-Toro, Noemi and Ternent, Tobias and Zhang, Peng and Buso, Nicola and Bandeira, Nuno and Deutsch, Eric W and Campbell, David S and Beavis, Ronald C and Salek, Reza M and Sarkans, Ugis and Petryszak, Robert and Keays, Maria and Fahy, Eoin and Sud, Manish and Subramaniam, Shankar and Barbera, Ariana and Jim{'e}nez, Rafael C and Nesvizhskii, Alexey I and Sansone, Susanna-Assunta and Steinbeck, Christoph and Lopez, Rodrigo and Vizca{'i}no, Juan A and Ping, Peipei and Hermjakob, Henning},
url = {http://www.nature.com/doifinder/10.1038/nbt.3790},
doi = {10.1038/nbt.3790},
year = {2017},
date = {2017-05-01},
journal = {Nature Biotechnology},
volume = {35},
number = {5},
pages = {406--409},
publisher = {Nature Research},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Haug, Kenneth; Salek, Reza M; Steinbeck, Christoph
Global open data management in metabolomics. Journal Article
In: Current Opinion in Chemical Biology, vol. 36, pp. 58–63, 2017.
@article{Haug:2017cb,
title = {Global open data management in metabolomics.},
author = {Haug, Kenneth and Salek, Reza M and Steinbeck, Christoph},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1367593116302083},
doi = {10.1016/j.cbpa.2016.12.024},
year = {2017},
date = {2017-02-01},
journal = {Current Opinion in Chemical Biology},
volume = {36},
pages = {58--63},
abstract = {Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way. Steady advancements in instrumentation towards high-throughput and highresolution methods have led to a revival of analytical chemistry methods for the measurement and analysis of the metabolome of organisms. This steady growth of metabolomics as a field is leading to a similar accumulation of big data across laboratories worldwide as can be observed in all of the other omics areas. This calls for the development of methods and technologies for handling and dealing with such large datasets, for efficiently distributing them and for enabling re-analysis. Here we describe the recently emerging ecosystem of global open-access databases and data exchange efforts between them, as well as the foundations and obstacles that enable or prevent the data sharing and reanalysis of this data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Larralde, Martin; Lawson, Thomas N; Weber, Ralf J M; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R; Steinbeck, Christoph; Salek, Reza M
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data. Journal Article
In: Bioinformatics, 2017.
@article{Larralde:2017di,
title = {mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.},
author = {Larralde, Martin and Lawson, Thomas N and Weber, Ralf J M and Moreno, Pablo and Haug, Kenneth and Rocca-Serra, Philippe and Viant, Mark R and Steinbeck, Christoph and Salek, Reza M},
url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx169},
doi = {10.1093/bioinformatics/btx169},
year = {2017},
date = {2017-01-01},
journal = {Bioinformatics},
abstract = {Summary:Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets.
Availability and Implementation:mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools . Documentation is available from http://2isa.readthedocs.io/en/latest/ .
Contact:reza.salek@ebi.ac.uk or isatools@googlegroups.com.
Supplementary information:Supplementary data are available at Bioinformatics online.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Availability and Implementation:mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools . Documentation is available from http://2isa.readthedocs.io/en/latest/ .
Contact:reza.salek@ebi.ac.uk or isatools@googlegroups.com.
Supplementary information:Supplementary data are available at Bioinformatics online.
Willighagen, Egon L; Mayfield, John W; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomás; Rojas-Chertó, Miquel; Spjuth, Ola; Torrance, Gilleain; Evelo, Chris T; Guha, Rajarshi; Steinbeck, Christoph
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching Journal Article
In: Journal of cheminformatics, vol. 9, no. 1, pp. 33, 2017.
@article{Willighagen:2017ge,
title = {The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching},
author = {Willighagen, Egon L and Mayfield, John W and Alvarsson, Jonathan and Berg, Arvid and Carlsson, Lars and Jeliazkova, Nina and Kuhn, Stefan and Pluskal, Tomás and Rojas-Chertó, Miquel and Spjuth, Ola and Torrance, Gilleain and Evelo, Chris T and Guha, Rajarshi and Steinbeck, Christoph},
url = {https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0220-4},
doi = {10.1186/s13321-017-0220-4},
year = {2017},
date = {2017-01-01},
journal = {Journal of cheminformatics},
volume = {9},
number = {1},
pages = {33},
publisher = {Springer International Publishing},
abstract = {The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10~years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, Janna; Steinbeck, Christoph
Ontologies in Chemoinformatics Book Section
In: Handbook of Computational Chemistry, pp. 2163–2181, Springer International Publishing, Cham, 2017, ISBN: 978-3-319-27281-8.
@incollection{Hastings:2017cf,
title = {Ontologies in Chemoinformatics},
author = {Hastings, Janna and Steinbeck, Christoph},
url = {http://link.springer.com/referenceworkentry/10.1007/978-3-319-27282-5_55/fulltext.html},
doi = {10.1007/978-3-319-27282-5_55},
isbn = {978-3-319-27281-8},
year = {2017},
date = {2017-01-01},
booktitle = {Handbook of Computational Chemistry},
pages = {2163--2181},
publisher = {Springer International Publishing},
address = {Cham},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Weber, Ralf J M; Lawson, Thomas N; Salek, Reza M; Ebbels, Timothy M D; Glen, Robert C; Goodacre, Royston; Griffin, Julian L; Haug, Kenneth; Koulman, Albert; Moreno, Pablo; Ralser, Markus; Steinbeck, Christoph; Dunn, Warwick B; Viant, Mark R
Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy. Journal Article
In: Metabolomics, vol. 13, no. 2, pp. 12, 2017.
@article{Weber:2017fga,
title = {Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.},
author = {Weber, Ralf J M and Lawson, Thomas N and Salek, Reza M and Ebbels, Timothy M D and Glen, Robert C and Goodacre, Royston and Griffin, Julian L and Haug, Kenneth and Koulman, Albert and Moreno, Pablo and Ralser, Markus and Steinbeck, Christoph and Dunn, Warwick B and Viant, Mark R},
url = {http://link.springer.com/10.1007/s11306-016-1147-x},
doi = {10.1007/s11306-016-1147-x},
year = {2017},
date = {2017-01-01},
journal = {Metabolomics},
volume = {13},
number = {2},
pages = {12},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Salek, Reza M; Conesa, Pablo; Cochrane, Keeva; Haug, Kenneth; Williams, Mark; Kale, Namrata; Moreno, Pablo; Jayaseelan, Kalai; Macias, Jose Ramon; Nainala, Venkata Chandrasekhar; Hall, Robert D; Reed, Laura K; Viant, Mark R; O'Donovan, Claire; Steinbeck, Christoph
Automated Assembly of Species Metabolomes through Data Submission into a Public Repository Journal Article
In: GigaScience, 2017.
@article{Salek:2017ex,
title = {Automated Assembly of Species Metabolomes through Data Submission into a Public Repository},
author = {Reza M Salek and Pablo Conesa and Keeva Cochrane and Kenneth Haug and Mark Williams and Namrata Kale and Pablo Moreno and Kalai Jayaseelan and Jose Ramon Macias and Venkata Chandrasekhar Nainala and Robert D Hall and Laura K Reed and Mark R Viant and Claire O'Donovan and Christoph Steinbeck},
url = {https://academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/gix062},
doi = {10.1093/gigascience/gix062},
year = {2017},
date = {2017-01-01},
journal = {GigaScience},
abstract = {Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2013
Foster, Joseph M; Moreno, Pablo; Fabregat, Antonio; Hermjakob, Henning; Steinbeck, Christoph; Apweiler, Rolf; Wakelam, Michael J O; Vizca'ino, Juan Antonio
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. Journal Article
In: PLoS ONE, vol. 8, no. 5, pp. e61951, 2013.
@article{Foster:2013bc,
title = {LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.},
author = {Foster, Joseph M and Moreno, Pablo and Fabregat, Antonio and Hermjakob, Henning and Steinbeck, Christoph and Apweiler, Rolf and Wakelam, Michael J O and Vizca{'i}no, Juan Antonio},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=23667450&retmode=ref&cmd=prlinks},
doi = {10.1371/journal.pone.0061951},
year = {2013},
date = {2013-01-01},
journal = {PLoS ONE},
volume = {8},
number = {5},
pages = {e61951},
abstract = {Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
De Matos, Paula; Cham, Jennifer A; Cao, Hong; Alcantara, Rafael; Rowland, Francis; Lopez, Rodrigo; Steinbeck, Christoph
The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics Journal Article
In: BMC Bioinformatics, vol. 14, no. 1, pp. 103, 2013.
@article{DeMatos:2013jp,
title = {The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics},
author = {De Matos, Paula and Cham, Jennifer A and Cao, Hong and Alcantara, Rafael and Rowland, Francis and Lopez, Rodrigo and Steinbeck, Christoph},
url = {http://www.biomedcentral.com/1471-2105/14/103},
doi = {10.1186/1471-2105-14-103},
year = {2013},
date = {2013-01-01},
journal = {BMC Bioinformatics},
volume = {14},
number = {1},
pages = {103},
publisher = {BioMed Central Ltd},
abstract = {User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users' requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, 'canvas sort' card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2012
Markley, John L; Akutsu, Hideo; Asakura, Tetsuo; Baldus, Marc; Boelens, Rolf; Bonvin, Alexandre; Kaptein, Robert; Bax, Ad; Bezsonova, Irina; Gryk, Michael R; Hoch, Jeffrey C; Korzhnev, Dmitry M; Maciejewski, Mark W; Case, Dave; Chazin, Walter J; Cross, Timothy A; Dames, Sonja; Kessler, Horst; Lange, Oliver; Madl, Tobias; Reif, Bernd; Sattler, Michael; Eliezer, David; Fersht, Alan; Forman-Kay, Julie; Kay, Lewis E; Fraser, James; Gross, John; Kortemme, Tanja; Sali, Andrej; Fujiwara, Toshimichi; Gardner, Kevin; Luo, Xuelian; Rizo-Rey, Jose; Rosen, Michael; Gil, Roberto R; Ho, Chien; Rule, Gordon; Gronenborn, Angela M; Ishima, Rieko; Klein-Seetharaman, Judith; Tang, Pei; van der Wel, Patrick; Xu, Yan; Grzesiek, Stephan; Hiller, Sebastian; Seelig, Joachim; Laue, Ernest D; Mott, Helen; Nietlispach, Daniel; Barsukov, Igor; Lian, Lu-Yun; Middleton, David; Blumenschein, Tharin; Moore, Geoffrey; Campbell, Iain; Schnell, Jason; Vakonakis, Ioannis John; Watts, Anthony; Conte, Maria R; Mason, James; Pfuhl, Mark; Sanderson, Mark R; Craven, Jeremy; Williamson, Michael; Dominguez, Cyril; Roberts, Gordon; Günther, Ulrich; Overduin, Michael; Werner, Joern; Williamson, Philip; Blindauer, Claudia; Crump, Matthew; Driscoll, Paul; Frenkiel, Tom; Golovanov, Alexander; Matthews, Steve; Parkinson, John; Uhrin, Dusan; Williams, Mark; Neuhaus, David; Oschkinat, Hartmut; Ramos, Andres; Shaw, David E; Steinbeck, Christoph; Vendruscolo, Michele; Vuister, Geerten W; Walters, Kylie J; Weinstein, Harel; Wüthrich, Kurt; Yokoyama, Shigeyuki
In support of the BMRB. Journal Article
In: Nature structural & molecular biology, vol. 19, no. 9, pp. 854–860, 2012.
@article{Markley:2012jf,
title = {In support of the BMRB.},
author = {Markley, John L and Akutsu, Hideo and Asakura, Tetsuo and Baldus, Marc and Boelens, Rolf and Bonvin, Alexandre and Kaptein, Robert and Bax, Ad and Bezsonova, Irina and Gryk, Michael R and Hoch, Jeffrey C and Korzhnev, Dmitry M and Maciejewski, Mark W and Case, Dave and Chazin, Walter J and Cross, Timothy A and Dames, Sonja and Kessler, Horst and Lange, Oliver and Madl, Tobias and Reif, Bernd and Sattler, Michael and Eliezer, David and Fersht, Alan and Forman-Kay, Julie and Kay, Lewis E and Fraser, James and Gross, John and Kortemme, Tanja and Sali, Andrej and Fujiwara, Toshimichi and Gardner, Kevin and Luo, Xuelian and Rizo-Rey, Jose and Rosen, Michael and Gil, Roberto R and Ho, Chien and Rule, Gordon and Gronenborn, Angela M and Ishima, Rieko and Klein-Seetharaman, Judith and Tang, Pei and van der Wel, Patrick and Xu, Yan and Grzesiek, Stephan and Hiller, Sebastian and Seelig, Joachim and Laue, Ernest D and Mott, Helen and Nietlispach, Daniel and Barsukov, Igor and Lian, Lu-Yun and Middleton, David and Blumenschein, Tharin and Moore, Geoffrey and Campbell, Iain and Schnell, Jason and Vakonakis, Ioannis John and Watts, Anthony and Conte, Maria R and Mason, James and Pfuhl, Mark and Sanderson, Mark R and Craven, Jeremy and Williamson, Michael and Dominguez, Cyril and Roberts, Gordon and G{ü}nther, Ulrich and Overduin, Michael and Werner, Joern and Williamson, Philip and Blindauer, Claudia and Crump, Matthew and Driscoll, Paul and Frenkiel, Tom and Golovanov, Alexander and Matthews, Steve and Parkinson, John and Uhrin, Dusan and Williams, Mark and Neuhaus, David and Oschkinat, Hartmut and Ramos, Andres and Shaw, David E and Steinbeck, Christoph and Vendruscolo, Michele and Vuister, Geerten W and Walters, Kylie J and Weinstein, Harel and W{ü}thrich, Kurt and Yokoyama, Shigeyuki},
url = {http://www.nature.com/doifinder/10.1038/nsmb.2371},
doi = {10.1038/nsmb.2371},
year = {2012},
date = {2012-09-01},
journal = {Nature structural & molecular biology},
volume = {19},
number = {9},
pages = {854--860},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Steinbeck, Christoph; Conesa, Pablo; Haug, Kenneth; Mahendraker, Tejasvi; Williams, Mark; Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Salek, Reza M; Griffin, Julian L
MetaboLights: towards a new COSMOS of metabolomics data management Journal Article
In: Metabolomics, vol. 8, no. 5, pp. 757–760, 2012.
@article{steinbeck2012metabolights,
title = {MetaboLights: towards a new COSMOS of metabolomics data management},
author = {Steinbeck, Christoph and Conesa, Pablo and Haug, Kenneth and Mahendraker, Tejasvi and Williams, Mark and Maguire, Eamonn and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Salek, Reza M and Griffin, Julian L},
url = {http://www.springerlink.com/index/10.1007/s11306-012-0462-0},
doi = {10.1007/s11306-012-0462-0},
year = {2012},
date = {2012-09-01},
journal = {Metabolomics},
volume = {8},
number = {5},
pages = {757--760},
abstract = {Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pavelin, Katrina; Cham, Jennifer A; De Matos, Paula; Brooksbank, Cath; Cameron, Graham; Steinbeck, Christoph
Bioinformatics Meets User-Centred Design: A Perspective Journal Article
In: PLoS Computational Biology, vol. 8, no. 7, pp. e1002554, 2012.
@article{pavelin2012bioinformatics,
title = {Bioinformatics Meets User-Centred Design: A Perspective},
author = {Pavelin, Katrina and Cham, Jennifer A and De Matos, Paula and Brooksbank, Cath and Cameron, Graham and Steinbeck, Christoph},
url = {http://dx.plos.org/10.1371/journal.pcbi.1002554.pdf},
doi = {10.1371/journal.pcbi.1002554},
year = {2012},
date = {2012-07-01},
journal = {PLoS Computational Biology},
volume = {8},
number = {7},
pages = {e1002554},
publisher = {Public Library of Science},
abstract = {Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn; Maguire, Eamonn; Taylor, Chris; Hofmann, Oliver; Fang, Hong; Neumann, Steffen; Tong, Weida; Amaral-Zettler, Linda; Begley, Kimberly; Booth, Tim; Bougueleret, Lydie; Burns, Gully; Chapman, Brad; Clark, Tim; Coleman, Lee-Ann; Copeland, Jay; Das, Sudeshna; de Daruvar, Antoine; De Matos, Paula; Dix, Ian; Edmunds, Scott; Evelo, Chris T; Forster, Mark J; Gaudet, Pascale; Gilbert, Jack; Goble, Carole; Griffin, Julian L; Jacob, Daniel; Kleinjans, Jos; Harland, Lee; Haug, Kenneth; Hermjakob, Henning; Sui, Shannan J Ho; Laederach, Alain; Liang, Shaoguang; Marshall, Stephen; McGrath, Annette; Merrill, Emily; Reilly, Dorothy; Roux, Magali; Shamu, Caroline E; Shang, Catherine A; Steinbeck, Christoph; Trefethen, Anne; Williams-Jones, Bryn; Wolstencroft, Katherine; Xenarios, Ioannis; Hide, Winston
Toward interoperable bioscience data Journal Article
In: Nat Genet, vol. 44, no. 2, pp. 121–126, 2012.
@article{sansone2012toward,
title = {Toward interoperable bioscience data},
author = {Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Field, Dawn and Maguire, Eamonn and Taylor, Chris and Hofmann, Oliver and Fang, Hong and Neumann, Steffen and Tong, Weida and Amaral-Zettler, Linda and Begley, Kimberly and Booth, Tim and Bougueleret, Lydie and Burns, Gully and Chapman, Brad and Clark, Tim and Coleman, Lee-Ann and Copeland, Jay and Das, Sudeshna and de Daruvar, Antoine and De Matos, Paula and Dix, Ian and Edmunds, Scott and Evelo, Chris T and Forster, Mark J and Gaudet, Pascale and Gilbert, Jack and Goble, Carole and Griffin, Julian L and Jacob, Daniel and Kleinjans, Jos and Harland, Lee and Haug, Kenneth and Hermjakob, Henning and Sui, Shannan J Ho and Laederach, Alain and Liang, Shaoguang and Marshall, Stephen and McGrath, Annette and Merrill, Emily and Reilly, Dorothy and Roux, Magali and Shamu, Caroline E and Shang, Catherine A and Steinbeck, Christoph and Trefethen, Anne and Williams-Jones, Bryn and Wolstencroft, Katherine and Xenarios, Ioannis and Hide, Winston},
url = {http://www.nature.com/doifinder/10.1038/ng.1054},
doi = {10.1038/ng.1054},
year = {2012},
date = {2012-01-01},
journal = {Nat Genet},
volume = {44},
number = {2},
pages = {121--126},
publisher = {Nature Publishing Group},
abstract = {To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chepelev, Leonid L; Hastings, Janna; Ennis, Marcus; Steinbeck, Christoph; Dumontier, Michel
Self-organizing ontology of biochemically relevant small molecules. Journal Article
In: BMC Bioinformatics, vol. 13, no. 1, pp. 3, 2012.
@article{chepelev2012self,
title = {Self-organizing ontology of biochemically relevant small molecules.},
author = {Chepelev, Leonid L and Hastings, Janna and Ennis, Marcus and Steinbeck, Christoph and Dumontier, Michel},
url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-3},
doi = {10.1186/1471-2105-13-3},
year = {2012},
date = {2012-01-01},
journal = {BMC Bioinformatics},
volume = {13},
number = {1},
pages = {3},
abstract = {BACKGROUND:The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest.
RESULTS:To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development.
CONCLUSIONS:We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
RESULTS:To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development.
CONCLUSIONS:We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development.
Hastings, Janna; Magka, Despoina; Batchelor, Colin; Duan, Lian; Stevens, Robert; Ennis, Marcus; Steinbeck, Christoph
Structure-based classification and ontology in chemistry. Journal Article
In: Journal of cheminformatics, vol. 4, no. 1, pp. 8, 2012.
@article{hastings2012structure,
title = {Structure-based classification and ontology in chemistry.},
author = {Hastings, Janna and Magka, Despoina and Batchelor, Colin and Duan, Lian and Stevens, Robert and Ennis, Marcus and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=22480202&retmode=ref&cmd=prlinks},
doi = {10.1186/1758-2946-4-8},
year = {2012},
date = {2012-01-01},
journal = {Journal of cheminformatics},
volume = {4},
number = {1},
pages = {8},
abstract = {BACKGROUND:Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures), while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. RESULTS:We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. CONCLUSION:Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic-based tools. For the task of automatic structure-based classification of chemical entities, essential to managing the vast swathes of chemical data being brought online, systems which are capable of hybrid reasoning combining several different approaches are crucial. We provide a thorough review of the available tools and methodologies, and identify areas of open research.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alcantara, Rafael; Axelsen, Kristian B; Morgat, Anne; Belda, Eugeni; Coudert, Elisabeth; Bridge, Alan; Cao, Hong; De Matos, Paula; Ennis, Marcus; Turner, Steve; Owen, Gareth; Bougueleret, Lydie; Xenarios, Ioannis; Steinbeck, Christoph
Rhea--a manually curated resource of biochemical reactions. Journal Article
In: Nucleic Acids Research, vol. 40, no. Database issue, pp. D754–60, 2012.
@article{alcantara2012rhea,
title = {Rhea--a manually curated resource of biochemical reactions.},
author = {Alcantara, Rafael and Axelsen, Kristian B and Morgat, Anne and Belda, Eugeni and Coudert, Elisabeth and Bridge, Alan and Cao, Hong and De Matos, Paula and Ennis, Marcus and Turner, Steve and Owen, Gareth and Bougueleret, Lydie and Xenarios, Ioannis and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=22135291&retmode=ref&cmd=prlinks},
doi = {10.1093/nar/gkr1126},
year = {2012},
date = {2012-01-01},
journal = {Nucleic Acids Research},
volume = {40},
number = {Database issue},
pages = {D754--60},
abstract = {Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions. Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference. Rhea includes enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list), transport reactions and spontaneously occurring reactions. Rhea reactions are described using chemical species from the Chemical Entities of Biological Interest ontology (ChEBI) and are stoichiometrically balanced for mass and charge. They are extensively manually curated with links to source literature and other public resources on metabolism including enzyme and pathway databases. This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic networks and models.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jayaseelan, Kalai Vanii; Moreno, Pablo; Truszkowski, Andreas; Ertl, Peter; Steinbeck, Christoph
Natural product-likeness score revisited: an open-source, open-data implementation. Journal Article
In: BMC Bioinformatics, vol. 13, no. 1, pp. 106, 2012.
@article{Jayaseelan:2012ig,
title = {Natural product-likeness score revisited: an open-source, open-data implementation.},
author = {Jayaseelan, Kalai Vanii and Moreno, Pablo and Truszkowski, Andreas and Ertl, Peter and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=22607271&retmode=ref&cmd=prlinks},
doi = {10.1186/1471-2105-13-106},
year = {2012},
date = {2012-01-01},
journal = {BMC Bioinformatics},
volume = {13},
number = {1},
pages = {106},
abstract = {BACKGROUND:Natural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead compounds. A closed source implementation of a natural product-likeness score, that finds its application in virtual screening, library design and compound selection, has been previously reported by one of us. In this note, we report an open-source and open-data re-implementation of this scoring system, illustrate its efficiency in ranking small molecules for natural product likeness and discuss its potential applications. RESULTS:The Natural-Product-Likeness scoring system is implemented as Taverna 2.2 workflows, and is available under Creative Commons Attribution-Share Alike 3.0 Unported License at http://www.myexperiment.org/packs/183.html. It is also available for download as executable standalone java package from http://sourceforge.net/projects/np-likeness/under Academic Free License. CONCLUSIONS:Our open-source, open-data Natural-Product-Likeness scoring system can be used as a filter for metabolites in Computer Assisted Structure Elucidation or to select natural-product-like molecules from molecular libraries for the use as leads in drug discovery.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, Janna; Josephs, Zara; Steinbeck, Christoph
Accessing and using chemical property databases. Journal Article
In: Methods in molecular biology (Clifton, N.J.), vol. 929, no. Chapter 9, pp. 193–219, 2012, ISBN: 978-1-62703-049-6.
@article{Hastings:2012ft,
title = {Accessing and using chemical property databases.},
author = {Hastings, Janna and Josephs, Zara and Steinbeck, Christoph},
url = {http://link.springer.com/10.1007/978-1-62703-050-2_9},
doi = {10.1007/978-1-62703-050-2_9},
isbn = {978-1-62703-049-6},
year = {2012},
date = {2012-01-01},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {929},
number = {Chapter 9},
pages = {193--219},
publisher = {Humana Press},
address = {Totowa, NJ},
abstract = {Chemical compounds participate in all the processes of life. Understanding the complex interactions of small molecules such as metabolites and drugs and the biological macromolecules that consume and produce them is key to gaining a wider understanding in a systemic context. Chemical property databases collect information on the biological effects and physicochemical properties of chemical entities. Accessing and using such databases is key to understanding the chemistry of toxic molecules. In this chapter, we present methods to search, understand, download, and manipulate the wealth of information available in public chemical property databases, with particular focus on the database of Chemical Entities of Biological Interest (ChEBI).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
De Matos, Paula; Adams, Nico; Hastings, Janna; Moreno, Pablo; Steinbeck, Christoph
A database for chemical proteomics: ChEBI. Journal Article
In: Methods in molecular biology (Clifton, N.J.), vol. 803, no. Chapter 19, pp. 273–296, 2012, ISBN: 978-1-61779-363-9.
@article{de2012database,
title = {A database for chemical proteomics: ChEBI.},
author = {De Matos, Paula and Adams, Nico and Hastings, Janna and Moreno, Pablo and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=22065232&retmode=ref&cmd=prlinks},
doi = {10.1007/978-1-61779-364-6_19},
isbn = {978-1-61779-363-9},
year = {2012},
date = {2012-01-01},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {803},
number = {Chapter 19},
pages = {273--296},
publisher = {Humana Press},
address = {Totowa, NJ},
abstract = {Chemical proteomics is concerned with the identification of protein targets interacting with small molecules. Hence, the availability of a high quality and free resource storing small molecules is essential for the future development of 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, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. These entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. In addition, ChEBI contains a chemical ontology which relates the small molecules with each other thereby making it easier for users to discover data. The ontology also describes the biological roles that the small molecules are active in. The ChEBI database also provides a central reference point in which to access a variety of bioinformatics data points such as pathways and their biochemical reactions; expression data; protein sequence and structures.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2011
Orchard, Sandra; Al-Lazikani, Bissan; Bryant, Steve; Clark, Dominic; Calder, Elizabeth; Dix, Ian; Engkvist, Ola; Forster, Mark; Gaulton, Anna; Gilson, Michael; Glen, Robert; Grigorov, Martin; Hammond-Kosack, Kim; Harland, Lee; Hopkins, Andrew; Larminie, Christopher; Lynch, Nick; Mann, Romeena K; Murray-Rust, Peter; Lo Piparo, Elena; Southan, Christopher; Steinbeck, Christoph; Wishart, David; Hermjakob, Henning; Overington, John; Thornton, Janet
Minimum information about a bioactive entity (MIABE) Journal Article
In: Nature Reviews Drug Discovery, vol. 10, no. 9, pp. 661–669, 2011.
@article{orchard2011minimum,
title = {Minimum information about a bioactive entity (MIABE)},
author = {Orchard, Sandra and Al-Lazikani, Bissan and Bryant, Steve and Clark, Dominic and Calder, Elizabeth and Dix, Ian and Engkvist, Ola and Forster, Mark and Gaulton, Anna and Gilson, Michael and Glen, Robert and Grigorov, Martin and Hammond-Kosack, Kim and Harland, Lee and Hopkins, Andrew and Larminie, Christopher and Lynch, Nick and Mann, Romeena K and Murray-Rust, Peter and Lo Piparo, Elena and Southan, Christopher and Steinbeck, Christoph and Wishart, David and Hermjakob, Henning and Overington, John and Thornton, Janet},
url = {http://www.nature.com/doifinder/10.1038/nrd3503},
doi = {10.1038/nrd3503},
year = {2011},
date = {2011-01-01},
journal = {Nature Reviews Drug Discovery},
volume = {10},
number = {9},
pages = {661--669},
publisher = {Nature Publishing Group},
abstract = {Bioactive molecules such as drugs, pesticides and food additives are produced in large numbers by many commercial and academic groups around the world. Enormous quantities of data are generated on the biological properties and quality of these molecules. Access to such data - both on licensed and commercially available compounds, and also on those that fail during development - is crucial for understanding how improved molecules could be developed. For example, computational analysis of aggregated data on molecules that are investigated in drug discovery programmes has led to a greater understanding of the properties of successful drugs. However, the information required to perform these analyses is rarely published, and when it is made available it is often missing crucial data or is in a format that is inappropriate for efficient data-mining. Here, we propose a solution: the definition of reporting guidelines for bioactive entities - the Minimum Information About a Bioactive Entity (MIABE) - which has been developed by representatives of pharmaceutical companies, data resource providers and academic groups.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, J; Batchelor, C R; Steinbeck, C; Schulz, S
IOS Press Ebooks - Modularization Requirements in Bio-Ontologies: A Case Study of ChEbi Journal Article
In: WoMO, 2011.
@article{Hastings:2011hx,
title = {IOS Press Ebooks - Modularization Requirements in Bio-Ontologies: A Case Study of ChEbi},
author = {Hastings, J and Batchelor, C R and Steinbeck, C and Schulz, S},
url = {http://ebooks.iospress.nl/publication/6516},
doi = {10.3233/978-1-60750-799-4-63},
year = {2011},
date = {2011-01-01},
journal = {WoMO},
abstract = {Abstract Bio-ontologies such as the Gene Ontology and ChEBI are characterized by large sizes and relatively low expressivity. However, ongoing efforts aim to increase the formalisation of these ontologies by adding full definitions (equivalent classes). This increase in complexity results in a decrease of performance for standard reasoning tasks. In this paper, we explore the contribution which modularization can play in the evolution of ...},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Griffin, Julian L; Atherton, Helen J; Steinbeck, Chris; Salek, Reza M
A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.". Journal Article
In: BMC Research Notes, vol. 4, no. 1, pp. 272, 2011.
@article{Griffin:2011es,
title = {A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".},
author = {Griffin, Julian L and Atherton, Helen J and Steinbeck, Chris and Salek, Reza M},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=21801423&retmode=ref&cmd=prlinks},
doi = {10.1186/1756-0500-4-272},
year = {2011},
date = {2011-01-01},
journal = {BMC Research Notes},
volume = {4},
number = {1},
pages = {272},
abstract = {BACKGROUND:Metabolomics is a rapidly developing functional genomic tool that has a wide range of applications in diverse fields in biology and medicine. However, unlike transcriptomics and proteomics there is currently no central repository for the depositing of data despite efforts by the Metabolomics Standard Initiative (MSI) to develop a standardised description of a metabolomic experiment. FINDINGS:In this manuscript we describe how the MSI description has been applied to a published dataset involving the identification of cross-species metabolic biomarkers associated with type II diabetes. The study describes sample collection of urine from mice, rats and human volunteers, and the subsequent acquisition of data by high resolution 1H NMR spectroscopy. The metadata is described to demonstrate how the MSI descriptions could be applied in a manuscript and the spectra have also been made available for the mouse and rat studies to allow others to process the data. CONCLUSIONS:The intention of this manuscript is to stimulate discussion as to whether the MSI description is sufficient to describe the metadata associated with metabolomic experiments and encourage others to make their data available to other researchers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, Janna; Batchelor, Colin; Neuhaus, Fabian; Steinbeck, Christoph
Whattextquoterights in an textquoteleftis abouttextquoterightlink? Chemical diagrams and the IAO Journal Article
In: Proceedings of the International Conference on Biomedical Ontology (ICBO2011), Buffalo, USA, 2011.
@article{hastings2011s,
title = {Whattextquoterights in an textquoteleftis abouttextquoterightlink? Chemical diagrams and the IAO},
author = {Hastings, Janna and Batchelor, Colin and Neuhaus, Fabian and Steinbeck, Christoph},
url = {http://www.google.de/search?client=safari&rls=10_7_4&q=Whats+in+an+is+aboutlink+Chemical+diagrams+and+the+IAO&ie=UTF-8&oe=UTF-8&redir_esc=&ei=Mvm5ULHuCKyL4gSDi4CoCg},
year = {2011},
date = {2011-01-01},
journal = {Proceedings of the International Conference on Biomedical Ontology (ICBO2011), Buffalo, USA},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
O'Boyle, Noel M; Guha, Rajarshi; Willighagen, Egon L; Adams, Samuel E; Alvarsson, Jonathan; Bradley, Jean-Claude; Filippov, Igor V; Hanson, Robert M; Hanwell, Marcus D; Hutchison, Geoffrey R; James, Craig A; Jeliazkova, Nina; Lang, Andrew Sid; Langner, Karol M; Lonie, David C; Lowe, Daniel M; Pansanel, Jerome; Pavlov, Dmitry; Spjuth, Ola; Steinbeck, Christoph; Tenderholt, Adam L; Theisen, Kevin J; Murray-Rust, Peter
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal Article
In: Journal of cheminformatics, vol. 3, no. 1, pp. 37, 2011.
@article{o2011open,
title = {Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.},
author = {O'Boyle, Noel M and Guha, Rajarshi and Willighagen, Egon L and Adams, Samuel E and Alvarsson, Jonathan and Bradley, Jean-Claude and Filippov, Igor V and Hanson, Robert M and Hanwell, Marcus D and Hutchison, Geoffrey R and James, Craig A and Jeliazkova, Nina and Lang, Andrew Sid and Langner, Karol M and Lonie, David C and Lowe, Daniel M and Pansanel, Jerome and Pavlov, Dmitry and Spjuth, Ola and Steinbeck, Christoph and Tenderholt, Adam L and Theisen, Kevin J and Murray-Rust, Peter},
url = {http://www.jcheminf.com/content/3/1/37},
doi = {10.1186/1758-2946-3-37},
year = {2011},
date = {2011-01-01},
journal = {Journal of cheminformatics},
volume = {3},
number = {1},
pages = {37},
abstract = {BACKGROUND:The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. RESULTS:This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. CONCLUSIONS:We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Truszkowski, Andreas; Jayaseelan, Kalai Vanii; Neumann, Stefan; Willighagen, Egon L; Zielesny, Achim; Steinbeck, Christoph
New developments on the cheminformatics open workflow environment CDK-Taverna. Journal Article
In: Journal of cheminformatics, vol. 3, no. 1, pp. 54, 2011.
@article{truszkowski2011new,
title = {New developments on the cheminformatics open workflow environment CDK-Taverna.},
author = {Truszkowski, Andreas and Jayaseelan, Kalai Vanii and Neumann, Stefan and Willighagen, Egon L and Zielesny, Achim and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=22166170&retmode=ref&cmd=prlinks},
doi = {10.1186/1758-2946-3-54},
year = {2011},
date = {2011-01-01},
journal = {Journal of cheminformatics},
volume = {3},
number = {1},
pages = {54},
abstract = {BACKGROUND:The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Legotexttrademark-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public. RESULTS:The CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios. CONCLUSIONS:CDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Taverna community and published on myexperiment.org enables molecular scientists to quickly calculate, process and analyse molecular data as typically found in e.g. today's systems biology scenarios.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. Journal Article
In: PLoS ONE, vol. 6, no. 10, pp. e25513, 2011.
@article{hastings2011chemical,
title = {The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.},
author = {Hastings, Janna and Chepelev, Leonid and Willighagen, Egon and Adams, Nico and Steinbeck, Christoph and Dumontier, Michel},
url = {http://dx.plos.org/10.1371/journal.pone.0025513.pdf},
doi = {10.1371/journal.pone.0025513},
year = {2011},
date = {2011-01-01},
journal = {PLoS ONE},
volume = {6},
number = {10},
pages = {e25513},
abstract = {Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2010
Apweiler, Rolf; Armstrong, Richard; Bairoch, Amos; Cornish-Bowden, Athel; Halling, Peter J; Hofmeyr, Jan-Hendrik S; Kettner, Carsten; Leyh, Thomas S; Rohwer, Johann; Schomburg, Dietmar; Steinbeck, Christoph; Tipton, Keith
A large-scale protein-function database. Journal Article
In: Nature Chemical Biology, vol. 6, no. 11, pp. 785–785, 2010.
@article{apweiler2010large,
title = {A large-scale protein-function database.},
author = {Apweiler, Rolf and Armstrong, Richard and Bairoch, Amos and Cornish-Bowden, Athel and Halling, Peter J and Hofmeyr, Jan-Hendrik S and Kettner, Carsten and Leyh, Thomas S and Rohwer, Johann and Schomburg, Dietmar and Steinbeck, Christoph and Tipton, Keith},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=20956966&retmode=ref&cmd=prlinks},
doi = {10.1038/nchembio.460},
year = {2010},
date = {2010-11-01},
journal = {Nature Chemical Biology},
volume = {6},
number = {11},
pages = {785--785},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, Janna; Batchelor, Colin; Steinbeck, Christoph; Schulz, Stefan
What are chemical structures and their relations? Journal Article
In: pp. 257–270, 2010, ISBN: 978-1-60750-534-1.
@article{Hastings:2010uk,
title = {What are chemical structures and their relations?},
author = {Hastings, Janna and Batchelor, Colin and Steinbeck, Christoph and Schulz, Stefan},
url = {http://dl.acm.org/citation.cfm?id=1804715.1804742},
isbn = {978-1-60750-534-1},
year = {2010},
date = {2010-07-01},
pages = {257--270},
publisher = {IOS Press},
abstract = {Abstract In chemistry, advances in computational technologies have allowed research into molecules that have not been synthesized yet, and may never be, to become widespread. These are described in terms of their structures, which are expressed as chemical graphs. ...},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Griffin, Julian L; Steinbeck, Christoph
So what have data standards ever done for us? The view from metabolomics. Journal Article
In: Genome medicine, vol. 2, no. 6, pp. 38, 2010.
@article{griffin2010so,
title = {So what have data standards ever done for us? The view from metabolomics.},
author = {Griffin, Julian L and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=20587079&retmode=ref&cmd=prlinks},
doi = {10.1186/gm159},
year = {2010},
date = {2010-01-01},
journal = {Genome medicine},
volume = {2},
number = {6},
pages = {38},
abstract = {The standardization of reporting of data promises to revolutionize biology by allowing community access to data generated in laboratories across the globe. This approach has already influenced genomics and transcriptomics. Projects that have previously been viewed as being too big to implement can now be distributed across multiple sites. There are now public databases for gene sequences, transcriptomic profiling and proteomic experiments. However, progress in the metabolomic community has seemed to falter recently, and whereas there are ontologies to describe the metadata for metabolomics there are still no central repositories for the datasets themselves. Here, we examine some of the challenges and potential benefits of further efforts towards data standardization in metabolomics and metabonomics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, Janna; Dumontier, Michel; Hull, Duncan; Horridge, Matthew; Steinbeck, Christoph; Sattler, Ulrike; Stevens, Robert; Hörne, Tertia; Britz, Katarina
Representing chemicals using OWL, description graphs and rules Journal Article
In: CEUR Workshop Proceedings, vol. 614, 2010.
@article{hastings2010representing,
title = {Representing chemicals using OWL, description graphs and rules},
author = {Hastings, Janna and Dumontier, Michel and Hull, Duncan and Horridge, Matthew and Steinbeck, Christoph and Sattler, Ulrike and Stevens, Robert and H{ö}rne, Tertia and Britz, Katarina},
url = {http://researchspace.csir.co.za/dspace/handle/10204/4919},
year = {2010},
date = {2010-01-01},
journal = {CEUR Workshop Proceedings},
volume = {614},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kuhn, Thomas; Willighagen, Egon L; Zielesny, Achim; Steinbeck, Christoph
CDK-Taverna: an open workflow environment for cheminformatics. Journal Article
In: BMC Bioinformatics, vol. 11, no. 1, pp. 159, 2010.
@article{kuhn2010cdk,
title = {CDK-Taverna: an open workflow environment for cheminformatics.},
author = {Kuhn, Thomas and Willighagen, Egon L and Zielesny, Achim and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=20346188&retmode=ref&cmd=prlinks},
doi = {10.1186/1471-2105-11-159},
year = {2010},
date = {2010-01-01},
journal = {BMC Bioinformatics},
volume = {11},
number = {1},
pages = {159},
publisher = {BioMed Central},
abstract = {BACKGROUND:Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.
RESULTS:Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.
CONCLUSIONS:The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
RESULTS:Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.
CONCLUSIONS:The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.
De Matos, Paula; Alcantara, Rafael; Dekker, Adriano; Ennis, Marcus; Hastings, Janna; Haug, Kenneth; Spiteri, Inmaculada; Turner, Steve; Steinbeck, Christoph
Chemical Entities of Biological Interest: an update. Journal Article
In: Nucleic Acids Research, vol. 38, no. Database issue, pp. D249–54, 2010.
@article{de2010chemical,
title = {Chemical Entities of Biological Interest: an update.},
author = {De Matos, Paula and Alcantara, Rafael and Dekker, Adriano and Ennis, Marcus and Hastings, Janna and Haug, Kenneth and Spiteri, Inmaculada and Turner, Steve and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19854951&retmode=ref&cmd=prlinks},
doi = {10.1093/nar/gkp886},
year = {2010},
date = {2010-01-01},
journal = {Nucleic Acids Research},
volume = {38},
number = {Database issue},
pages = {D249--54},
abstract = {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 products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by 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 molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/. This article reports on new features in ChEBI since the last NAR report in 2007, including substructure and similarity searching, a submission tool for authoring of ChEBI datasets by the community and a 30-fold increase in the number of chemical structures stored in ChEBI.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hastings, Janna; Steinbeck, Christoph; Jansen, Ludger; Schulz, Stefan
Substance concentrations as conditions for the realization of dispositions Journal Article
In: Semantic Applications in Life Sciences: Proceedings of the 4th International Workshop on Formal Biomedical Knowledge Representation, KR-MED, pp. 9–10, 2010.
@article{hastings2010substance,
title = {Substance concentrations as conditions for the realization of dispositions},
author = {Hastings, Janna and Steinbeck, Christoph and Jansen, Ludger and Schulz, Stefan},
url = {http://www.google.de/search?client=safari&rls=10_7_4&q=Substance+concentrations+as+conditions+for+the+realization+of+dispositions&ie=UTF-8&oe=UTF-8&redir_esc=&ei=Mvm5UIjSE-nE4gTnx4DACA},
year = {2010},
date = {2010-01-01},
journal = {Semantic Applications in Life Sciences: Proceedings of the 4th International Workshop on Formal Biomedical Knowledge Representation, KR-MED},
pages = {9--10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Batchelor, Colin; Hastings, Janna; Steinbeck, Christoph
Ontological dependence, dispositions and institutional reality in chemistry Journal Article
In: Proceeding of the 2010 conference on Formal Ontology in Information Systems, pp. 271–284, 2010.
@article{batchelor2010ontological,
title = {Ontological dependence, dispositions and institutional reality in chemistry},
author = {Batchelor, Colin and Hastings, Janna and Steinbeck, Christoph},
url = {http://www.google.de/search?client=safari&rls=10_7_4&q=Ontological+dependence+dispositions+and+institutional+reality+in+chemistry&ie=UTF-8&oe=UTF-8&redir_esc=&ei=Mvm5UOfuEcSJ4ATM8oH4Aw},
year = {2010},
date = {2010-01-01},
journal = {Proceeding of the 2010 conference on Formal Ontology in Information Systems},
pages = {271--284},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2009
Rijnbeek, Mark; Steinbeck, Christoph
OrChem - An open source chemistry search engine for Oracle(R). Journal Article
In: Journal of cheminformatics, vol. 1, no. 1, pp. 17, 2009.
@article{Rijnbeek:2009jy,
title = {OrChem - An open source chemistry search engine for Oracle(R).},
author = {Rijnbeek, Mark and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=20298521&retmode=ref&cmd=prlinks},
doi = {10.1186/1758-2946-1-17},
year = {2009},
date = {2009-01-01},
journal = {Journal of cheminformatics},
volume = {1},
number = {1},
pages = {17},
abstract = {UNLABELLED:ABSTRACT: BACKGROUND:Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. RESULTS:Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. AVAILABILITY:OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Spjuth, Ola; Alvarsson, Jonathan; Berg, Arvid; Eklund, Martin; Kuhn, Stefan; Masak, Carl; Torrance, Gilleain; Wagener, Johannes; Willighagen, Egon L; Steinbeck, Christoph; Wikberg, Jarl E S
Bioclipse 2: a scriptable integration platform for the life sciences. Journal Article
In: BMC Bioinformatics, vol. 10, no. 1, pp. 397, 2009.
@article{spjuth2009bioclipse,
title = {Bioclipse 2: a scriptable integration platform for the life sciences.},
author = {Spjuth, Ola and Alvarsson, Jonathan and Berg, Arvid and Eklund, Martin and Kuhn, Stefan and Masak, Carl and Torrance, Gilleain and Wagener, Johannes and Willighagen, Egon L and Steinbeck, Christoph and Wikberg, Jarl E S},
url = {http://www.biomedcentral.com/1471-2105/10/397},
doi = {10.1186/1471-2105-10-397},
year = {2009},
date = {2009-01-01},
journal = {BMC Bioinformatics},
volume = {10},
number = {1},
pages = {397},
abstract = {BACKGROUND:Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks. RESULTS:Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments. CONCLUSION:Bioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today's powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked (Web/Cloud) services for more demanding calculations or retrieval of data. The fact that Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, making it easy to add new algorithms, visualizations, as well as scripting commands. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative research.Bioclipse 2 is released under the Eclipse Public License (EPL), a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2008
Blinov, K A; Smurnyy, Y D; Elyashberg, M E; Churanova, T S; Kvasha, M; Steinbeck, C; Lefebvre, B A; Williams, A J
Performance validation of neural network based (13)c NMR prediction using a publicly available data source. Journal Article
In: Journal of Chemical Information and Modeling, vol. 48, no. 3, pp. 550–555, 2008.
@article{Blinov:2008jf,
title = {Performance validation of neural network based (13)c NMR prediction using a publicly available data source.},
author = {Blinov, K A and Smurnyy, Y D and Elyashberg, M E and Churanova, T S and Kvasha, M and Steinbeck, C and Lefebvre, B A and Williams, A J},
url = {http://pubs.acs.org/doi/abs/10.1021/ci700363r},
doi = {10.1021/ci700363r},
year = {2008},
date = {2008-03-01},
journal = {Journal of Chemical Information and Modeling},
volume = {48},
number = {3},
pages = {550--555},
publisher = {American Chemical Society},
abstract = {The validation of the performance of a neural network based 13C NMR prediction algorithm using a test set available from an open source publicly available database, NMRShiftDB, is described. The validation was performed using a version of the database containing ca. 214,000 chemical shifts as well as for two subsets of the database to compare performance when overlap with the training set is taken into account. The first subset contained ca. 93,000 chemical shifts that were absent from the ACDCNMR DB, the "excluded shift set" used for training of the neural network and the ACDCNMR prediction algorithm, while the second contained ca. 121,000 shifts that were present in the ACDCNMR DB training set, the "included shift set". This work has shown that the mean error between experimental and predicted shifts for the entire database is 1.59 ppm, while the mean deviation for the subset with included shifts is 1.47 and 1.74 ppm for excluded shifts. Since similar work has been reported online for another algorithm we compared the results with the errors determined using Robien's CNMR Neural Network Predictor using the entire NMRShiftDB for program validation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kuhn, Stefan; Egert, Björn; Neumann, Steffen; Steinbeck, Christoph
Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction. Journal Article
In: BMC Bioinformatics, vol. 9, no. 1, pp. 400, 2008.
@article{kuhn2008building,
title = {Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.},
author = {Kuhn, Stefan and Egert, Bj{ö}rn and Neumann, Steffen and Steinbeck, Christoph},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=18817546&retmode=ref&cmd=prlinks},
doi = {10.1186/1471-2105-9-400},
year = {2008},
date = {2008-01-01},
journal = {BMC Bioinformatics},
volume = {9},
number = {1},
pages = {400},
abstract = {BACKGROUND:Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB. RESULTS:A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error. CONCLUSION:NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Blinov, K A; Smurnyy, Y D; Elyashberg, M E; Churanova, T S; Kvasha, M; Steinbeck, C; Lefebvre, B A; Williams, A J
Performance Validation of Neural Network Based 13C NMR Prediction Using a Publicly Available Data Source Journal Article
In: Journal of Chemical Information and Modeling, vol. 48, no. 3, pp. 550–555, 2008.
@article{blinov2008performance,
title = {Performance Validation of Neural Network Based 13C NMR Prediction Using a Publicly Available Data Source},
author = {Blinov, K A and Smurnyy, Y D and Elyashberg, M E and Churanova, T S and Kvasha, M and Steinbeck, C and Lefebvre, B A and Williams, A J},
url = {http://www.google.de/search?client=safari&rls=10_7_4&q=Performance+Validation+of+Neural+Network+Based+13C+NMR+Prediction+Using+a+Publicly+Available+Data+Source&ie=UTF-8&oe=UTF-8&redir_esc=&ei=Mvm5UPGdF7H14QT-oIDYDQ},
year = {2008},
date = {2008-01-01},
journal = {Journal of Chemical Information and Modeling},
volume = {48},
number = {3},
pages = {550--555},
publisher = {ACS Publications},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2007
Kuhn, Stefan; Helmus, Tobias; Lancashire, Robert J; Murray-Rust, Peter; Rzepa, Henry S; Steinbeck, Christoph; Willighagen, Egon L
Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data. Journal Article
In: Journal of Chemical Information and Modeling, vol. 47, no. 6, pp. 2015–2034, 2007.
@article{kuhn2007chemical,
title = {Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data.},
author = {Kuhn, Stefan and Helmus, Tobias and Lancashire, Robert J and Murray-Rust, Peter and Rzepa, Henry S and Steinbeck, Christoph and Willighagen, Egon L},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=17887743&retmode=ref&cmd=prlinks},
doi = {10.1021/ci600531a},
year = {2007},
date = {2007-01-01},
journal = {Journal of Chemical Information and Modeling},
volume = {47},
number = {6},
pages = {2015--2034},
abstract = {CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Spjuth, Ola; Helmus, Tobias; Willighagen, Egon L; Kuhn, Stefan; Eklund, Martin; Wagener, Johannes; Murray-Rust, Peter; Steinbeck, Christoph; Wikberg, Jarl E S
Bioclipse: an open source workbench for chemo- and bioinformatics. Journal Article
In: BMC Bioinformatics, vol. 8, no. 1, pp. 59, 2007.
@article{spjuth2007bioclipse,
title = {Bioclipse: an open source workbench for chemo- and bioinformatics.},
author = {Spjuth, Ola and Helmus, Tobias and Willighagen, Egon L and Kuhn, Stefan and Eklund, Martin and Wagener, Johannes and Murray-Rust, Peter and Steinbeck, Christoph and Wikberg, Jarl E S},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=17316423&retmode=ref&cmd=prlinks},
doi = {10.1186/1471-2105-8-59},
year = {2007},
date = {2007-01-01},
journal = {BMC Bioinformatics},
volume = {8},
number = {1},
pages = {59},
abstract = {BACKGROUND:There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS:Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION:Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Willighagen, E L; O'Boyle, N M; Gopalakrishnan, H; Jiao, D; Guha, R; Steinbeck, C; Wild, D J
Userscripts for the life sciences Journal Article
In: BMC Bioinformatics, vol. 8, no. 1, pp. 487, 2007.
@article{willighagen2007userscripts,
title = {Userscripts for the life sciences},
author = {Willighagen, E L and O'Boyle, N M and Gopalakrishnan, H and Jiao, D and Guha, R and Steinbeck, C and Wild, D J},
url = {http://www.google.de/search?client=safari&rls=10_7_4&q=Userscripts+for+the+life+sciences&ie=UTF-8&oe=UTF-8&redir_esc=&ei=Mvm5UMyfGsfU4QS6voDYBA},
year = {2007},
date = {2007-01-01},
journal = {BMC Bioinformatics},
volume = {8},
number = {1},
pages = {487},
publisher = {BioMed Central Ltd},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Schenk, Ang'ela; Xu, Zhongli; Pfeiffer, Corina; Steinbeck, Christoph; Hertweck, Christian
Geminal bismethylation prevents polyketide oxidation and dimerization in the benastatin pathway. Journal Article
In: Angewandte Chemie. International Ed. in English, vol. 46, no. 37, pp. 7035–7038, 2007.
@article{Schenk:2007kha,
title = {Geminal bismethylation prevents polyketide oxidation and dimerization in the benastatin pathway.},
author = {Schenk, Ang{'e}la and Xu, Zhongli and Pfeiffer, Corina and Steinbeck, Christoph and Hertweck, Christian},
url = {http://doi.wiley.com/10.1002/anie.200702033},
doi = {10.1002/anie.200702033},
year = {2007},
date = {2007-01-01},
journal = {Angewandte Chemie. International Ed. in English},
volume = {46},
number = {37},
pages = {7035--7038},
publisher = {WILEY-VCH Verlag},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2006
Steinbeck, Christoph; Hoppe, Christian; Kuhn, Stefan; Guha, Rajarshi; Willighagen, Egon L
Recent Developments of The Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics Journal Article
In: Current pharmaceutical design, vol. 12, no. 17, pp. 2111–2120, 2006.
@article{steinbeck2006recent,
title = {Recent Developments of The Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics},
author = {Steinbeck, Christoph and Hoppe, Christian and Kuhn, Stefan and Guha, Rajarshi and Willighagen, Egon L},
url = {http://dx.doi.org/10.2174/138161206777585274},
doi = {10.2174/138161206777585274},
year = {2006},
date = {2006-01-01},
journal = {Current pharmaceutical design},
volume = {12},
number = {17},
pages = {2111--2120},
publisher = {Bentham Science Publishers},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hoppe, C; Steinbeck, C; Wohlfahrt, G
Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials Journal Article
In: Journal of Molecular Graphics & Modelling, vol. 24, no. 5, pp. 328–340, 2006.
@article{hoppe2006classification,
title = {Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials},
author = {Hoppe, C and Steinbeck, C and Wohlfahrt, G},
url = {http://dx.doi.org/10.1016/j.jmgm.2005.09.013},
doi = {10.1016/j.jmgm.2005.09.013},
year = {2006},
date = {2006-01-01},
journal = {Journal of Molecular Graphics & Modelling},
volume = {24},
number = {5},
pages = {328--340},
publisher = {Elsevier},
abstract = {We describe the application of knowledge-based potentials implemented in the MOE program to compare the ligand-binding sites of several proteins. The binding probabilities for a polar and a hydrophobic probe are calculated on a grid to allow easy comparison of binding sites of superimposed related proteins. The method is fast and simple enough to simultaneously use structural information of multiple proteins of a target family. The method can be used to rapidly cluster proteins into subfamilies according to the similarity of hydrophobic and polar fields of their ligand-binding sites. Regions of the binding site which are common within a protein family can be identified and analysed for the design of family-targeted libraries or those which differ for improvement of ligand selectivity. The field-based hierarchical clustering is demonstrated for three protein families: the ligand-binding domains of nuclear receptors, the ATP-binding sites of protein kinases and the substrate binding sites of proteases. More detailed comparisons are presented for serine proteases of the chymotrypsin family, for the peroxisome proliferator-activated receptor subfamily of nuclear receptors and for progesterone and androgen receptor. The results are in good accordance with structure-based analysis and highlight important differences of the binding sites, which have been also described in the literature.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Guha, Rajarshi; Howard, Michael T; Hutchison, Geoffrey R; Murray-Rust, Peter; Rzepa, Henry; Steinbeck, Christoph; Wegner, Joerg; Willighagen, Egon L
The Blue Obelisk - Interoperability in Chemical Informatics Journal Article
In: Journal of Chemical Information and Modeling, vol. 46, no. 3, pp. 991–998, 2006.
@article{guha2006blue,
title = {The Blue Obelisk - Interoperability in Chemical Informatics},
author = {Guha, Rajarshi and Howard, Michael T and Hutchison, Geoffrey R and Murray-Rust, Peter and Rzepa, Henry and Steinbeck, Christoph and Wegner, Joerg and Willighagen, Egon L},
url = {http://dx.doi.org/10.1021/ci050400b},
doi = {10.1021/ci050400b},
year = {2006},
date = {2006-01-01},
journal = {Journal of Chemical Information and Modeling},
volume = {46},
number = {3},
pages = {991--998},
publisher = {ACS Publications},
abstract = {The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2005
Steinbeck, C; Kuhn, Stefan
Eine offene NMR-Datenbank Journal Article
In: Nachrichten Aus Der Chemie, vol. 53, pp. 1039–1040, 2005.
@article{NMRShiftDB2005,
title = {Eine offene NMR-Datenbank},
author = {Steinbeck, C and Kuhn, Stefan},
year = {2005},
date = {2005-09-01},
journal = {Nachrichten Aus Der Chemie},
volume = {53},
pages = {1039--1040},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2004
Steinbeck, Christoph; Kuhn, Stefan
NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database. Journal Article
In: Phytochemistry, vol. 65, no. 19, pp. 2711–2717, 2004.
@article{Steinbeck:2004do,
title = {NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database.},
author = {Steinbeck, Christoph and Kuhn, Stefan},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=15464159&retmode=ref&cmd=prlinks},
doi = {10.1016/j.phytochem.2004.08.027},
year = {2004},
date = {2004-10-01},
journal = {Phytochemistry},
volume = {65},
number = {19},
pages = {2711--2717},
abstract = {Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Steinbeck, C
Recent developments in automated structure elucidation of natural products Journal Article
In: Natural Product Reports, vol. 21, no. 4, pp. 512–518, 2004.
@article{steinbeck2004recent,
title = {Recent developments in automated structure elucidation of natural products},
author = {Steinbeck, C},
url = {http://www.google.de/search?client=safari&rls=10_7_4&q=Recent+developments+in+automated+structure+elucidation+of+natural+products&ie=UTF-8&oe=UTF-8&redir_esc=&ei=Mvm5UKjFHoaF4ASe-YDgAg},
year = {2004},
date = {2004-01-01},
journal = {Natural Product Reports},
volume = {21},
number = {4},
pages = {512--518},
publisher = {Royal Society of Chemistry},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Han, Y Q; Steinbeck, C
Evolutionary-algorithm-based strategy for computer-assisted structure elucidation Journal Article
In: Journal of Chemical Information & Computer Sciences, vol. 44, no. 2, pp. 489–498, 2004.
@article{han2004evolutionary,
title = {Evolutionary-algorithm-based strategy for computer-assisted structure elucidation},
author = {Han, Y Q and Steinbeck, C},
url = {http://dx.doi.org/10.1021/ci034132y},
doi = {10.1021/ci034132y},
year = {2004},
date = {2004-01-01},
journal = {Journal of Chemical Information & Computer Sciences},
volume = {44},
number = {2},
pages = {489--498},
publisher = {ACS Publications},
abstract = {An evolutionary algorithm (EA) using a graph-based data structure to explore the molecular constitution space is presented. The EA implementation proves to be a promising alternative to deterministic approaches to the problem of computer-assisted structure elucidation (CASE). While not relying on any external database, the EA-guided CASE program SENECA is able to find correct solutions within calculation times comparable to that of other CASE expert systems. The implementation presented here significantly expands the size limit of constitutional optimization problems treatable with evolutionary algorithms by introducing novel efficient graph-based genetic operators. The new EA-based search strategy is discussed including the underlying data structures, component design, parameter optimization, and evolution process control. Typical structure elucidation examples are given to demonstrate the algorithm's performance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2003
Steinbeck, C
Correlations between Chemical Structures and NMR Data Book Section
In: Gasteiger, Johann; Engel, Thomas (Ed.): pp. 1368–1377, John Wiley & Sons, Weinheim, 2003, ISBN: 3527618279.
@incollection{steinbeck2003correlations,
title = {Correlations between Chemical Structures and NMR Data},
author = {Steinbeck, C},
editor = {Gasteiger, Johann and Engel, Thomas},
url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527618279.ch42c/summary},
isbn = {3527618279},
year = {2003},
date = {2003-01-01},
pages = {1368--1377},
publisher = {John Wiley & Sons},
address = {Weinheim},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Steinbeck, C; Krause, S; Kuhn, S
NMRShiftDB - Constructing a free chemical information system with open-source components Journal Article
In: Journal of Chemical Information & Computer Sciences, vol. 43, no. 6, pp. 1733–1739, 2003.
@article{steinbeck2003nmrshiftdb,
title = {NMRShiftDB - Constructing a free chemical information system with open-source components},
author = {Steinbeck, C and Krause, S and Kuhn, S},
url = {http://dx.doi.org/10.1021/ci0341363},
doi = {10.1021/ci0341363},
year = {2003},
date = {2003-01-01},
journal = {Journal of Chemical Information & Computer Sciences},
volume = {43},
number = {6},
pages = {1733--1739},
publisher = {ACS Publications},
abstract = {The process of designing and implementing NMRShiftDB, an open-source, open-content database for chemical structures and their NMR data based solely on free software is described. NMRShiftDB is available to the community on http://www.nmrshiftdb.org. It allows for open submission and retrieval of data sets by its user community. The software and the content itself is freely distributable, allowing for the establishment of a highly available mirror system of databases in collaborating laboratories.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Steinbeck, C; Han, Y Q; Kuhn, S; Horlacher, O; Luttmann, E; Willighagen, E
The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics Journal Article
In: Journal of Chemical Information & Computer Sciences, vol. 43, no. 2, pp. 493–500, 2003.
@article{steinbeck2003chemistry,
title = {The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics},
author = {Steinbeck, C and Han, Y Q and Kuhn, S and Horlacher, O and Luttmann, E and Willighagen, E},
url = {http://dx.doi.org/10.1021/ci025584y},
doi = {10.1021/ci025584y},
year = {2003},
date = {2003-01-01},
journal = {Journal of Chemical Information & Computer Sciences},
volume = {43},
number = {2},
pages = {493--500},
publisher = {ACS Publications},
abstract = {The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given. [References: 48]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Steinbeck, C
Correlations between Chemical Structures and NMR Data Book Section
In: pp. 1368–1377, John Wiley & Sons, Weinheim, 2003, ISBN: 3527618279.
@incollection{steinbeck2003correlationsb,
title = {Correlations between Chemical Structures and NMR Data},
author = {Steinbeck, C},
url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527618279.ch42c/summary},
isbn = {3527618279},
year = {2003},
date = {2003-01-01},
pages = {1368--1377},
publisher = {John Wiley & Sons},
address = {Weinheim},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
2001
Steinbeck, C
The automation of natural product structure elucidation. Journal Article
In: Current Opinion in Drug Discovery and Development, vol. 4, no. 3, pp. 338–342, 2001.
@article{Steinbeck:2001uq,
title = {The automation of natural product structure elucidation.},
author = {Steinbeck, C},
url = {http://europepmc.org/abstract/MED/11560068},
year = {2001},
date = {2001-05-01},
journal = {Current Opinion in Drug Discovery and Development},
volume = {4},
number = {3},
pages = {338--342},
abstract = {The last two or three years have seen exciting developments in the field of computer-assisted structure elucidation (CASE) with a number of programs becoming commercially or freely available. This was the conditio sine qua non for CASE to be widely applied in the daily work of bench chemists and spectroscopists. A number of promising applications have been published in the area of structure generators, deterministic and stochastic CASE tools and property predictions, including the automatic distinction between natural products and artificial compounds, as well as the determination of 3-D structure from a connection table based on IR spectroscopy. Advancements in coupling techniques between chromatographic and spectroscopic methods demonstrate progress towards a fully automated structure elucidation or identification process starting at the earliest steps of obtaining crude extracts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Yankep, E; Mbafor, J T; Fomum, Z T; Steinbeck, C; Messanga, B B; Nyasse, B; Budzikiewicz, H; Lenz, C; Schmickler, H
Further isoflavonoid metabolites from Millettia griffoniana (Bail) Journal Article
In: Phytochemistry, vol. 56, no. 4, pp. 363–368, 2001.
@article{yankep2001further,
title = {Further isoflavonoid metabolites from Millettia griffoniana (Bail)},
author = {Yankep, E and Mbafor, J T and Fomum, Z T and Steinbeck, C and Messanga, B B and Nyasse, B and Budzikiewicz, H and Lenz, C and Schmickler, H},
url = {http://dx.doi.org/10.1016/S0031-9422(00)00400-3},
doi = {10.1016/S0031-9422(00)00400-3},
year = {2001},
date = {2001-01-01},
journal = {Phytochemistry},
volume = {56},
number = {4},
pages = {363--368},
publisher = {Elsevier},
abstract = {Three new isoflavonoids, griffonianone A (1), B (2) and C (4) were isolated from the root bark of Millettia griffoniama, along with the known maximaisoflavone G (5) and 7-hydroxy-6-methoxy-3',4'-methylenedioxyisoflavone (6). Their structures were assigned on the basis of spectroscopic data and chemical transformations. (C) 2001 Elsevier Science Ltd. All rights reserved. [References: 13]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Steinbeck, C
SENECA: A platform-independent, distributed, and parallel system for computer-assisted structure elucidation in organic chemistry Journal Article
In: Journal of Chemical Information & Computer Sciences, vol. 41, no. 6, pp. 1500–1507, 2001.
@article{steinbeck2001seneca,
title = {SENECA: A platform-independent, distributed, and parallel system for computer-assisted structure elucidation in organic chemistry},
author = {Steinbeck, C},
url = {http://dx.doi.org/10.1021/ci000407n},
doi = {10.1021/ci000407n},
year = {2001},
date = {2001-01-01},
journal = {Journal of Chemical Information & Computer Sciences},
volume = {41},
number = {6},
pages = {1500--1507},
publisher = {ACS Publications},
abstract = {The program package SENECA for Computer-Assisted Structure Elucidation (CASE) of organic molecules is described. SENECA is written completely in the programming language Java and divided into a server, a client, and a gatekeeper part. While the client allows for input of spectroscopic information, the server part performs the actual structure elucidation by stochastically walking through constitution space while optimizing the molecule toward agreement with given spectral properties. The convergence is guided by simulated annealing. The gatekeeper administers a list of server processes, which can be retrieved by the client. The package is completely platform-independent and its server part can be distributed over the Internet or an intranet using a heterogeneous network of almost any number and type of computers, thus allowing for parallel CASE computations on ordinary networks, present in almost any institution. [References: 23]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}