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==Background==
==Background==
In the field of organic chemistry, like in any research area, the availability of digital data is a prerequisite for sustainable and successful research as it allows for the access of results, the search for information, and the processing of obtained research data.<ref name="Winkler-NeesStatus13">{{cite book |url=https://books.google.com/books?id=Nf35AgAAQBAJ&pg=PA18&lpg=PA18 |chapter=Status of Discussion and Current Activities: National Developments |title=Digital Curation of Research Data: Experiences of a Baseline Study in Germany |author=Winkler-Nees, S. |editor=Neuroth, H.; Strathmann, S.; Oßwald, A.; Ludwig, J. |publisher=Universitätsverlag Göttingen |pages=18–36 |year=2013 |isbn=9783864880544}}</ref><ref name="StajichOpen06">{{cite journal |title=Open source tools and toolkits for bioinformatics: Significance, and where are we? |journal=Briefings in Bioinformatics |author=Stajich, J.E.; Lapp, H. |volume=7 |issue=3 |pages=287–96 |year=2006 |doi=10.1093/bib/bbl026 |pmid=16899494}}</ref><ref name="OwensData16">{{cite journal |title=Data sharing: Access all areas |journal=Nature |author=Owens, B. |volume=533 |issue=7602 |pages=S71-2 |year=2016 |doi=10.1038/533S71a |pmid=27167398}}</ref> Due to the ever-growing accumulation of information resulting from the constant saving and recording of data, it is imperative to improve data management with a digital system. Following the data life cycle, this enables the increase of knowledge by computing methods.<ref name="PirhadiOpen16">{{cite journal |title=Open source molecular modeling |journal=Journal of Molecular Graphics & Modeling |author=Pirhadi, S.; Sunseri, J.; Koes, D.R. |volume=69 |pages=127–43 |year=2016 |doi=10.1016/j.jmgm.2016.07.008 |pmid=27631126 |pmc=PMC5037051}}</ref><ref name="SeglerNeural17">{{cite journal |title=Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction |journal=Chemistry |author=Segler, M.H.S.; Waller, M.P. |volume=23 |issue=25 |pages=5966-5971 |year=2017 |doi=10.1002/chem.201605499 |pmid=28134452}}</ref><ref name="ChristMining12">{{cite journal |title=Mining electronic laboratory notebooks: analysis, retrosynthesis, and reaction based enumeration |journal=Journal of Chemical Information and Modeling |author=Christ, C.D.; Zentgraf, M.; Kriegl, J.M. |volume=52 |issue=7 |pages=1745-56 |year=2012 |doi=10.1021/ci300116p |pmid=22657734}}</ref> However, the lack of accessible and sufficiently mapped data limits current research, and the need to improve the situation has been stated many times before.<ref name="NAData09">{{cite journal |title=Data's shameful neglect |journal=Nature |author=NA |volume=461 |issue=7261 |pages=145 |year=2009 |doi=10.1038/461145a |pmid=19741659}}</ref><ref name="BirdChemical13">{{cite journal |title=Chemical information matters: An e-Research perspective on information and data sharing in the chemical sciences |journal=Chemical Society Reviews |author=Bird, C.L.; Frey, J.G. |volume=42 |issue=16 |pages=6754-76 |year=2013 |doi=10.1039/c3cs60050e |pmid=23686012}}</ref><ref name="AlsheikhPublic11">{{cite journal |title=Public availability of published research data in high-impact journals |journal=PLoS One |author=Alsheikh-Ali, A.A.; Qureshi, W.; Al-Mallah, M.H.; Ioannidis, J.P. |volume=6 |issue=9 |pages=e24357 |year=2011 |doi=10.1371/journal.pone.0024357 |pmid=21915316 |pmc=PMC3168487}}</ref>
In the field of organic chemistry, like in any research area, the availability of digital data is a prerequisite for sustainable and successful research as it allows for the access of results, the search for information, and the processing of obtained research data.<ref name="Winkler-NeesStatus13">{{cite book |url=https://books.google.com/books?id=Nf35AgAAQBAJ&pg=PA18&lpg=PA18 |chapter=Status of Discussion and Current Activities: National Developments |title=Digital Curation of Research Data: Experiences of a Baseline Study in Germany |author=Winkler-Nees, S. |editor=Neuroth, H.; Strathmann, S.; Oßwald, A.; Ludwig, J. |publisher=Universitätsverlag Göttingen |pages=18–36 |year=2013 |isbn=9783864880544}}</ref><ref name="StajichOpen06">{{cite journal |title=Open source tools and toolkits for bioinformatics: Significance, and where are we? |journal=Briefings in Bioinformatics |author=Stajich, J.E.; Lapp, H. |volume=7 |issue=3 |pages=287–96 |year=2006 |doi=10.1093/bib/bbl026 |pmid=16899494}}</ref><ref name="OwensData16">{{cite journal |title=Data sharing: Access all areas |journal=Nature |author=Owens, B. |volume=533 |issue=7602 |pages=S71-2 |year=2016 |doi=10.1038/533S71a |pmid=27167398}}</ref> Due to the ever-growing accumulation of information resulting from the constant saving and recording of data, it is imperative to improve data management with a digital system. Following the data life cycle, this enables the increase of knowledge by computing methods.<ref name="PirhadiOpen16">{{cite journal |title=Open source molecular modeling |journal=Journal of Molecular Graphics & Modeling |author=Pirhadi, S.; Sunseri, J.; Koes, D.R. |volume=69 |pages=127–43 |year=2016 |doi=10.1016/j.jmgm.2016.07.008 |pmid=27631126 |pmc=PMC5037051}}</ref><ref name="SeglerNeural17">{{cite journal |title=Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction |journal=Chemistry |author=Segler, M.H.S.; Waller, M.P. |volume=23 |issue=25 |pages=5966-5971 |year=2017 |doi=10.1002/chem.201605499 |pmid=28134452}}</ref><ref name="ChristMining12">{{cite journal |title=Mining electronic laboratory notebooks: analysis, retrosynthesis, and reaction based enumeration |journal=Journal of Chemical Information and Modeling |author=Christ, C.D.; Zentgraf, M.; Kriegl, J.M. |volume=52 |issue=7 |pages=1745-56 |year=2012 |doi=10.1021/ci300116p |pmid=22657734}}</ref> However, the lack of accessible and sufficiently mapped data limits current research, and the need to improve the situation has been stated many times before.<ref name="NAData09">{{cite journal |title=Data's shameful neglect |journal=Nature |author=NA |volume=461 |issue=7261 |pages=145 |year=2009 |doi=10.1038/461145a |pmid=19741659}}</ref><ref name="BirdChemical13">{{cite journal |title=Chemical information matters: An e-Research perspective on information and data sharing in the chemical sciences |journal=Chemical Society Reviews |author=Bird, C.L.; Frey, J.G. |volume=42 |issue=16 |pages=6754-76 |year=2013 |doi=10.1039/c3cs60050e |pmid=23686012}}</ref><ref name="AlsheikhPublic11">{{cite journal |title=Public availability of published research data in high-impact journals |journal=PLoS One |author=Alsheikh-Ali, A.A.; Qureshi, W.; Al-Mallah, M.H.; Ioannidis, J.P. |volume=6 |issue=9 |pages=e24357 |year=2011 |doi=10.1371/journal.pone.0024357 |pmid=21915316 |pmc=PMC3168487}}</ref> Therefore, the maintenance of systems for digital data acquisition, management, and storage is a key factor for efficient research activity.<ref name="SzymkućComputer16">{{cite journal |title=Computer-Assisted Synthetic Planning: The End of the Beginning |journal=Angewandte Chemie |author=Szymkuć, S.; Gajewska, E.P.; Klucznik, T. et al. |volume=55 |issue=20 |pages=5904-37 |year=2016 |doi=10.1002/anie.201506101 |pmid=27062365}}</ref><ref name="BorgmanTheCon12">{{cite journal |title=The conundrum of sharing research data |journal=Journal of the Association for Information Science and Technology |author=Borgman, C.L. |volume=63 |issue=6 |pages=1059–1078 |year=2012 |doi=10.1002/asi.22634}}</ref><ref name="GhoshSoftware11">{{cite journal |title=Software for systems biology: From tools to integrated platforms |journal=Nature Reviews Genetics |author=Ghosh, S.; Matsuoka, Y.; Asai, Y. et al. |volume=12 |issue=12 |pages=821-32 |year=2011 |doi=10.1038/nrg3096 pmid=22048662}}</ref>


==References==
==References==

Revision as of 23:35, 30 October 2017

Full article title Chemotion ELN: An open-source electronic lab notebook for chemists in academia
Journal Journal of Chemoinformatics
Author(s) Tremouilhac, Pierre; Nguyen, An; Huang, Yu-Chieh; Kotov, Serhii; Lütjohann, Dominic Sebastian; Hübsch, Florian; Jung, Nicole; Bräse, Stefan
Author affiliation(s) Karlsruhe Institute of Technology, Cubuslab GmbH, Ninja-Concept GmbH
Primary contact Email: nicole dot jung at kit dot edu
Year published 2017
Volume and issue 9
Page(s) 54
DOI 10.1186/s13321-017-0240-0
ISSN 1758-2946
Distribution license Creative Commons Attribution 4.0 International
Website https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0240-0
Download https://jcheminf.springeropen.com/track/pdf/10.1186/s13321-017-0240-0 (PDF)
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Abstract

The development of an electronic laboratory notebook (ELN) for researchers working in the field of chemical sciences is presented. The web-based application is available as open-source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state-of-the-art research infrastructure, the ELN allows the search for molecules and reactions not only within the user’s data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing open- source instruments to record and reuse research data. The current version of the ELN has been used for over half of a year in our chemistry research group, serving as a common infrastructure for chemistry research and enabling chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms.

Keywords: Electronic lab notebook, digitization, open source, Ruby on Rails, compound management

Background

In the field of organic chemistry, like in any research area, the availability of digital data is a prerequisite for sustainable and successful research as it allows for the access of results, the search for information, and the processing of obtained research data.[1][2][3] Due to the ever-growing accumulation of information resulting from the constant saving and recording of data, it is imperative to improve data management with a digital system. Following the data life cycle, this enables the increase of knowledge by computing methods.[4][5][6] However, the lack of accessible and sufficiently mapped data limits current research, and the need to improve the situation has been stated many times before.[7][8][9] Therefore, the maintenance of systems for digital data acquisition, management, and storage is a key factor for efficient research activity.[10][11][12]

References

  1. ↑ Winkler-Nees, S. (2013). "Status of Discussion and Current Activities: National Developments". In Neuroth, H.; Strathmann, S.; Oßwald, A.; Ludwig, J.. Digital Curation of Research Data: Experiences of a Baseline Study in Germany. Universitätsverlag Göttingen. pp. 18–36. ISBN 9783864880544. https://books.google.com/books?id=Nf35AgAAQBAJ&pg=PA18&lpg=PA18. 
  2. ↑ Stajich, J.E.; Lapp, H. (2006). "Open source tools and toolkits for bioinformatics: Significance, and where are we?". Briefings in Bioinformatics 7 (3): 287–96. doi:10.1093/bib/bbl026. PMID 16899494. 
  3. ↑ Owens, B. (2016). "Data sharing: Access all areas". Nature 533 (7602): S71-2. doi:10.1038/533S71a. PMID 27167398. 
  4. ↑ Pirhadi, S.; Sunseri, J.; Koes, D.R. (2016). "Open source molecular modeling". Journal of Molecular Graphics & Modeling 69: 127–43. doi:10.1016/j.jmgm.2016.07.008. PMC PMC5037051. PMID 27631126. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5037051. 
  5. ↑ Segler, M.H.S.; Waller, M.P. (2017). "Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction". Chemistry 23 (25): 5966-5971. doi:10.1002/chem.201605499. PMID 28134452. 
  6. ↑ Christ, C.D.; Zentgraf, M.; Kriegl, J.M. (2012). "Mining electronic laboratory notebooks: analysis, retrosynthesis, and reaction based enumeration". Journal of Chemical Information and Modeling 52 (7): 1745-56. doi:10.1021/ci300116p. PMID 22657734. 
  7. ↑ NA (2009). "Data's shameful neglect". Nature 461 (7261): 145. doi:10.1038/461145a. PMID 19741659. 
  8. ↑ Bird, C.L.; Frey, J.G. (2013). "Chemical information matters: An e-Research perspective on information and data sharing in the chemical sciences". Chemical Society Reviews 42 (16): 6754-76. doi:10.1039/c3cs60050e. PMID 23686012. 
  9. ↑ Alsheikh-Ali, A.A.; Qureshi, W.; Al-Mallah, M.H.; Ioannidis, J.P. (2011). "Public availability of published research data in high-impact journals". PLoS One 6 (9): e24357. doi:10.1371/journal.pone.0024357. PMC PMC3168487. PMID 21915316. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168487. 
  10. ↑ Szymkuć, S.; Gajewska, E.P.; Klucznik, T. et al. (2016). "Computer-Assisted Synthetic Planning: The End of the Beginning". Angewandte Chemie 55 (20): 5904-37. doi:10.1002/anie.201506101. PMID 27062365. 
  11. ↑ Borgman, C.L. (2012). "The conundrum of sharing research data". Journal of the Association for Information Science and Technology 63 (6): 1059–1078. doi:10.1002/asi.22634. 
  12. ↑ Ghosh, S.; Matsuoka, Y.; Asai, Y. et al. (2011). "Software for systems biology: From tools to integrated platforms". Nature Reviews Genetics 12 (12): 821-32. doi:10.1038/nrg3096 pmid=22048662. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. In some cases, the authors directly referenced a citation number; the author and year of the citation was inserted along with the citation for completeness.

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