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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> 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>
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> The need for digitalization of data and its systematic storage presents challenges for the scientist, their institution providing the research infrastructure, and their scientific community. In the past, the discussion about the generation of and access to digital research information was mainly limited to published research data.<ref name="SzymkućComputer16" /><ref name="ButlerGates17">{{cite journal |title=Gates Foundation announces open-access publishing venture |journal=Nature |author=Butler, D. |volume=543 |issue=7647 |pages=599 |year=2017 |doi=10.1038/nature.2017.21700 |pmid=28358109}}</ref><ref name="LawrenceOpen17">{{cite journal |title=Open Access is Evolving and ChemistryOpen is Too! |journal=ChemistryOpen |author=Lawrence, K. |volume=6 |issue=1 |pages=3–4 |year=2017 |doi=10.1002/open.201600165 |pmid=28168141 |pmc=PMC5288765}}</ref> During the last two decades this accessibility has been improved drastically due to the availability of publications in online editions of scientific journals and the online-support of standard commercial databases like SciFinder<ref name="SciFinder">{{cite web |url=http://www.cas.org/products/scifinder |title=SciFinder |publisher=Chemical Abstracts Service |accessdate=2017}}</ref> and Reaxys<ref name="Reaxys">{{cite web |url=https://www.elsevier.com/solutions/reaxys |title=Reaxys |publisher=Elsevier |accessdate=2017}}</ref>, as examples in chemical research. These developments have facilitated the search for published information, whereas solutions for a comprehensive digital storage and availability of all other research data, including data directly recorded in the [[laboratory|laboratories]], are still missing or lagging due to the challenging requirements of the research infrastructure in academia. The establishment of infrastructure in academic institutions is particularly difficult due to missing standards or policies in data handling and storage, diverse work practices, the prevalence of used equipment, and the limited budget for fundamental improvements. In natural sciences, the digitization of research data, as the basis for a later availability of the results and procedures, has to be implemented directly in the daily routine of scientists. Specific aspects of laboratory work have to be reflected in the [[Electronic data capture|electronic data acquisition]] and storage system depending on the research field. Although several electronic lab notebooks (ELNs) have been developed during the last few years, offering intelligent solutions for the documentation of research data (like [[sciNote]]<ref name="SciNote">{{cite web |url=https://github.com/biosistemika/scinote-web |title=biosistemika/scinote-web |publisher=GitHub, Inc |accessdate=2017}}</ref>, [[Dassault Systemes SA|Biovia ELN]]<ref name="Biovia">{{cite web |url=http://accelrys.com/products/unified-lab-management/biovia-electronic-lab-notebooks/ |title=BIOVIA Electronic Laboratory Notebooks |publisher=Dassault Systemes |accessdate=2017}}</ref>, EMEN<ref name="ReesEMEN2_13">{{cite journal |title=EMEN2: An object oriented database and electronic lab notebook |journal=Microscopy and Microanalysis |author=Rees, I.; Langley, E.; Chiu, W.; Ludtke, S.J. |volume=19 |issue=1 |pages=1–10 |year=2013 |doi=10.1017/S1431927612014043 |pmid=23360752 |pmc=PMC3907281}}</ref>, [[openBIS]] ELN-LIMS<ref name="BarillariOpenBIS16">{{cite journal |journal=Bioinformatics |title=openBIS ELN-LIMS: An open-source database for academic laboratories |author=Barillari, C.; Ottoz, D.S.M.; Fuentes-Serna, J.M. et al. |volume=32 |issue=4 |pages=638–640 |year=2016 |doi=10.1093/bioinformatics/btv606 |pmid=26508761 |pmc=PMC4743625}}</ref>, [[Labfolder GmbH|LabFolder]]<ref name="LabFolder">{{cite web |url=https://www.labfolder.com/ |title=LabFolder |publisher=LabFolder GmbH |accessdate=2017}}</ref>, and others<ref name="ZengImpact11">{{cite journal |title=Impact of the implementation of a well-designed electronic laboratory notebook on bioanalytical laboratory function |journal=Bioanalysis |author=Zeng, J.; Hillman, M.; Arnold, M. |volume=3 |issue=13 |pages=1501–11 |year=2011 |doi=10.4155/bio.11.116 |pmid=21728774}}</ref><ref name="BeatoGoing11">{{cite journal |title=Going paperless: Implementing an electronic laboratory notebook in a bioanalytical laboratory |journal=Bioanalysis |author=Beato, B.; Pisek, A.; White, J. et al. |volume=3 |issue=13 |pages=1457–70 |year=2011 |doi=10.4155/bio.11.117 |pmid=21702721}}</ref><ref name="RubachaARev11">{{cite journal |title=A review of electronic laboratory notebooks available in the market today |journal=Journal of Laboratory Automation |author=Rubacha, M.; Rattan, A.K.; Hosselet, S.C. |volume=16 |issue=1 |pages=90–98 |year=2011 |doi=10.1016/j.jala.2009.01.002 |pmid=21609689}}</ref><ref name="TaylorTheStatus">{{cite journal |title=The status of electronic laboratory notebooks for chemistry and biology |journal=Current Opinion in Drug Discovery & Development |author=Taylor, K.T. |volume=9 |issue=3 |pages=348–53 |year=2006 |pmid=16729731}}</ref><ref name="vanEikerenIntell04">{{cite journal |title=Intelligent Electronic Laboratory Notebooks for Accelerated Organic Process R&D |journal=Organic Process Research & Development |author=van Eikeren, P. |volume=8 |issue=6 |pages=1015–23 |year=2004 |doi=10.1021/op049890j}}</ref><ref name="AchourSanofi04">{{cite journal |title=Sanofi-Synthelabo Chemical Development and the Development of an Electronic Laboratory Notebook |journal=Organic Process Research & Development |author=Achor, Z.; Ladboeur, T.; Gien, O. et al. |volume=8 |issue=6 |pages=983–97 |year=2004 |doi=10.1021/op040012v}}</ref><ref name="WalshUsing13">{{cite journal |title=Using Evernote as an electronic lab notebook in a translational science laboratory |journal=Journal of Laboratory Automation |author=Walsh, E.; Choi, I. |volume=18 |issue=3 |year=2013 |pages=229-34 |doi=10.1177/2211068212471834 |pmid=23271786}}</ref><ref name="GoddardECat09">{{cite journal |title=eCAT: Online electronic lab notebook for scientific research |journal=Automated Experimentation |author=Goddard, N.H.; Macneil, R.; Ritchie, J. |volume=1 |pages=4 |year=2009 |doi=10.1186/1759-4499-1-4}}</ref>), only a scant few electronic lab notebooks are dedicated to the chemical sciences.<ref name="BirdLab13">{{cite journal |title=Laboratory notebooks in the digital era: The role of ELNs in record keeping for chemistry and other sciences |journal=Chemical Society Reviews |author=Bird, C.L.; Willoughby, C.; Frey, J.G. |volume=42 |issue=20 |pages=8157–75 |year=2013 |doi=10.1039/c3cs60122f |pmid=23864106}}</ref><ref name="VoegeleAUniversal13">{{cite journal |title=A universal open-source electronic laboratory notebook |journal=Bioinformatics |author=Voegele, C.; Bouchereau, B.; Robinot, N. et al. |volume=29 |issue=13 |year=2013 |pages=1710-2 |doi=10.1093/bioinformatics/btt253 |pmid=23645817}}</ref> In the [[Chemical industry|chemical sciences]] in particular, challenges arise with the drawing and processing of chemical structures, a crucial and central step for the correlation of research data with the corresponding chemical transformation or structure.<ref name="ColesFirst13">{{cite journal |title=First steps towards semantic descriptions of electronic laboratory notebook records |journal=Journal of Cheminformatics |author=Coles, S.J.; Frey, J.G.; Bird, C.L. et al. |volume=5 |issue=1 |pages=52 |year=2013 |doi=10.1186/1758-2946-5-52 |pmid=24360292 |pmc=PMC3878183}}</ref> Examples for systems in chemistry that offer the necessary support of chemical structures are the [[PerkinElmer Inc.|PerkinElmer]] E-Notebook for Chemistry<ref name="E-Notebook">{{cite web |url=https://www.cambridgesoft.com/Ensemble_for_Chemistry/ENotebookforChemistry/ |title=E-Notebook for Chemistry |publisher=PerkinElmer, Inc |accessdate=2017}}</ref>, [[Indigo ELN]]<ref name="IndigoELN">{{cite web |url=https://github.com/epam/Indigo |title=epam/Indigo |publisher=GitHub, Inc |accessdate=2017}}</ref>, [[LabTrove]]<ref name="DayChemTrove15">{{cite journal |title=ChemTrove: Enabling a generic ELN to support chemistry through the use of transferable plug-ins and online data sources |journal=Journal of Chemical Information and Modeling |author=Day, A.E.; Coles, S.J.; Bird, C.L. et al. |volume=55 |issue=3 |pages=501–9 |year=2015 |doi=10.1021/ci5005948 |pmid=25679543}}</ref><ref name="FreySample14">{{cite journal |title=Sample management with the LabTrove ELN |journal=Conference Proceedings from the 247th ACS National Meeting & Exposition |author=Frey, J.G.; Coles, S.J.; Bird, C.L. et al. |year=2014 |url=https://eprints.soton.ac.uk/368133/}}</ref><ref name="WilloughbyCreating14">{{cite journal |title=Creating context for the experiment record. User-defined metadata: investigations into metadata usage in the LabTrove ELN |journal=Journal of Chemical Information and Modeling |author=Willoughby, C.; Bird, C.L.; Coles, S.J.; Frey, J.G. |volume=54 |issue=12 |pages=3268–83 |year=2014 |doi=10.1021/ci500469f |pmid=25405258}}</ref>, and [[open enventory]].<ref name="RudolphiElectronic12">{{cite journal |title=Electronic laboratory notebook: The academic point of view |journal=Journal of Chemical Information and Modeling |author=Rudolphi, F.; Goossen, L.J. |volume=52 |issue=2 |pages=293–301 |year=2012 |doi=10.1021/ci2003895 |pmid=22077095}}</ref> These existing systems have already been in use by several groups and researchers. However, the sporadic implementation still reflects a mismatch between the offered solutions and the actual needs and resources of the chemists and their research facilities. This might be due to the high specific requirements for the software to reflect fast moving research: suitable ELNs have to be readily obtainable, adaptable, and modular without incurring additional costs. These features can probably only be offered by an open source project. In addition, a suitable, state-of-the-art system for sustainable research management should support communication with additional external databases and repositories, as well as connections to external devices and storage systems<ref name="LütjohannOpenSource15">{{cite journal |title=Open source life science automation: Design of experiments and data acquisition via “dial-a-device” |journal=Chemometrics and Intelligent Laboratory Systems |author=Lütjohann, D.S.; Jung, N.; Bräse, S. |volume=144 |pages=100–107 |year=2015 |doi=10.1016/j.chemolab.2015.04.002}}</ref> of analytical results. Other important aspects are the embedding of calculation methods, and the possible extension of source code to the needs of other fields of chemistry (e.g., surface chemistry) and related domains of research (e.g., biology). As the identified criteria for a system to face the challenges of professional data management in academia could not be fulfilled by the currently available open-source systems, we initiated the development of a powerful ELN for chemical sciences. Such an ELN should offer the features, currently lacking in available systems, while being flexible, referring to the internal structure. Future extensions and adaptions to the needs of progressive chemistry research should be possible with minimal effort. The development of the Chemotion ELN resulted in a system with modern infrastructure that offers intelligent support of academic research projects as key instruments for the acquisition, storage, and management of digital data in chemistry.


==References==
==References==

Revision as of 19:32, 1 November 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] The need for digitalization of data and its systematic storage presents challenges for the scientist, their institution providing the research infrastructure, and their scientific community. In the past, the discussion about the generation of and access to digital research information was mainly limited to published research data.[10][13][14] During the last two decades this accessibility has been improved drastically due to the availability of publications in online editions of scientific journals and the online-support of standard commercial databases like SciFinder[15] and Reaxys[16], as examples in chemical research. These developments have facilitated the search for published information, whereas solutions for a comprehensive digital storage and availability of all other research data, including data directly recorded in the laboratories, are still missing or lagging due to the challenging requirements of the research infrastructure in academia. The establishment of infrastructure in academic institutions is particularly difficult due to missing standards or policies in data handling and storage, diverse work practices, the prevalence of used equipment, and the limited budget for fundamental improvements. In natural sciences, the digitization of research data, as the basis for a later availability of the results and procedures, has to be implemented directly in the daily routine of scientists. Specific aspects of laboratory work have to be reflected in the electronic data acquisition and storage system depending on the research field. Although several electronic lab notebooks (ELNs) have been developed during the last few years, offering intelligent solutions for the documentation of research data (like sciNote[17], Biovia ELN[18], EMEN[19], openBIS ELN-LIMS[20], LabFolder[21], and others[22][23][24][25][26][27][28][29]), only a scant few electronic lab notebooks are dedicated to the chemical sciences.[30][31] In the chemical sciences in particular, challenges arise with the drawing and processing of chemical structures, a crucial and central step for the correlation of research data with the corresponding chemical transformation or structure.[32] Examples for systems in chemistry that offer the necessary support of chemical structures are the PerkinElmer E-Notebook for Chemistry[33], Indigo ELN[34], LabTrove[35][36][37], and open enventory.[38] These existing systems have already been in use by several groups and researchers. However, the sporadic implementation still reflects a mismatch between the offered solutions and the actual needs and resources of the chemists and their research facilities. This might be due to the high specific requirements for the software to reflect fast moving research: suitable ELNs have to be readily obtainable, adaptable, and modular without incurring additional costs. These features can probably only be offered by an open source project. In addition, a suitable, state-of-the-art system for sustainable research management should support communication with additional external databases and repositories, as well as connections to external devices and storage systems[39] of analytical results. Other important aspects are the embedding of calculation methods, and the possible extension of source code to the needs of other fields of chemistry (e.g., surface chemistry) and related domains of research (e.g., biology). As the identified criteria for a system to face the challenges of professional data management in academia could not be fulfilled by the currently available open-source systems, we initiated the development of a powerful ELN for chemical sciences. Such an ELN should offer the features, currently lacking in available systems, while being flexible, referring to the internal structure. Future extensions and adaptions to the needs of progressive chemistry research should be possible with minimal effort. The development of the Chemotion ELN resulted in a system with modern infrastructure that offers intelligent support of academic research projects as key instruments for the acquisition, storage, and management of digital data in chemistry.

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. ↑ 10.0 10.1 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. 
  13. ↑ Butler, D. (2017). "Gates Foundation announces open-access publishing venture". Nature 543 (7647): 599. doi:10.1038/nature.2017.21700. PMID 28358109. 
  14. ↑ Lawrence, K. (2017). "Open Access is Evolving and ChemistryOpen is Too!". ChemistryOpen 6 (1): 3–4. doi:10.1002/open.201600165. PMC PMC5288765. PMID 28168141. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288765. 
  15. ↑ "SciFinder". Chemical Abstracts Service. http://www.cas.org/products/scifinder. Retrieved 2017. 
  16. ↑ "Reaxys". Elsevier. https://www.elsevier.com/solutions/reaxys. Retrieved 2017. 
  17. ↑ "biosistemika/scinote-web". GitHub, Inc. https://github.com/biosistemika/scinote-web. Retrieved 2017. 
  18. ↑ "BIOVIA Electronic Laboratory Notebooks". Dassault Systemes. http://accelrys.com/products/unified-lab-management/biovia-electronic-lab-notebooks/. Retrieved 2017. 
  19. ↑ Rees, I.; Langley, E.; Chiu, W.; Ludtke, S.J. (2013). "EMEN2: An object oriented database and electronic lab notebook". Microscopy and Microanalysis 19 (1): 1–10. doi:10.1017/S1431927612014043. PMC PMC3907281. PMID 23360752. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907281. 
  20. ↑ Barillari, C.; Ottoz, D.S.M.; Fuentes-Serna, J.M. et al. (2016). "openBIS ELN-LIMS: An open-source database for academic laboratories". Bioinformatics 32 (4): 638–640. doi:10.1093/bioinformatics/btv606. PMC PMC4743625. PMID 26508761. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743625. 
  21. ↑ "LabFolder". LabFolder GmbH. https://www.labfolder.com/. Retrieved 2017. 
  22. ↑ Zeng, J.; Hillman, M.; Arnold, M. (2011). "Impact of the implementation of a well-designed electronic laboratory notebook on bioanalytical laboratory function". Bioanalysis 3 (13): 1501–11. doi:10.4155/bio.11.116. PMID 21728774. 
  23. ↑ Beato, B.; Pisek, A.; White, J. et al. (2011). "Going paperless: Implementing an electronic laboratory notebook in a bioanalytical laboratory". Bioanalysis 3 (13): 1457–70. doi:10.4155/bio.11.117. PMID 21702721. 
  24. ↑ Rubacha, M.; Rattan, A.K.; Hosselet, S.C. (2011). "A review of electronic laboratory notebooks available in the market today". Journal of Laboratory Automation 16 (1): 90–98. doi:10.1016/j.jala.2009.01.002. PMID 21609689. 
  25. ↑ Taylor, K.T. (2006). "The status of electronic laboratory notebooks for chemistry and biology". Current Opinion in Drug Discovery & Development 9 (3): 348–53. PMID 16729731. 
  26. ↑ van Eikeren, P. (2004). "Intelligent Electronic Laboratory Notebooks for Accelerated Organic Process R&D". Organic Process Research & Development 8 (6): 1015–23. doi:10.1021/op049890j. 
  27. ↑ Achor, Z.; Ladboeur, T.; Gien, O. et al. (2004). "Sanofi-Synthelabo Chemical Development and the Development of an Electronic Laboratory Notebook". Organic Process Research & Development 8 (6): 983–97. doi:10.1021/op040012v. 
  28. ↑ Walsh, E.; Choi, I. (2013). "Using Evernote as an electronic lab notebook in a translational science laboratory". Journal of Laboratory Automation 18 (3): 229-34. doi:10.1177/2211068212471834. PMID 23271786. 
  29. ↑ Goddard, N.H.; Macneil, R.; Ritchie, J. (2009). "eCAT: Online electronic lab notebook for scientific research". Automated Experimentation 1: 4. doi:10.1186/1759-4499-1-4. 
  30. ↑ Bird, C.L.; Willoughby, C.; Frey, J.G. (2013). "Laboratory notebooks in the digital era: The role of ELNs in record keeping for chemistry and other sciences". Chemical Society Reviews 42 (20): 8157–75. doi:10.1039/c3cs60122f. PMID 23864106. 
  31. ↑ Voegele, C.; Bouchereau, B.; Robinot, N. et al. (2013). "A universal open-source electronic laboratory notebook". Bioinformatics 29 (13): 1710-2. doi:10.1093/bioinformatics/btt253. PMID 23645817. 
  32. ↑ Coles, S.J.; Frey, J.G.; Bird, C.L. et al. (2013). "First steps towards semantic descriptions of electronic laboratory notebook records". Journal of Cheminformatics 5 (1): 52. doi:10.1186/1758-2946-5-52. PMC PMC3878183. PMID 24360292. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878183. 
  33. ↑ "E-Notebook for Chemistry". PerkinElmer, Inc. https://www.cambridgesoft.com/Ensemble_for_Chemistry/ENotebookforChemistry/. Retrieved 2017. 
  34. ↑ "epam/Indigo". GitHub, Inc. https://github.com/epam/Indigo. Retrieved 2017. 
  35. ↑ Day, A.E.; Coles, S.J.; Bird, C.L. et al. (2015). "ChemTrove: Enabling a generic ELN to support chemistry through the use of transferable plug-ins and online data sources". Journal of Chemical Information and Modeling 55 (3): 501–9. doi:10.1021/ci5005948. PMID 25679543. 
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  37. ↑ Willoughby, C.; Bird, C.L.; Coles, S.J.; Frey, J.G. (2014). "Creating context for the experiment record. User-defined metadata: investigations into metadata usage in the LabTrove ELN". Journal of Chemical Information and Modeling 54 (12): 3268–83. doi:10.1021/ci500469f. PMID 25405258. 
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  39. ↑ Lütjohann, D.S.; Jung, N.; Bräse, S. (2015). "Open source life science automation: Design of experiments and data acquisition via “dial-a-device”". Chemometrics and Intelligent Laboratory Systems 144: 100–107. doi:10.1016/j.chemolab.2015.04.002. 

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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