Standards for Reporting Enzymology Data

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Standards for Reporting Enzymology Data (STRENDA) is an initiative as part of the Minimum Information Standards which specifically focuses on the development of guidelines for reporting (describing metadata) enzymology experiments. The initiative is supported by the Beilstein Institute for the Advancement of Chemical Sciences. [1] STRENDA establishes both publication standards for enzyme activity data and STRENDA DB, an electronic validation and storage system for enzyme activity data. Launched in 2004, the foundation of STRENDA is the result of a detailed analysis of the quality of enzymology data in written and electronic publications. [2] [3]

Contents

Organization

The STRENDA project is driven by 15 scientists from all over the world forming the STRENDA Commission [4] and supporting the work with expertises in biochemistry, enzyme nomenclature, bioinformatics, systems biology, modelling, mechanistic enzymology and theoretical biology.

Reporting guidelines

The STRENDA Guidelines [5] propose those minimum information that is needed to comprehensively report kinetic and equilibrium data from investigations of enzyme activities including corresponding experimental conditions. This minimum information is suggested to be addressed in a scientific publication when enzymology research data is reported to ensure that data sets are comprehensively described. This allows scientists not only to review, interpret and corroborate the data but also to reuse the data for modelling and simulation of biocatalytic pathways. In addition, the guidelines support researchers making their experimental data reproducible and transparent. [6] [7] [8] [9]

As of March 2020, more than 55 international biochemistry journal included the STRENDA Guidelines in their authors' instructions as recommendations when reporting enzymology data. [10] The STRENDA project is registered with FAIRsharing.org [11] and the Guidelines are part of the FAIRDOM Community standards for Systems Biology. [12]

Applications

STRENDA DB

STRENDA DB [13] is a web-based storage and search platform that has incorporated the Guidelines and automatically checks the submitted data on compliance with the STRENDA Guidelines thus ensuring that the manuscript data sets are complete and valid. A valid data set is awarded a STRENDA Registry Number (SRN) and a fact sheet (PDF) is created containing all submitted data. Each dataset is registered at Datacite and assigned a DOI to refer and track the data. After the publication of the manuscript in a peer-reviewed journal the data in STRENDA DB are made open accessible. [14] [15] STRENDA DB is a repository recommended by re3data and OpenDOAR. It is harvested by OpenAIRE. The database service is recommended in the authors' instructions of more than 10 biochemistry journals, including Nature, The Journal of Biological Chemistry, eLife, and PLoS. It has been referred as a standard tool for the validation and storage of enzyme kinetics data in multifold publications [16] [17] [18] [19] [20] [21] A recent study examining eleven publications, including Supporting Information, from two leading journals revealed that at least one omission was found in every one of these papers. The authors concluded that using STRENDA DB in the current version would ensure that about 80% auf the relevant information would be made available. [22]

Data Management

STRENDA DB is considered a tool for research data management by the research community (e.g. EU project CARBAFIN [23] ).

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References

  1. ↑ "Strenda - Projects - Beilstein-Institut zur Förderung der Chemischen Wissenschaften". www.beilstein-institut.de.
  2. ↑ Kettner, Carsten; Hicks, Martin (1 June 2005). "The Dilemma of Modern Functional Enzymology". Current Enzyme Inhibition. 1 (2): 171–181. doi:10.2174/1573408054022234.
  3. ↑ Apweiler, R; Cornish-Bowden, A; Hofmeyr, JH; Kettner, C; Leyh, TS; Schomburg, D; Tipton, K (January 2005). "The importance of uniformity in reporting protein-function data". Trends in Biochemical Sciences. 30 (1): 11–2. doi:10.1016/j.tibs.2004.11.002. PMID   15653320.
  4. ↑ "Commission - Strenda - Projects - Beilstein-Institut zur Förderung der Chemischen Wissenschaften". www.beilstein-institut.de.
  5. ↑ "Guidelines - Strenda - Projects - Beilstein-Institut zur Förderung der Chemischen Wissenschaften". www.beilstein-institut.de.
  6. ↑ Tipton, Keith F.; Armstrong, Richard N.; Bakker, Barbara M.; Bairoch, Amos; Cornish-Bowden, Athel; Halling, Peter J.; Hofmeyr, Jan-Hendrik; Leyh, Thomas S.; Kettner, Carsten; Raushel, Frank M.; Rohwer, Johann; Schomburg, Dietmar; Steinbeck, Christoph (May 2014). "Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful". Perspectives in Science. 1 (1–6): 131–137. doi: 10.1016/j.pisc.2014.02.012 .
  7. ↑ Gardossi, Lucia; Poulsen, Pout B.; Ballesteros, Antonio; Hult, Karl; Svedas, Vytas K.; Vasic-Racki, Durda; Carrea, Giacomo; Magnusson, Anders; Schmid, Andreas; Wohlgemuth, Roland; Halling, Peter J. (April 2010). "Guidelines for reporting of biocatalytic reactions". Trends in Biotechnology. 28 (4): 171–180. doi:10.1016/j.tibtech.2010.01.001. PMID   20149467.
  8. ↑ Erb, Tobias J. (February 2019). "Back to the future: Why we need enzymology to build a synthetic metabolism for the future". Beilstein Journal of Organic Chemistry. 15: 551–557. doi: 10.3762/bjoc.15.49 . PMC   6404388 . PMID   30873239. S2CID   76665217.
  9. ↑ Gygli, Gudrun; Pleiss, Juergen (April 2020). "Simulation Foundry: Automated and FAIR molecular modeling". Journal of Chemical Information and Modeling. 60 (4): 1922–1927. doi:10.1021/acs.jcim.0c00018. PMID   32240586. S2CID   214772277.
  10. ↑ "Journals - Strenda - Projects - Beilstein-Institut zur Förderung der Chemischen Wissenschaften". www.beilstein-institut.de.
  11. ↑ FAIRsharing Team (2015). "STRENDA at FAIRsharing.org". FAIRsharing. doi:10.25504/FAIRsharing.8ntfwm.{{cite journal}}: Cite journal requires |journal= (help)
  12. ↑ "FAIRDOM Community Standards for Systems Biology".
  13. ↑ "STRENDA DB Home". www.beilstein-strenda-db.org.
  14. ↑ 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 (18 October 2010). "A large-scale protein-function database". Nature Chemical Biology. 6 (11): 785. doi: 10.1038/nchembio.460 . PMC   3245624 . PMID   20956966.
  15. ↑ Swainston, Neil; Baici, Antonio; Bakker, Barbara M.; Cornish‐Bowden, Athel; Fitzpatrick, Paul F.; Halling, Peter; Leyh, Thomas S.; O'Donovan, Claire; Raushel, Frank M.; Reschel, Udo; Rohwer, Johann M.; Schnell, Santiago; Schomburg, Dietmar; Tipton, Keith F.; Tsai, Ming‐Daw; Westerhoff, Hans V.; Wittig, Ulrike; Wohlgemuth, Roland; Kettner, Carsten (23 March 2018). "STRENDA DB: enabling the validation and sharing of enzyme kinetics data". The FEBS Journal. 285 (12): 2193–2204. doi: 10.1111/febs.14427 . PMC   6005732 . PMID   29498804.
  16. ↑ Fademrecht, Silvia; Pleiss, Jürgen (2018). "Enzymmodellierung: von der Sequenz zum Substratkomplex". Einführung in die Enzymtechnologie (in German). Springer. pp. 35–51. doi:10.1007/978-3-662-57619-9_3. ISBN   978-3-662-57619-9.
  17. ↑ Cornish-Bowden, Athel (2012). Fundamentals of enzyme kinetics (4th., rev. and enlarged ed.). Wiley-VCH. pp. 413–450. ISBN   978-3-527-33074-4.
  18. ↑ Emmerich, Christoph H.; Harris, Christopher M. (2020). "Minimum Information and Quality Standards for Conducting, Reporting, and Organizing In Vitro Research". Good Research Practice in Non-Clinical Pharmacology and Biomedicine. Handbook of Experimental Pharmacology. Vol. 257. Springer International Publishing. pp. 177–196. doi: 10.1007/164_2019_284 . ISBN   978-3-030-33656-1. PMID   31628600.
  19. ↑ Punekar, N. S. (2018). "Good Kinetic Practices". ENZYMES: Catalysis, Kinetics and Mechanisms. Springer. pp. 131–142. doi:10.1007/978-981-13-0785-0_13. ISBN   978-981-13-0785-0.
  20. ↑ National Academies of Sciences, Engineering (2018). Open Science by Design: Realizing a Vision for 21st Century Research. ISBN   978-0-309-47624-9.
  21. ↑ Harmer, Nicholas J.; Vega, Mirella Vivoli (2019). "Reaction Chemical Kinetics in Biology". Biomolecular and Bioanalytical Techniques. John Wiley & Sons, Ltd. pp. 179–217. doi:10.1002/9781119483977.ch9. ISBN   978-1-119-48397-7. S2CID   133422670.
  22. ↑ Halling, Peter; Fitzpatrick, Paul F.; Raushel, Frank M.; Rohwer, Johann; Schnell, Santiago; Wittig, Ulrike; Wohlgemuth, Roland; Kettner, Carsten (November 2018). "An empirical analysis of enzyme function reporting for experimental reproducibility: Missing/incomplete information in published papers". Biophysical Chemistry. 242: 22–27. doi:10.1016/j.bpc.2018.08.004. PMC   6258184 . PMID   30195215.
  23. ↑ "Documents download module". ec.europa.eu.

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