Standards for Reporting Enzymology Data

The STRENDA project is driven by 15 scientists from all over the world forming the STRENDA Commission{{Cite web|url=https://www.beilstein-institut.de/en/projects/strenda/commission|title=Commission - Strenda - Projects - Beilstein-Institut zur Förderung der Chemischen Wissenschaften|website=www.beilstein-institut.de}} and supporting the work with expertises in biochemistry, [https://www.qmul.ac.uk/sbcs/iubmb/enzyme/ enzyme nomenclature], bioinformatics, systems biology, modelling, mechanistic enzymology and theoretical biology.

The STRENDA Guidelines{{Cite web|url=https://www.beilstein-institut.de/en/projects/strenda/guidelines|title=Guidelines - Strenda - Projects - Beilstein-Institut zur Förderung der Chemischen Wissenschaften|website=www.beilstein-institut.de}} 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.{{cite journal |last1=Tipton |first1=Keith F. |last2=Armstrong |first2=Richard N. |last3=Bakker |first3=Barbara M. |last4=Bairoch |first4=Amos |last5=Cornish-Bowden |first5=Athel |last6=Halling |first6=Peter J. |last7=Hofmeyr |first7=Jan-Hendrik |last8=Leyh |first8=Thomas S. |last9=Kettner |first9=Carsten |last10=Raushel |first10=Frank M. |last11=Rohwer |first11=Johann |last12=Schomburg |first12=Dietmar |last13=Steinbeck |first13=Christoph |title=Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful |journal=Perspectives in Science |date=May 2014 |volume=1 |issue=1–6 |pages=131–137 |doi=10.1016/j.pisc.2014.02.012 |doi-access=free}}{{cite journal |last1=Gardossi |first1=Lucia |last2=Poulsen |first2=Pout B. |last3=Ballesteros |first3=Antonio |last4=Hult |first4=Karl |last5=Svedas |first5=Vytas K. |last6=Vasic-Racki |first6=Durda |last7=Carrea |first7=Giacomo |last8=Magnusson |first8=Anders |last9=Schmid |first9=Andreas |last10=Wohlgemuth |first10=Roland |last11=Halling |first11=Peter J. |title=Guidelines for reporting of biocatalytic reactions |journal=Trends in Biotechnology |date=April 2010 |volume=28 |issue=4 |pages=171–180 |doi=10.1016/j.tibtech.2010.01.001|pmid=20149467 }}{{cite journal |last1=Erb |first1=Tobias J. |title=Back to the future: Why we need enzymology to build a synthetic metabolism for the future |journal=Beilstein Journal of Organic Chemistry |date=February 2019 |volume=15 |pages=551–557 |doi=10.3762/bjoc.15.49 |doi-access=free |pmid=30873239 |pmc=6404388 |s2cid=76665217 }}{{cite journal |last1=Gygli |first1=Gudrun |last2=Pleiss |first2=Juergen |title=Simulation Foundry: Automated and FAIR molecular modeling |journal=Journal of Chemical Information and Modeling |date=April 2020 |volume=60 |issue=4 |pages=1922–1927 |doi=10.1021/acs.jcim.0c00018|pmid=32240586 |s2cid=214772277 }}

As of March 2020, more than 55 international biochemistry journal included the STRENDA Guidelines in their authors' instructions as recommendations when reporting enzymology data.{{Cite web|url=https://www.beilstein-institut.de/en/projects/strenda/journals|title=Journals - Strenda - Projects - Beilstein-Institut zur Förderung der Chemischen Wissenschaften|website=www.beilstein-institut.de}}

The STRENDA project is registered with FAIRsharing.org{{cite journal |title=STRENDA at FAIRsharing.org |year=2015|doi=10.25504/FAIRsharing.8ntfwm|author1=FAIRsharing Team|publisher=FAIRsharing}} and the Guidelines are part of the FAIRDOM Community standards for Systems Biology.{{cite web |title=FAIRDOM Community Standards for Systems Biology |url=https://fairsharing.org/collection/FAIRDOM}}

STRENDA DB

STRENDA DB{{Cite web|url=https://www.beilstein-strenda-db.org/strenda/index.xhtml|title=STRENDA DB Home|website=www.beilstein-strenda-db.org}} 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 [https://datacite.org 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.{{cite journal |last1=Apweiler |first1=Rolf |last2=Armstrong |first2=Richard |last3=Bairoch |first3=Amos |last4=Cornish-Bowden |first4=Athel |last5=Halling |first5=Peter J |last6=Hofmeyr |first6=Jan-Hendrik S |last7=Kettner |first7=Carsten |last8=Leyh |first8=Thomas S |last9=Rohwer |first9=Johann |last10=Schomburg |first10=Dietmar |last11=Steinbeck |first11=Christoph |last12=Tipton |first12=Keith |title=A large-scale protein-function database |journal=Nature Chemical Biology |date=18 October 2010 |volume=6 |issue=11 |pages=785 |doi=10.1038/nchembio.460 |doi-access=free |pmid=20956966 |pmc=3245624 }}{{cite journal |last1=Swainston |first1=Neil |last2=Baici |first2=Antonio |last3=Bakker |first3=Barbara M. |last4=Cornish-Bowden |first4=Athel |last5=Fitzpatrick |first5=Paul F. |last6=Halling |first6=Peter |last7=Leyh |first7=Thomas S. |last8=O'Donovan |first8=Claire |last9=Raushel |first9=Frank M. |last10=Reschel |first10=Udo |last11=Rohwer |first11=Johann M. |last12=Schnell |first12=Santiago |last13=Schomburg |first13=Dietmar |last14=Tipton |first14=Keith F. |last15=Tsai |first15=Ming-Daw |last16=Westerhoff |first16=Hans V. |last17=Wittig |first17=Ulrike |last18=Wohlgemuth |first18=Roland |last19=Kettner |first19=Carsten |title=STRENDA DB: enabling the validation and sharing of enzyme kinetics data |journal=The FEBS Journal |date=23 March 2018 |volume=285 |issue=12 |pages=2193–2204 |doi=10.1111/febs.14427 |doi-access=free |pmid=29498804 |pmc=6005732 }}

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 [https://nature.com Nature], [https://www.jbc.org The Journal of Biological Chemistry], [https://elifesciences.org eLife], and [https://www.plos.org PLoS]. It has been referred as a standard tool for the validation and storage of enzyme kinetics data in multifold publications {{cite book |last1=Fademrecht |first1=Silvia |last2=Pleiss |first2=Jürgen |title=Einführung in die Enzymtechnologie |date=2018 |publisher=Springer |isbn=978-3-662-57619-9 |pages=35–51 |language=de |chapter=Enzymmodellierung: von der Sequenz zum Substratkomplex|doi=10.1007/978-3-662-57619-9_3 }}{{cite book |last1=Cornish-Bowden |first1=Athel |title=Fundamentals of enzyme kinetics |date=2012 |publisher=Wiley-VCH |isbn=978-3-527-33074-4 |pages=413–450 |edition=4th., rev. and enlarged}}{{cite book |last1=Emmerich |first1=Christoph H. |last2=Harris |first2=Christopher M. |title=Good Research Practice in Non-Clinical Pharmacology and Biomedicine |date=2020 |publisher=Springer International Publishing |isbn=978-3-030-33656-1 |pages=177–196 |language=en |chapter=Minimum Information and Quality Standards for Conducting, Reporting, and Organizing In Vitro Research|series=Handbook of Experimental Pharmacology |volume=257 |doi=10.1007/164_2019_284 |doi-access=free |pmid=31628600 }}{{cite book |last1=Punekar |first1=N. S. |title=ENZYMES: Catalysis, Kinetics and Mechanisms |date=2018 |publisher=Springer |isbn=978-981-13-0785-0 |pages=131–142 |language=en |chapter=Good Kinetic Practices|doi=10.1007/978-981-13-0785-0_13 }}{{cite book |last1=National Academies of Sciences |first1=Engineering |title=Open Science by Design: Realizing a Vision for 21st Century Research |date=2018 |isbn=978-0-309-47624-9 |url=https://www.nap.edu/catalog/25116/open-science-by-design-realizing-a-vision-for-21st-century |language=en}}{{cite book |last1=Harmer |first1=Nicholas J. |last2=Vega |first2=Mirella Vivoli |title=Biomolecular and Bioanalytical Techniques |date=2019 |publisher=John Wiley & Sons, Ltd |isbn=978-1-119-48397-7 |pages=179–217 |language=en |chapter=Reaction Chemical Kinetics in Biology|doi=10.1002/9781119483977.ch9 |s2cid=133422670 }}

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.{{cite journal |last1=Halling |first1=Peter |last2=Fitzpatrick |first2=Paul F. |last3=Raushel |first3=Frank M. |last4=Rohwer |first4=Johann |last5=Schnell |first5=Santiago |last6=Wittig |first6=Ulrike |last7=Wohlgemuth |first7=Roland |last8=Kettner |first8=Carsten |title=An empirical analysis of enzyme function reporting for experimental reproducibility: Missing/incomplete information in published papers |journal=Biophysical Chemistry |date=November 2018 |volume=242 |pages=22–27 |doi=10.1016/j.bpc.2018.08.004|pmid=30195215 |pmc=6258184 }}

Data Management

STRENDA DB is considered a tool for research data management by the research community (e.g. EU project CARBAFIN{{Cite web|url=https://ec.europa.eu/research/participants/documents/downloadPublic?documentIds=080166e5bbcee782&appId=PPGMS|title=Documents download module|website=ec.europa.eu}}).

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• Record in FAIRSharing.org for STRENDA DB, https://fairsharing.org/FAIRsharing.ekj9zx

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Category:Biochemistry

Category:Proteins

Category:Enzymes

Category:Standards

Category:Biological databases