Kettner, C.

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OPEN SCIENCE DAYS 2017 BERLIN 16 & 17 OCTOBER 2017 CARSTEN KETTNER STRENDA DB: THE PDB FOR ENZYME FUNCTION DATA? BEILSTEIN-INSTITUT  Publications in enzymology  02000400060008000100001200014000enzyme kinetics metabolic pathway analysis Systems BiologySource: PubMed (http://www.ncbi.nlm.nih.gov/pubmed), March 2017 2 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Is this information useful?  PeerJ 1:e148; DOI 10.7717/peerj.148 October 2014 | Volume 11 | Issue 10 | e1001747 3 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT   Missing and imprecise information …on the assay conditions… no indication of UniProtKB AC 85% Missing enzyme concentration 63% no indication of temperature  12% "room temperature" 6% incomplete biochemical reactions (missing substrates/ products) 14% no standard units for concentrations of compounds 20% experimental conditions in references 10% inconsistent experimental conditions within the publication 6% Survey in SABIO-RK, as for September 2017 4 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Science, Nov. 2014, 346(6210) http://www.nih.gov/about/reporting-preclinical-research.htm 5 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  STandards for Reporting ENzymology DAta Barbara M. Bakker,  Antonio Baici, Athel Cornish-Bowden,  Paul F. Fitzpatrick,  Peter Halling,  Thomas S. Leyh, Claire O’Donovan, Frank M. Raushel Johann M. Rohwer, Santiago Schnell  Dietmar Schomburg,  Neil Swainston,  Ming-Daw Tsai, Roland Wohlgemuth, Ulrike Wittig,  Carsten Kettner  founded in 2003 and supported by the Beilstein-Institut  www.beilstein-strenda.org  6 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Mission: 1. Development of experimental standard conditions; (1)  Definition of minimum information for reporting enzyme functional data (STRENDA Guidelines); (2)  Generation of a comprehensive data acquisition system  (STRENDA DB). Standards for Reporting ENzymology DAta 7 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Standards for Reporting ENzymology DAta http://www.beilstein-institut.de/en/projects/strenda/guidelines/ Mission: 1.  Development of experimental standard conditions; 2.  Definition of minimum information for reporting enzyme  function data (STRENDA Guidelines); 3.  Generation of a comprehensive data acquisition system  (STRENDA DB). 8 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Guidelines highly recommended by:  ACS Catalysis Archives in Biochemistry and Biophysics Antimicrobial Agents and Chemotherapy BBA (all nine sections) Biochem. and Biophys. Res. Communications Biochemical Journal Biochemistry Biophysical Chemistry Clinical and Vaccine Immunology eLife FEBS Journal Free Radical Research Infection and Immunity Journal of the American Chemical Society mBio Molecular and Cellular Biology Proceedings of the National Academy of Sciences The Journal of Bacteriology The Journal of Biological Chemistry The Journal of Virology Trends in Biotechnology […] FAIRsharing.org PLoS Journals BioMedCentral Journals Beilstein J. Org. Chem. eLife FEBS Lett. J. Biomed. Sci. Nature OMICS Science 9 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Standards are…  … demanded and appreciated by the community … created by the community after internal and  external consultation … recommended by journals … included in instructions for authors Standards are… 10 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Standards are…  … demanded and appreciated by the community … created by the community after internal and  external consultation … recommended by journals … included in instructions for authors Standards are… In addition, they are… … often (comprehensively) long … too complicated … for experts only 11 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Standards are useful…  …BUT… Bosch Fawstin, http://fawstin.blogspot.de 12 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Standards are useful…  …BUT… …they are disregarded since • “nobody” reads instructions • not consistently enforced by editors • time consuming for editors, reviewers and authors • not made mandatory in editorial practice (expertise required) • no additional impact nor benefits for authors • competitive reasons 1. Sufficiency.  Comprehensive and relevant 2. Practicability.  Useful but not too burdensome 3. Stability.   Long-term access and support Some prerequisites for acceptance  13 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Making standards useful  14 Missions: 1. Development of experimental standard conditions; 2. Definition of minimum information for reporting enzyme functional data (STRENDA Guidelines); 3. Generation of a comprehensive data validation system      (STRENDA DB). OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Making standards applicable  Mission: 1. Development of experimental standard conditions; 2. Definition of minimum information for reporting enzyme function data (STRENDA Guidelines); 3. Generation of a comprehensive data validation system       (STRENDA DB). • Assessment tool for authors and journals • Direct data submission by authors • Storage of data in a freely accessible database • STRENDA DB: the “PDB for enzyme function” • Customize, transform and update guidelines 15 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Overview identifier source organism modifications reaction assayed methodology & techniques assay conditions temperature, pH, etc. kinetic params inhibition activitation Check for compliance with STRENDA guidelines Review/ correction 1 PDB: 1BDG, hexokinase 2 Acker & Auld (2014) Perspectives in Science 1(1-6):56-73. 1 2 IMPORTANT:  • not a substitute for the review process! • emphasis on monitoring information rather than defining acceptance criteria 16 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment 17 Definition of • Type of Experiment • Methodology • Techniques OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment 18 Definition of • Type of Experiment • Methodology • Techniques OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment Protein data:  • Identifier • Source • Modifications • Reaction 19 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment1 Experiment2 Protein data:  • Identifier • Source • Modifications • Reaction Experiment3 Protein data:  • Identifier • Source • Modifications • Reaction Protein data:  • Identifier • Source • Modifications • Reaction 20 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment • Assay components • Temperature • pH 21 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment Results Assay Conditions • Kinetic params • Inhibition • Activation 22 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment Results Assay Conditions Dataset 23 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment Results Assay Conditions Results Assay Conditions Results Assay Conditions Results Assay Conditions Dataset1 Dataset2 Dataset3 Datasetn e.g. pH profile of protein X: Exp1: pH 5 Exp2: pH 6 … e.g. Temp. profile of protein Y: Exp1 @ 15 °C Exp2 @ 20 °C … Examples 24 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment Results Assay Conditions Results Assay Conditions Results Assay Conditions Results Assay Conditions Dataset1 Dataset2 Dataset3 Datasetn e.g. pH profile of protein X: Exp1: pH 5 Exp2: pH 6 … e.g. Temp. profile of protein Y: Exp1 @ 15 °C Exp2 @ 20 °C … Examples 25 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment Results Assay Conditions Results Assay Conditions Results Assay Conditions Results Assay Conditions non-public PMID Dataset3 Datasetn Dataset2 Dataset1 SRN/ DOI 26 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Experiment Results Assay Conditions Results Assay Conditions Results Assay Conditions Results Assay Conditions PMID non-public Dataset1 Dataset2 Dataset3 Datasetn SRN/ DOI 27 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Enzyme Results Assay Conditions Results Assay Conditions Results Assay Conditions Results Assay Conditions SRN/ DOI PMID public 28 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  https://www.strenda-db.org STRENDA DB:  Data Overview 29 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Submit Data „closed“ DB (unpublished data) STRENDA DB User/ Author Publication of data Transfer of  complete and published  data set Bibliographical data (PMID) Submit Manuscript Publication Process (depends on data workflow) Editor(s)? Reviewer(s)? Read access STRENDA Registry No. STRENDA DB:  Interaction of stakeholders 30 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  STRENDA DB: Perspectives and benefits STRENDA DB other DBs Web services  (read access) • free access to data • low burden for authors  • data input prior or during publication • uniform structure of information • comparison of kinetic data • access to assay conditions • comprehensive information  on proteins • data summary sheet as SI Perspectives • LIMS • Archive • ELN e.g.  • BRENDA • SABIO-RK • … 31 OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  Successes & Progesses 32 Compliant with and harvested from Registered with: Recommended by: OPEN SCIENCE DAYS 2017, BERLIN BEILSTEIN-INSTITUT  https://www.strenda-db.org Contact: strenda@beilstein-institut.de First data coming in … 33 OPEN SCIENCE DAYS 2017, BERLIN 

STRENDA DB: The PDB for Enzyme Function Data?

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