CARSTEN KETTNER STRENDA DB: THE PDB FOR ENZYME FUNCTION DATA? OPEN SCIENCE DAYS 2017 BERLIN 16 & 17 OCTOBER 2017
BEILSTEIN-INSTITUT Publications in enzymology 14000 enzyme kinetics metabolic pathway analysis Systems Biology 12000 10000 8000 6000 4000 2000 0 Source: PubMed (http://www.ncbi.nlm.nih.gov/pubmed), March 2017 OPEN SCIENCE DAYS 2017, BERLIN 2
BEILSTEIN-INSTITUT Is this information useful? October 2014 | Volume 11 | Issue 10 | e1001747 PeerJ 1:e148; DOI 10.7717/peerj.148 OPEN SCIENCE DAYS 2017, BERLIN 3
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/ 14% products) 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 OPEN SCIENCE DAYS 2017, BERLIN 4
BEILSTEIN-INSTITUT Science , Nov. 2014, 346(6210) http://www.nih.gov/about/reporting-preclinical-research.htm OPEN SCIENCE DAYS 2017, BERLIN 5
BEILSTEIN-INSTITUT STandards for Reporting ENzymology DAta founded in 2003 and supported by the Beilstein-Institut www.beilstein-strenda.org Barbara M. Bakker, Johann M. Rohwer, Antonio Baici, Santiago Schnell Athel Cornish-Bowden, Dietmar Schomburg, Paul F. Fitzpatrick, Neil Swainston, Peter Halling, Ming-Daw Tsai, Thomas S. Leyh, Roland Wohlgemuth, Claire O’Donovan, Ulrike Wittig, Frank M. Raushel Carsten Kettner OPEN SCIENCE DAYS 2017, BERLIN 6
BEILSTEIN-INSTITUT Standards for Reporting ENzymology DAta 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). OPEN SCIENCE DAYS 2017, BERLIN 7
BEILSTEIN-INSTITUT Standards for Reporting ENzymology DAta 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). http://www.beilstein-institut.de/en/projects/strenda/guidelines/ OPEN SCIENCE DAYS 2017, BERLIN 8
BEILSTEIN-INSTITUT Guidelines highly recommended by: ACS Catalysis FAIRsharing.org Archives in Biochemistry and Biophysics Antimicrobial Agents and Chemotherapy BBA (all nine sections) Biochem. and Biophys. Res. Communications PLoS Journals Biochemical Journal Biochemistry BioMedCentral Journals Biophysical Chemistry Clinical and Vaccine Immunology Beilstein J. Org. Chem. eLife eLife FEBS Journal FEBS Lett. Free Radical Research Infection and Immunity J. Biomed. Sci. Journal of the American Chemical Society Nature mBio OMICS Molecular and Cellular Biology Science Proceedings of the National Academy of Sciences The Journal of Bacteriology The Journal of Biological Chemistry The Journal of Virology Trends in Biotechnology […] OPEN SCIENCE DAYS 2017, BERLIN 9
BEILSTEIN-INSTITUT Standards are… 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 OPEN SCIENCE DAYS 2017, BERLIN 10
BEILSTEIN-INSTITUT Standards are… 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 In addition, they are… … often (comprehensively) long … too complicated … for experts only OPEN SCIENCE DAYS 2017, BERLIN 11
BEILSTEIN-INSTITUT Standards are useful… …BUT… Bosch Fawstin, http://fawstin.blogspot.de OPEN SCIENCE DAYS 2017, BERLIN 12
BEILSTEIN-INSTITUT Standards are useful… …BUT… …they are disregarded since • “nobody” reads instructions • not consistently enforced by editors • time consuming for editors, reviewers and Some prerequisites for acceptance authors • not made mandatory in editorial practice (expertise required) 1. Sufficiency. Comprehensive and relevant • no additional impact nor benefits for 2. Practicability. Useful but not too burdensome authors 3. Stability. Long-term access and support • competitive reasons OPEN SCIENCE DAYS 2017, BERLIN 13
BEILSTEIN-INSTITUT Making standards useful 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 14
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). • Customize, transform and update guidelines • 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” OPEN SCIENCE DAYS 2017, BERLIN 15
BEILSTEIN-INSTITUT Overview 2 1 identifier methodology & techniques kinetic params source assay conditions inhibition IMPORTANT: organism temperature, pH, etc. activitation • not a substitute for the review process! modifications Review/ • emphasis on monitoring information rather than defining reaction assayed correction acceptance criteria Check for compliance with STRENDA guidelines 1 PDB: 1BDG, hexokinase 2 Acker & Auld (2014) Perspectives in Science 1 (1-6):56-73. OPEN SCIENCE DAYS 2017, BERLIN 16
BEILSTEIN-INSTITUT Definition of • Type of Experiment Experiment • Methodology • Techniques OPEN SCIENCE DAYS 2017, BERLIN 17
BEILSTEIN-INSTITUT Definition of • Type of Experiment Experiment • Methodology • Techniques OPEN SCIENCE DAYS 2017, BERLIN 18
BEILSTEIN-INSTITUT Protein data: • Identifier Experiment • Source • Modifications • Reaction OPEN SCIENCE DAYS 2017, BERLIN 19
BEILSTEIN-INSTITUT Protein data: • Identifier Experiment 1 • Source • Modifications • Reaction Protein data: • Identifier Experiment 2 • Source • Modifications • Reaction Protein data: • Identifier Experiment 3 • Source • Modifications • Reaction OPEN SCIENCE DAYS 2017, BERLIN 20
BEILSTEIN-INSTITUT • Assay components • Temperature Experiment • pH OPEN SCIENCE DAYS 2017, BERLIN 21
BEILSTEIN-INSTITUT • Kinetic Assay Experiment Results params Conditions • Inhibition • Activation OPEN SCIENCE DAYS 2017, BERLIN 22
BEILSTEIN-INSTITUT Assay Experiment Results Conditions Dataset OPEN SCIENCE DAYS 2017, BERLIN 23
BEILSTEIN-INSTITUT Dataset 1 Assay Experiment Results Conditions Dataset 2 Assay Results Conditions Dataset 3 Assay Results Conditions Examples e.g. pH profile of protein X : Dataset n Exp 1 : pH 5 Assay Results Exp 2 : pH 6 Conditions … e.g. Temp. profile of protein Y : Exp 1 @ 15 °C Exp 2 @ 20 °C … OPEN SCIENCE DAYS 2017, BERLIN 24
BEILSTEIN-INSTITUT Dataset 1 Assay Experiment Results Conditions Dataset 2 Assay Results Conditions Dataset 3 Assay Results Conditions Examples e.g. pH profile of protein X : Dataset n Exp 1 : pH 5 Assay Results Exp 2 : pH 6 Conditions … e.g. Temp. profile of protein Y : Exp 1 @ 15 °C Exp 2 @ 20 °C … OPEN SCIENCE DAYS 2017, BERLIN 25
BEILSTEIN-INSTITUT Dataset 1 Assay Experiment Results Conditions Dataset 2 Assay Results Conditions Dataset 3 SRN/ DOI Assay Results Conditions Dataset n Assay Results Conditions non-public PMID OPEN SCIENCE DAYS 2017, BERLIN 26
BEILSTEIN-INSTITUT Dataset 1 Assay Experiment Results Conditions Dataset 2 Assay Results Conditions Dataset 3 SRN/ DOI Assay Results Conditions Dataset n Assay Results Conditions non-public PMID OPEN SCIENCE DAYS 2017, BERLIN 27
BEILSTEIN-INSTITUT Assay Enzyme Results Conditions Assay Results Conditions SRN/ DOI Assay Results Conditions Assay Results Conditions public PMID OPEN SCIENCE DAYS 2017, BERLIN 28
BEILSTEIN-INSTITUT STRENDA DB: Data Overview https://www.strenda-db.org OPEN SCIENCE DAYS 2017, BERLIN 29
BEILSTEIN-INSTITUT STRENDA DB: Interaction of stakeholders Transfer of Submit „closed“ DB STRENDA complete and published Data (unpublished DB data set data) Bibliographical data (PMID) User/ Read access STRENDA Author Registry No. Submit Publication Manuscript of data Editor(s)? Publication Process Reviewer(s)? (depends on data workflow) OPEN SCIENCE DAYS 2017, BERLIN 30
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