STRENDA DB: THE PDB FOR ENZYME FUNCTION DATA? OPEN SCIENCE DAYS - - PowerPoint PPT Presentation

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STRENDA DB: THE PDB FOR ENZYME FUNCTION DATA? OPEN SCIENCE DAYS - - PowerPoint PPT Presentation

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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

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OPEN SCIENCE DAYS 2017 BERLIN 16 & 17 OCTOBER 2017

CARSTEN KETTNER

STRENDA DB: THE PDB FOR ENZYME FUNCTION DATA?

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BEILSTEIN-INSTITUT

Publications in enzymology

2000 4000 6000 8000 10000 12000 14000

enzyme kinetics metabolic pathway analysis Systems Biology

Source: PubMed (http://www.ncbi.nlm.nih.gov/pubmed), March 2017

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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

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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

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Science, Nov. 2014, 346(6210) http://www.nih.gov/about/reporting-preclinical-research.htm

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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

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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

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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

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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

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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…

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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

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Standards are useful…

…BUT…

Bosch Fawstin, http://fawstin.blogspot.de

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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

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Making standards useful

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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

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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

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Overview

identifier source

  • rganism

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

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Experiment

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Definition of

  • Type of Experiment
  • Methodology
  • Techniques

OPEN SCIENCE DAYS 2017, BERLIN

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Experiment

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Definition of

  • Type of Experiment
  • Methodology
  • Techniques

OPEN SCIENCE DAYS 2017, BERLIN

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Experiment

Protein data:

  • Identifier
  • Source
  • Modifications
  • Reaction

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Experiment1 Experiment2

Protein data:

  • Identifier
  • Source
  • Modifications
  • Reaction

Experiment3

Protein data:

  • Identifier
  • Source
  • Modifications
  • Reaction

Protein data:

  • Identifier
  • Source
  • Modifications
  • Reaction

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Experiment

  • Assay components
  • Temperature
  • pH

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Experiment Results Assay Conditions

  • Kinetic

params

  • Inhibition
  • Activation

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Experiment Results Assay Conditions

Dataset

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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

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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

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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

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Experiment Results Assay Conditions Results Assay Conditions Results Assay Conditions Results Assay Conditions PMID

non-public Dataset1 Dataset2 Dataset3 Datasetn

SRN/ DOI

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Enzyme Results Assay Conditions Results Assay Conditions Results Assay Conditions Results Assay Conditions SRN/ DOI PMID

public

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https://www.strenda-db.org

STRENDA DB: Data Overview

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Submit Data „closed“ DB (unpublished data) STRENDA DB User/ Author Publication

  • f 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

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STRENDA DB: Perspectives and benefits

STRENDA DB

  • ther 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
  • n proteins
  • data summary sheet as SI

Perspectives

  • LIMS
  • Archive
  • ELN

e.g.

  • BRENDA
  • SABIO-RK
  • …

31 OPEN SCIENCE DAYS 2017, BERLIN

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Successes & Progesses

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Compliant with and harvested from

Registered with: Recommended by:

OPEN SCIENCE DAYS 2017, BERLIN

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https://www.strenda-db.org

Contact: strenda@beilstein-institut.de First data coming in …

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