examples of community-based data reporting...

STRENDA AND MIRAGE

EXAMPLES OF COMMUNITY-BASED DATA REPORTING STANDARDIZATION INITIATIVES

ACS 2016, SAN DIEGO

CARSTEN KETTNER & MARTIN HICKS

BEILSTEIN-INSTITUT

Number of publications doubles every nine years

ACS MEETING 2016, SAN DIEGO 2

Segmented growth of the annual number of cited references from 1650 to 2012 (citing publications from 1980 to 2012)

(From: Bornman L, Mutz, R (2015) JAIST, 66(11):2215)

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Publications in enzymology


0

5000

10000

15000

20000

25000

30000

1960 1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 2015Metabolic Pathway Analysis Enzymology Systems Biology

Publications per year

Source: PubMed analysis as for February 2016

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Publications in glycobiology/-chemistry


0

100

200

300

400

500

600

700

800

900

1970 1975 1980 1985 1990 1995 2000 2005 2010

Publications per Year

MS DataGlycomics

Source: PubMed analysis as for July 2014

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Is this information useful?

5 PeerJ 1:e148; DOI 10.7717/peerj.148

October 2014 | Volume 11 | Issue 10 | e1001747

ACS MEETING 2016, SAN DIEGO

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Pitfall – possible mis-interpretation of data


C. Burlak, et al. 2013. Xenotransplantation 20: 277–291 (Figure 3D)

Annotation of MALDI-TOF Mass Spectrum of N-glycans isolated from a transgenic pig

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Pitfall: possible mis-interpretation of data


OH

In-Source Fragmentation

OH

C

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Enzymology – insight into the issues

8

Tummler et al. (2014) FEBS J. 281:549-571


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Experimental results

9

• in particular no data at all

• broad data ranges

• fragmented functional data (among journals)


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Experimental conditions

10 ACS MEETING 2016, SAN DIEGO

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A couple of examples…

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“The reaction mixture contained 100 µL of 2 mM ATChI as substrate and 100µL of 2 mM DTNB as chromogen added in 1.8 mL of 0.1 M phosphate buffer, an appropriate amount of the enzyme.”

Examples taken from Peter Halling et al., Poster „Standards are boring…“ presented at Gordon Conference 2010.

“So the soak solution was prepared freshly by mixing 2 volumes of 25% aqueous glutaraldehyde with 3 volumes of 250 mM Na-cacodylate buffer pH 6.5 containing 25% v/v glycerol and, where required, 1.5 M salt.”

Was pH set before or after adding glycerol and salt?

If after, was electrode calibrated in their

presence, and if so, how?

What pH? What cation?


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…last question

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Values in these units depend on arbitrary

choice of reaction volume.

“The amounts of released soluble hydrolysis products were calculated based on the enzyme concentrations employed (mM/mg protein).”

Examples taken from Peter Halling et al., Poster „Standards are boring…“ presented at Gordon Conference 2010.


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Survey in SABIO-RK: missing and imprecise information in publications

no indication of UniProtKB AC 85%

no indication of temperature 12% "room temperature" 6% incomplete biochemical reactions (missing products) 14% no standard units for concentrations of compounds 20%

experimental conditions in references 10%

inconsistent experimental conditions within the publication 6%

as for September 2013

13 ACS MEETING 2016, SAN DIEGO

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Metadata – data about the data


Set up, Sample prep’s

Material & Technique

Software

Results

Interpre-tation &

Evaluation

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Paving the way(s) through bottom-up approaches


… for enzymology… …for glycomics

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Standards for Reporting ENzymology DAta

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Richard N. Armstrong, Amos Bairoch, Barbara M. Bakker, Athel Cornish-Bowden, Paul F. Fitzpatrick, Peter Halling, Thomas S. Leyh,

Claire O'Donovan, Frank M. Raushel, Johann M. Rohwer, Dietmar Schomburg, Neil Swainston, Ming-Daw Tsai, Carsten Kettner

founded in 2003 and supported by the Beilstein-Institut www.beilstein-strenda.org


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Organisation

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Systems biology

Nomenclature Databases

Enzyme superfamilies

Biocatalysis

Metabolic control analysis

Mechanistic enzymology

Software development

Synthetic proteins


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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 acquisition system

(STRENDA DB).



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(STRENDA DB).




(STRENDA DB).


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Guidelines highly recommended

ACS Catalysis Archives in Biochemistry and Biophysics Antimicrobial Agents and Chemotherapy BBA (all nine sections) Biochemical and Biophysical Research Communications Biochemical Journal Biochemistry Clinical and Vaccine Immunology FEBS Journal Free Radical Research Infection and Immunity Journal of the American Chemical Society mBio Molecular and Cellular Biology Nature Chemical Biology Proceedings of the National Academy of Sciences The Journal of Bacteriology The Journal of Biological Chemistry The Journal of Virology Trends in Biotechnology

PLoS BMC

OMICS

biosharing.org

20

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(STRENDA DB).




(STRENDA DB).


https://www.beilstein-strenda-db.org/strenda/

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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

22 ACS MEETING 2016, SAN DIEGO https://www.beilstein-strenda-db.org/strenda/

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Minimum Information Required for A Glycomics Experiment

founded in 2011 and supported by the Beilstein-Institut www.beilstein-mirage.org

Sanjay Agravat Matthew Campbell Stuart Haslam, Carsten Kettner Daniel Kolarich Yan Liu, Ryan McBride René Ranzinger Erdmann Rapp Weston Struwe Will York Joseph Zaia

Catherine Costello Anne Dell Ten Feizi Niclas Karlsson Kay-Hooi Khoo Milos Novotny Nicolle Packer James Paulson Pauline Rudd Michael Tiemeyer Lance Wells David Smith

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Aims & organisation


Interaction Analysis Subgroup Guidelines for biological interactions of

glycans with other macromolecules (Micro arrays, SPR, ELISA, ITC, flow

cytometry, NMR,…)

Structural Analysis Subgroup Guidelines for sample preparation and

identification of glycan structures (MS, LC, CE, sample preparations,…)

Bioinformatics Subgroup Integration of data processing

parameters into guidelines, definition of data exchange formats

(Exchange file formats, integration for db‘s,…)

Advisory Board Coordination

Working Groups

The development of publication guidelines for interaction and structural glycomics data as well as the development of data exchange formats.

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Workflow for the development of guidelines


Subgroups discussion and guideline draft

MIRAGE committee meetings Refinement of guideline draft

Review by Advisory board Specific inputs to guideline draft

Review and comments by broad scientific community

Publication of guidelines

Kolarich et al. (2013) Mol. Cell. Prot. 12(4):991-995

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MIRAGE MS guidelines


General features

Ion Sources

Ion transfer and detection

Spectrum and peak list generation

Interpretation and

validation

e.g. instrument manufacturer, customisation, software

e.g. source fragementation, degree of fragmentation (ESI, MALDI)

e.g. hardware options, detectors

e.g. description of analytical results

e.g. overview of software tools (and databases) used

Kolarich et al. (2013) Mol. Cell. Prot. 12(4):991-995

MS Guidelines

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1. Sufficiency. Comprehensive and relevant 2. Practicability. Useful but not too burdensome 3. Stability. Long-term access and support

Guidelines aren’t substitutes for the review process

Essential prerequisites for acceptance


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Some Prerequisites for Acceptance

• structured • easy to follow • short (maximum three pages per guideline) • ideally, with examples and/or comments

If longer, then customize!


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Some Prerequisites for Acceptance

• review on regular basis • track changes • provided on stable web sites • increase visibility by sharing on various web sites

(institutes, biosharing.org, etc.) • long-term funding of working groups • published in subject-related journals


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Two initiatives- on different ways


Organisation Simple and small Complex and large

Guidelines • More general • Functional enzymology • Ready to use • Rec’d by > 30 journals

• Methodology-focused; • Mass Spec, ready to use

but complex; • Adopted for journals’

guidelines;

Tools STRENDA DB

Pipeline • Standards for experimental conditions

• glycan arrays, LC, sample preparation, CE

• Software tools tbd.

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Conclusions


Aims

• improvement of data reporting

• data sharing and exchange

Benefits • by/for the community • experimentalists’

expertise • broad acceptance

Requirements • leaders in the fields • journals • funding agencies

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For the discussion:


How to enforce data publishing

in compliance with established guidelines?

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examples of community-based data reporting...

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