STRENDA AND MIRAGE
EXAMPLES OF COMMUNITY-BASED DATA REPORTING STANDARDIZATION INITIATIVES
ACS 2016, SAN DIEGO
CARSTEN KETTNER & MARTIN HICKS
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Number of publications doubles every nine years
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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
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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
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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
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Pitfall – possible mis-interpretation of data
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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
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OH
In-Source Fragmentation
OH
C
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Enzymology – insight into the issues
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Tummler et al. (2014) FEBS J. 281:549-571
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Experimental results
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• in particular no data at all
• broad data ranges
• fragmented functional data (among journals)
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Experimental conditions
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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
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Metadata – data about the data
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Set up, Sample prep’s
Material & Technique
Software
Results
Interpre-tation &
Evaluation
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Paving the way(s) through bottom-up approaches
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… 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).
Standards for Reporting ENzymology DAta
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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).
Standards for Reporting ENzymology DAta
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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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
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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).
Standards for Reporting ENzymology DAta
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).
ACS MEETING 2016, SAN DIEGO
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
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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
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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
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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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1. Sufficiency. Comprehensive and relevant 2. Practicability. Useful but not too burdensome 3. Stability. Long-term access and support
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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1. Sufficiency. Comprehensive and relevant 2. Practicability. Useful but not too burdensome 3. Stability. Long-term access and support
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
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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
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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:
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How to enforce data publishing
in compliance with established guidelines?
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