Data sharing - Data management - The SysMO-SEEK Story

Data sharing Data management The SysMO-SEEK Story Professor Carole Goble FREng FBCS CITP University of Manchester, UK [email_address]

13 teams
91 institutes, 300 scientists
Multi-site, multi-disciplinary
Each three year duration
Data generation
Data consumption
Data analysis
Data management:
Local – Shared – Long term
Pan European Systems Biology http://www.sysmo.net

Own data solutions. wikis, e-Groupware, PHProjekt, BaseCamp, PLONE, Alfresco, bespoke commercial … files and spreadsheets. Extreme caution over sharing. Modellers vs experimentalist tribalism Many institutions, many projects, overlapping memberships, changing membership. Projects ending, starting, carrying on the same, carrying on differently. Legacy Suspicion Dynamics Expert scientists, inexpert informaticians. Few resources. Skills Patchy standards, incomparable data, afterthought. Data

Scientist Lab Collaborators Competitors Programme Published Post- Publication Pre- Publication

Data mine-ing
“ my impression of researchers, and I can criticize myself in this, is that we’re much more interested in sharing data when we mean sharing somebody else’s as opposed [to] sharing ours.”
E-infrastructure - taking forward the strategy , RIN report, 2010

1. Sharing Competitive advantage. Adoption. Kudos & Credit. Help. Fame. Reputation. Being scooped. Scrutiny. Misinterpretation. Cost. Blame. Reputation. Rewards Risks Nature 461 , 145 (10 September 2009)

“ It’s not ready yet” “ I need to get (another) publication first” “ We don’t have the resources or skills to prepare it for others, esp. now we finished that project” “ Its faster/easier to do it myself, and will keep the credit/control too ” “ Its not described enough to be usable” “ I don’t trust the quality. Its not reliable enough. Its too noisy. “ Others won’t use it properly.” “ It’s not worth my while” “ They are my competitors!!”

Pseudo Sharing

2. Preparation for Use
Curation
Standards
Reusability
Reproducibility
Accountability & Quality
Data discipline Silo busting

CIMR C ore I nformation for M etabolomics R eporting
MIABE M inimal I nformation A bout a B ioactive E ntity
MIACA M inimal I nformation A bout a C ellular A ssay
MIAME M inimum I nformation A bout a M icroarray E xperiment
MIAME/Env MIAME / Env ironmental transcriptomic experiment
MIAME/Nutr MIAME / Nutr igenomics
MIAME/Plant MIAME / Plant transcriptomics
MIAME/Tox MIAME / Tox icogenomics
MIAPA M inimum I nformation A bout a P hylogenetic A nalysis
MIAPAR M inimum I nformation A bout a P rotein A ffinity R eagent
MIAPE M inimum I nformation A bout a P roteomics E xperiment
MIARE M inimum I nformation A bout a R NAi E xperiment
MIASE M inimum I nformation A bout a S imulation E xperiment
MIENS M inimum I nformation about an EN vironmental S equence
MIFlowCyt M inimum I nformation for a Flow Cyt ometry Experiment
MIGen M inimum I nformation about a Gen otyping Experiment
MIGS M inimum I nformation about a G enome S equence
MIMIx M inimum I nformation about a M olecular I nteraction E x periment
MIMPP M inimal I nformation for M ouse P henotyping P rocedures
MINI M inimum I nformation about a N euroscience I nvestigation
MINIMESS Mini mal Me tagenome S equence Analysis S tandard
MINSEQE M inimum I nformation about a high-throughput S e Q uencing E xperiment
MIPFE M inimal I nformation for P rotein F unctional E valuation
MIQAS M inimal I nformation for Q TLs and A ssociation S tudies
MIqPCR M inimum I nformation about a q uantitative P olymerase C hain R eaction experiment
MIRIAM M inimal I nformation R equired I n the A nnotation of biochemical M odels
MISFISHIE M inimum I nformation S pecification F or I n S itu H ybridization and I mmunohistochemistry E xperiments
STRENDA St andards for Re porting En zymology Da ta
TBC T ox B iology C hecklist
BioPAX : Biological Pathways Exchange http://www.biopax.org/
FuGE Functional Genomics Experiment
MGED: Microarray Experimental Conditions
Minimum Information for Biological and Biomedical Investigations http://www.mibbi.org/index.php/MIBBI_portal Metadata Minefield

Publishing Process http://usefulchem.wikispaces.com/page/code/EXPLAN001 http://www.mygrid.org.uk/tools/taverna/ models software methods scripts http://openwetware.org standard operating procedures

Community Curation Responsiblity

Blue Collar Science John Quackenbush
Difficult and time consuming
Poor Credit or Reward
Shabby Career Paths & Prospects

3. Credit Crisis
Reward sharing, curation and reuse rather than reinvention.
Credit. Attribution. Citation.
For software, methods and standards too.
Technical (DataCite.org).
Cultural (Respected policy).
Institutional.
Funding bodies.

4. Infrastructure, Capability & Capacity
Three year PhD/project cycle
Local data control
Realistic paths to adoption by busy people.
Spreadsheets, wikis, catalogues and yellow pages.
Content and Tools

5. Data Ecosystem http://www.biosharing.org Identity Management Sharednames DataCite LSID DOIs ORCID Resources

6. Sustained Resources
Three year projects.
Three year lifespan of data (and its software).
Sunsets and Sustains
Reinvention rewarded
Institution.
Funding councils.
Funding panels.
Publishers
Libraries
National data centres
International data centres

Incentives. Sensitivity to Behaviours Infrastructure Community building Trusted service Coordination Governance Policy Capability Community Integration

A Partnership
Software engineers
Computational scientists
Experimental Scientists
Domain informaticians
Service providers
Funding agencies
But the community credit crisis continues….

http://www.rcuk.ac.uk/escience/einfrastructure.htm Coordination Sustainability Interoperability Adoption Capacity Data

Service Software Content Repository Registry Community Skills Methodology Software engineers Computational scientists Scientists Service providers Funding agencies

Summary
Science is a complex social activity undertaken by tribes of people and dominated by trust issues.
Infrastructure has to be there and fit for purpose but its not the real the problem.
Need a cultural shift (on all sides) that truly honours data.

Data sharing - Data management - The SysMO-SEEK Story

by Research Information Network on Nov 19, 2010

Accessibility

Categories

Tags

Upload Details

Usage Rights

Statistics

Data sharing - Data management - The SysMO-SEEK Story — Presentation Transcript