a centre of expertise in digital information management ukoln is supported by: evolution or...
TRANSCRIPT
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A centre of expertise in digital information management
www.ukoln.ac.uk
UKOLN is supported by:
Evolution or revolution? The changing data landscape
Dr Liz Lyon, Associate Director, UK Digital Curation Centre Director, UKOLN, University of Bath, UK
3rd DCC Regional Roadshow, Glasgow, June 2011
.
This work is licensed under a Creative Commons LicenceAttribution-ShareAlike 2.0
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“Data sets are becoming the new instruments of science”
Dan Atkins, Univ Michigan
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Digital data as the new special collections?
Sayeed Choudhury, Johns Hopkins
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Research data : institutional
crown jewels?
http://www.flickr.com/photos/lifes__too_short__to__drink__cheap__wine/4754234186 /
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Perspectives• Environmental scan
– Scale and complexity– Infrastructure– Open science
• Policy– Funders– Institutions– Ethics & IP
• Practice Challenges– Storage– Incentives– Costs & Sustainability
http://www.flickr.com/photos/thegreenalbum/3997609142/
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“Surfing the Tsunami”Science: 11 February 2011
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“I worry there won’t be enough people around to do the analysis.” Chris Ponting, University of Oxford
“The costs of sequencing DNA has taken a nosedive...and is now dropping by 50% every 5 months”.
“A single sequencer can now generate in a day what it took 10 years to collect for the Human Genome Project”.
“The 1000 Genomes Project generated more DNA sequence data in its first 6 months than GenBank had accumulated in its entire 21 year existence”.
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PDB
GenBank
UniProt
Pfam
Spreadsheets, NotebooksLocal, Lost
High throughput experimental methodsIndustrial scaleCommons based productionPublicly data setsCherry picked resultsPreserved
CATH, SCOP(Protein Structure Classification)
ChemSpider
Data collections
Slide: Carole Goble
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Complexity challenges
• Data pipelines• Visualise: Cytoscape • Workflow: Taverna
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• Distributed gene expression & clinical traits data
• Workflows capture the complex model construction process
• Derive large-scale bionetwork models
• Use to predict disease patterns
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A centre of expertise in digital information management
www.ukoln.ac.uk
Structural Sciences Infrastructure
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Infrastructure Roadmap
Cross Organisations
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Infrastructure Roadmap
Cross Disciplines
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Infrastructure Roadmap
Open Science
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http://www.ukoln.ac.uk/ukoln/staff/e.j.lyon/publications.html#november-2009
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16
2011: Citizens getting involved in science
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Citizen as
scientist
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Classify galaxies…
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Working with academics
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Validate results data and publish
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Patients Participate!
• Bridging the Gap• Feasibility pilot study
• Stem cell research • Develop Use Cases
• Deliver advocacy, guidance• Report &
Recommendations• JISC funding
21
Citizen-patients producing crowd-sourced lay summaries of UK PubMed Central papersBlog : http://blogs.ukoln.ac.uk/patientsparticipate/
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Policy
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Funder Policy
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Funder Policy
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http://www.epsrc.ac.uk/about/standards/researchdata/Pages/expectations.aspx
EPSRC Expectations : implications for HEIs
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NSF-OCI TASK FORCE on Data and Visualization : Reporthttp://www.nsf.gov/od/oci/taskforces/
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INCREMENTAL ProjectInstitutional perspective
• Creating & organising data• Storage and access• Back-up• Preservation• Sharing and re-use
The majority of people felt that some form of policy or guidance was needed....
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Institutional Policy
Article in next issue Int J Digital Curation
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Institutional Policy
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Institutional Policy
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Policy Summary from DCC
http://www.dcc.ac.uk/resources/policy-and-legal
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Policy summary from ANDS
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International collaboration around the DCC DMPOnline tool
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“While many researchers are positive about sharing data inprinciple, they are almost universally reluctant in practice. ..... using these data to publish results before anyone else is theprimary way of gaining prestige in nearly all disciplines.” INCREMENTAL Project
“Data sharing was more readily discussed by early career researchers.”
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Alzheimer’s Disease Neuroimaging Initiative: a unique (open) $60M partnership between
NIH, FDA, universities and drug companies.
“It was unbelievable. Its not science the way most of us have practiced in our careers. But we all realised that we would never get biomarkers unless all of us parked our egos and intellectual property noses outside the door and agreed that all of our data would be public immediately.”
Dr John Trojanowski, University of Pennsylvania
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Data is headline news
JISC FoI FAQ
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P4 medicine: Predictive,
Personalised, Preventive,
Participatory.Leroy Hood –
Institute for Systems Biology
Your genome is basis for your medical record
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Open data and ethics
Buy a DIY kit?Share your data?
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Open data and ethics• Bring your genes to CAL• UC Berkeley personalised medicine initiative in 2010• >700 new students have submitted a genetic sample and a consent form• Aggregate analyses for three genes related to nutrition• Constrained by State Law• Implications for UK HE students & staff?
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Policy Gaps...• Is Policy disconnected
from Practice?– Data Sharing – Data Licensing– Ethics and Privacy – Citizen Science & Public
Engagement– Data Storage, Selection
& Appraisal– Data Citation and
Attribution
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“Departments don’t have guidelines or norms for personal back-up and researcher procedure, knowledge and diligence varies
tremendously. Many have experienced moderate to catastrophic data loss”
Incremental Project Report, June 2010
http://www.flickr.com/photos/mattimattila/3003324844/
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Data storage...
The case for cloud computing in genome informatics. Lincoln D Stein, May 2010
– Scaleable– Cost-effective (rent on-demand)– Secure (privacy and IPR)– Robust and resilient– Low entry barrier / ease-of-use– Has data-handling / transfer /
analysis capability
• Cloud services?
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Your data in the cloud
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Janet Brokerage
& Connectivity
Services
Janet Brokerage
& Connectivity
Services
Common Cloud Service Bus (CSB)Common Cloud Service Bus (CSB)
JISC Community CloudConsortium
EduservEduserv MIMASMIMAS OtherOther
Public CloudsAmazon
AWSAmazon
AWSMicrosoft
AzureMicrosoft
Azure
Private CloudsUniversity
AUniversity
AUniversity
BUniversity
BUniversity
CUniversity
CUniversity
DUniversity
DUniversity
EUniversity
EUniversity
FUniversity
FUniversity
GUniversity
G
Community Services
EduBoxEduBox Disaster RecoveryDisaster Recovery
VMlaunch pad
VMlaunch pad
DCC Services
DCC Services
Access ControlAccess Control
……
HEFCE UMF cloud infrastructure model : new DCC role
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Incentivising data
management
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Beyond the PDF Workshop, January 2011
• Concept of “reproducibility”• Executable papers• Data papers• Links to data, workflows, analyses (GenePattern) within a document • Post-publication peer review• Alternative impact metrics : downloads, slide reuse, data citation, YouTube views • La Jolla Manifesto : guiding principles for digital scholarship
Jodi Schneider, Ariadne, Issue 66, January 2011
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DataCite sagecitedemorepository
DataPro
duces
Regist
er
Generate landing page for data
DOIsDOIsDOIsDOIsMint
DataCite API Google API
Resolve to landing page
Taverna workflow
The relationships between data via DataCite DOIs with tools are captured by the provenance (OPM) produced by Taverna
1
2
3 4
5
6
Workflowmetadata
For referring to data reported in the provanance?
Slide : Peter Li
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KRDS
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Research Outputs
Citations, References
User registration data; Instrument allocation data etc.
Comments, annotations, ratings etc.
Risk assessment data; other sample data
Process &Analyse
Derived Data
Research Concept and/or
Experiment Design
Start Project
Peer-review Proposal
Conduct ExperimentGenerate, Create,
& Collect Raw Data
Check & CleanRaw Data
Interpret & Analyse
Results Data
Archive, Preservation & Curation(OAIS conformant; Representation Information etc.)
IPR, Embargo & Access Control
Discover, Access, Validate, Reuse
& Repurpose Data
Publish Research
Results Data Derived DataProcessed Data Raw Data
Documentation, Metadata & Storage (Reference, Provenance, Context, Calibration etc.)
Acquire Sample
Write Proposal
(include DMP)
Scholarly Knowledge
Write Usage Report
Research Activity Administrative Activity
Curation Activity
Information Flow
KEY:
Peer Review
Prepare Manuscript
Prepare Supplementary
Data
Publications Database
Publication Activity
An Idealised Scientific Research Activity Lifecycle Model
Appraisal & Quality Control
Programs (generate customised software)
Papers, articles, presentations, reports
An Idealised Scientific Research Data Lifecycle Model
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• KRDS/I2S2 Project • Extending the Benefits Framework• Developing Value Chain and Impact
Analysis tool• Applying to different domains• Workshop South Bank Univ, London 12
July
KRDS Activity Model Benefits & MetricsUse Case 1 : National Crystallography ServiceUse Case 2 : Researcher in the lab
http://beagrie.com/krds-i2s2.php
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Thank you…7th International Digital Curation Conference Dec 5-7, Bristol
http://www.flickr.com/photos/dvdmerwe/195985961/