Invited talk at the STM Publishers Conference London, 3rd Dec 2014

1. FAIRer Research
Professor Carole Goble CBE FREng FBCS
The University of Manchester, UK
carole.goble@manchester.ac.uk
STM Conference, London, 3rd Dec 2014

2. “An article about computational
science in a scientific publication
is not the scholarship itself, it is
merely advertising of the
scholarship. The actual
scholarship is the complete
software development
environment, [the complete
data] and the complete set of
instructions which generated the
figures.”
David Donoho, “Wavelab and Reproducible
Research,” 1995
datasets
data collections
standard operating
procedures
software
algorithms
configurations
tools and apps
codes
workflows
scripts
code libraries
services,
system software
infrastructure,
compilers
hardware

3. Systems Biology

4. Systems Biology
Modelling
Cycle
45 organisations 112 organisations 37 organisations

5. http://www.seek4science.org
Aggregated Commons
share and interlinking methods, models, data, samples…
multi-stewardship, multi-disciplinary, mixed
Standards
DCAT
FOAF
Data
Models Articles
External
Databases
Metadata
Yellow
Pages

6. Investigations
Assays
Studies
Towards Interoperable Bioscience Data, Nature Genetics, 2012
Standards, Structure, Interlink
Just Enough Results Model
for things produced and used
in experiments

7. http://www.fair-dom.org
Findable, Accessible,
Interoperable, Reusable
Data,
SOPs,
Models, Methods
Multi-tenant Commons
Platform
http://datafairport.org

8. Data discovery
Data assembly,
cleaning, and
refinement
Modeling
Statistical analysis
Data collection
Insights Scholarly Communication
& Reporting
Material & Methods

9. BioSTIF
instruments and laboratory
Data discovery
Data assembly,
cleaning, and
refinement
Modeling
Statistical analysis
Data collection
Insights Scholarly Communication
& Reporting
Material & Methods

10. Workflow
Commons

11. "Mapping present and future predicted distribution patterns for a meso-grazer
guild in the Baltic Sea" by Sonja Leidenberger et al

12. • 35 kinds of annotations
• 5 Main Workflows
• 14 Nested Workflows
• 11 Configuration files
• 25 Scripts
• 10 Software dependencies
• 1 Workflow management
system
• 1 Web Service
• Dataset: 90 galaxies observed
in 3 bands
José Enrique Ruiz (IAA-CSIC)
Galaxy
Luminosity
Profiling
Dependencies
Components

13. Rinse and Repeat Research
• Sweep Datasets
• Sweep Variables
• Sweep Steps

14. SHARING SENSITIVITY
SENSITIVE SHARING
IMPLICATIONS FOR METRICS
BEING FAIR

15. scientific ego-system for open science
trust, reciprocity, competition
fame
competitive
advantage
productivity
credit
adoption
kudos
for love
blame
scooped
uncredited
misinterpretation
scrutiny
shame
insecurity
cost/time/skills
distraction
responsibility
disruption
staff churn
inertia

16. Howard Ratner, STM Innovations Seminar 2012
was: Chair STM Future Labs Committee, CEO EVP Nature Publishing Group,
now: Director of Development for CHORUS (Clearinghouse for the Open Research of US)
http://www.youtube.com/watch?v=p-W4iLjLTrQ&list=PLC44A300051D052E5
http://www.myexperiment.org/packs/196.html

17. http://www.researchobject.org/
Outputs are first class
citizens to be managed,
credited and tracked:
data, software
A Framework to Bundle and Relate multi-hosted
(digital) resources of a scientific experiment or
investigation using standard mechanisms & uniform
access protocols. Carriers of Research Context
Research Objects

18. What is the RO Framework?
• A framework of models and
conventions
• Representations
• API specifications
• Implementations mapped into
legacy / commodity platforms

19. KnowledgeTurns
Unit of Scholarly Currency, RO Commons
Circulate in the Scholarly Ecosystem
Citation? Credit? Link to Publishers?
Goble, De Roure, Bechhofer, Accelerating Knowledge Turns, I3CK, 2013

20. Goble, De Roure, Bechhofer, Accelerating Knowledge Turns, I3CK, 2013
Collaboration to support safe use of
patient and research data for medical
research
Farr Commons
Research Object packages codes, study,
and metadata to exchange coded
descriptions of clinical study cohorts
KnowledgeTurns
Unit of Scholarly Currency, RO Commons
Circulate in the Scholarly Ecosystem
Citation? Credit? Link to Publishers?
arch, Discover, Index, Harvest, Port

21. Schopf, Treating Data Like Software: A Case for Production Quality Data, JCDL 2012Goble, De Roure, Bechhofer, Accelerating Knowledge Turns, I3CK, 2013
Profile Focus
Body of knowledge around methods, workflows,
software, data, person, rather than publication.
Citation, credit

22. Release Research
Evolution, Emergence, Discourse, Threaded
Comparison, Historical review, Anti-Salami
Forks, Merges, Fixivity, Citation? Credit?
Flow across groups, projects and articles
Schopf, Treating Data Like Software: A Case for Production Quality Data, JCDL 2012

23. Reproduce Research
Repeat, Replicate, Recompute, Reuse….
Entropy, Citation? Credit?
icanhascheezburger.com
Zhao, et al .Why workflows break - Understanding and combating
decay inTaverna workflows, 8th Intl Conf e-Science 2012
Can I repeat &
defend my
results?
Can I review, reproduce
and compare my
results/method with your
results/method?
Can I review,
replicate and certify
your results?
Can I transfer your
results into my
research and reuse
this method?
Hettne et al Structuring research methods and data with the research object model: genomics
workflows as a case study 2014 http://www.jbiomedsem.com/content/pdf/2041-1480-5-41.pdf

24. Reproduce
Repeat, Replicate, Recompute, Reuse….
Entropy, Citation? Credit?
icanhascheezburger.com

26. Checklists aka Minimum Information Models, Reporting Guidelines
Minim Checklist Ontology, http://purl.org/net/mim/ns
Zhao et. al. A Checklist-Based Approach for QualityAssessment of Scientific Information 3rd In.Workshop on Linked Science, 2013
Hettne et al Structuring research methods and data with the research object model: genomics
workflows as a case study 2014 http://www.jbiomedsem.com/content/pdf/2041-1480-5-41.pdf

27. Checklists
Versioning
Provenance
Dependencies
Progressive
Metadata
Profiles
Depth: how deeply
described
Coverage: how
much is covered.
More specialised
detail, fewer
services
More
Stakeholders & Services
Citation minimum
Library
Publishers
Experiments
Science
PROV
PAV
VoID GIT
PAV
NISO-JATS
Docker
DC
EXPO, ISA,
JERM, OBI
MIAME, SBML,
SED-ML
wfdesc
MIM Ontology
wfprov
VIVO-ISF
PID

28. Standards
Machine-processable
Technology Independent
Multi-platform
Incremental

29. W3C
OADM
DOIs
URIs
Handles
ORCID
OAI-
ORE
RRIDs

30. host
service
Open Source/Store
Sci as a Service
Integrative fws
Virtual Machines
Portable Packaging
ReproZip
Workflows,makefiles
ProvStore

31. OMEX archive
bundle

33. Nanopub: represents structured
data along with its provenance in a
single publishable and citable entry
Galaxy workflows: re-enact the analysis
Research Object:
aggregates the
(digital) resources
contributing to
findings of
(computational)
research (results,
data and software)
as citable
compound digital
objects
http://isa-tools.github.io/soapdenovo2/
http://sandbox.wf4ever-project.org/portal/ro?ro=http://sandbox.wf4ever-project.org/rodl/ROs/SOAP2denovo2-Aureus/
[Alejandra Gonzalez-Beltran
Philippe Rocca-Serra]

34. • Id & Cite fluid
things
• Uniform handling
1st class citizens
• Compound,
multi-authored
• Mixed, leaky
containers
• Span outcomes,
evolve outputs,
emergence
• Profiles
• Bridge
researchers,
platforms,
resources
Bechhofer,Why linked data is not enough for scientists, DOI: 10.1016/j.future.2011.08.004

35. [Norman Morrison]

36. Focus on
Personal
Productivity
not Public Good
Auto-magical
Stealthy not Sneaky
reduce the friction
instrumentation
Training Time

37. From made RO to born RO

38. • Open research is like Open software
• Multi-part, multi-contributor, updating
• Tardis & Commons
• Implications for metrics? publishing?
• Learning from open software development

39. http://www.force11.org

40. • Barend Mons
• Sean Bechhofer
• Philip Bourne
• Matthew Gamble
• Raul Palma
• Jun Zhao
• Alan Williams
• Stian Soiland-Reyes
• Paul Groth
• Tim Clark
• Juliana Freire
• Alejandra Gonzalez-Beltran
• Philippe Rocca-Serra
• Ian Cottam
• Susanna Sansone
• James Howison
• James Herbsleb
• Kristian Garza
All the members of the Wf4Ever team
iSOCO: Intelligent Software Components S.A.,
Spain
University of Manchester, School of Computer
Science, Manchester, United Kingdom
University of Oxford, Department of Zoology,
Oxford, UK
Poznan Supercomputing and Networking
Center. Poznan, Poland
IAA: Instituto de Astrofísica de Andalucía,
Granada, Spain
Leiden University Medical Centre, Centre for
Human and Clinical Genetics, The Netherlands
Colleagues in Manchester’s Information
Management Group
RO Advisory Board Members
http://www.researchobject.org
http://www.wf4ever-project.org
http://www.fair-dom.org
http://www.datafairport.org