data models for preserving and publishing digital research material beyond the pdf
DESCRIPTION
Slides for the Technology Track of ISMB/ECCB 2013 in Berlin on digital publishing, highlighting the Research Object model, Nanopublications, and ISA as a means to capture methods and results when research is carried out digitally. This work was supported by the EU workflow forever project (http://wf4ever-project.org).TRANSCRIPT
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Data models for digital preservation and publishing beyond the PDF
Jun Zhao, Mark Thompson, Kristina Hettne, Stian Soiland, Susana Garcia , Marco Roos
Acknowledging Harish Dharuri, Susanna Sansone, Philipe Rocca-Sera,
Alejandra Gonzales-Beltran, Albert Mons, Arie Baak, Erik Schultes, Carole Goble, Barend Mons
The Workflow Forever project (EU FP7 nr. 270192), Digital Libraries and Digital Preservation. (ICT-2009.4.1)
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Recording your computational steps…
Bioinformaticians have no labbooks!and no training on digital notekeeping
http://graemefielder.wordpress.com/2010/09/17/lab-books-evolution-required/
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State of the art study capture?
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How then?Workflows encapsulate in silico analysis
http://ap27-cgla.blogspot.nl/ http://openi.nlm.nih.gov/detailedresult.php?img=2743669_1471-2105-10-252-2&req=4
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Components to understand an experimentIs a workflow enough?
Workflow: Which biological pathways explain the
associations?
Interpret results(Interaction
pathways in the cell)
Research QuestionGenome Wide Association Studies (GWAS)
In 1000+ people: which gene mutations are associated with metabolic syndrome,
and why?
Download data- External DB
- Existing Knowledge
Hypothesis
Genes involved in inflammation pathways are
involved in the onset of metabolic syndrome.
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Components to understand an experimentIs a workflow enough?
Workflow: Which biological pathways explain the
associations?
Interpret results(Interaction
pathways in the cell)
Research QuestionGenome Wide Association Studies (GWAS)
In 1000+ people: which gene mutations are associated with metabolic syndrome,
and why?
Download data- External DB
- Existing Knowledge
Hypothesis
Genes involved in inflammation pathways are
involved in the onset of metabolic syndrome. Preserve
PreservePreserve
Preserve
Preserve
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Research Object
DataData
Method/Experimental
protocol
Method/Experimental
protocol
FindingsFindings
Types of resources
ISA-TAB/ISA2OWL
Nanopublication
ISA-TAB/ISA2OWLWfdesc
ISA-TAB/ISA2OWLWfdesc
Data Models
Capture more than workflows
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Research Object ModelPreservation for understanding
Preserve at least the:– Hypothesis
– A workflow-like sketch
– One or more workflows
– Input data
– Workflow runs
– Results
– Conclusion
My Research Book
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Fame and Glory
It was me, me,
me!
What I found
How I found
it
HDAC1 interacts with Parvb
Discovered by: me
Nanopublication
AssertionProvenance of Assertion
Metadata of nanopublication
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Prototyping the models
• Create: myExperiment• Better: Checklist service• Evolution: Digital Library software• Curation: Quality Monitoring Service• Credit original assertions: LandMark Tool• Applications by private partners
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myExperiment- create Research Objects
Prototyping the Research Object Data Model in
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Checklist service- make better Research Objects
Prototyping the Research Object Data Model in
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http://www.wf4ever-project.org/wiki/display/docs/RO+checklist+evaluation+API
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http://www.wf4ever-project.org/wiki/display/docs/RO+checklist+evaluation+API
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RELEASE! http://www.wf4ever-project.org/wiki/display/docs/RO+checklist+evaluation+API
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Digital Library software- evolution of a Research Object
Prototyping the Research Object Data Model in
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Research Object ‘under construction’
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Snaphots to record intermediate states
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Full copy ‘Ready for Release’
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Quality Monitoring Service- Long term curation
Prototyping the Research Object Data Model in
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Landmark Claim Tool- mark and credit the first discovery
Prototyping the Nanopublication Model
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Landmark Claim Tool
Core data
Attribution
Qualification
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Applications from private partners- Robust tools for business stakeholders
Prototyping the Nanopublication Model
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Nanopublication applicationsEuretos Company
Copyright Euretos b.v. 2013
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Releases planned for 2014
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Some gory detailData models ‘under the hood’
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Research Object Model at a glance
Research Object
ResourceResource
Resource
AnnotationAnnotation
Annotation
oa:hasTarget
ResourceResource
Annotation graphoa:hasBody
ore:aggregatesManifest
ore:isDescribedBy
For more information and extensions (Evolution model, MINIM) seehttp://wf4ever-project.org/
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Extensions
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Wf4Ever architecture
Semantic REST API
RDF triple store(RO structure, Annotations)
RO indexUploaded files
PortalChecklist service
Command line
Workflow runner
...
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Nanopublication Data Model
Assertion
Nanopublication URL
Provenance PublicationInfo
assertion
opm:was
DerivedFrom
http://rdf.biosemantics.org/…profiles_matching_198
0_2010
opm:wasGene-ratedBy
thisnanopub
dcterms:created
2012-03-28T11:32
^̂ xsd:dateTime
pav:authored-
By
associa-tion
a sio:statis-ticalAssociation
sio:has-measurementValue
Association_1_p_value
a
Sio:probability-value
sio:has-value
6.56 e-5
^̂ xsd:float
sio:refers-to
http://bio2rdf.org/
omim:210600
researcherid.com/rB-6035-
2012
dcterms:DOI
http://dx.doi.org/
….
…http://
bio2rdf.org/geneid:55835
Integrity Key
An Individual association between concepts:• statement or declaration• measurement• hypothetical inference• quantitative or qalitative
Guarantee immutabilityafter publication
Unique, persistent and resolvable identifier
How this assertion came to be, methods,
evidence, context, etc.
• Detailed attribution for authors, institutions, lab technicians, curators
• License info• Publication date
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Assertion
http://www.store.net/mynanopub.rdf
Provenance Publication-Info
SoapDenovo 2 increases correct
assembly length by 3-80 times over Soapdenovo 1
pav:authoredBydc:rights
dc:created
A Galaxy workflow
results
slides
hypothesis
ro:aggregate
s
Research object can link to a nanopub as
an experimental result
ro:aggregates
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Assertion
http://www.store.net/mynanopub.rdf
Provenance Publication-Info
SoapDenovo 2 increases correct
assembly length by 3-80 times over Soapdenovo 1
pav:authoredBydc:rights
dc:created
A Galaxy workflow
results
slides
hypothesis
ro:aggregate
s
Nanopublication gains detailed
workflow provenance by
linking to RO
ro:aggregates
rdf:describedBy
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Assertion
http://www.store.net/mynanopub.rdf
Provenance Publication-Info
SoapDenovo 2 increases correct
assembly length by 3-80 times over Soapdenovo 1
pav:authoredBydc:rights
dc:created
A Galaxy workflow
results
ro:aggregates
slides
hypothesis
ro:aggregate
s
Extend your provenance!
E.g. link the claim to the original data elements
from which it was derived
rdf:describedBy
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Assertion
http://www.store.net/mynanopub.rdf
Provenance Publication-Info
SoapDenovo 2 increases correct
assembly length by 3-80 times over Soapdenovo 1
pav:authoredBydc:rights
dc:created
A Galaxy workflow
results
ro:aggregates
slides
hypothesis
ro:aggregate
s
?rdf:describedBy
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Community effort
• Research Objectshttp://researchobjects.org/http://wf4ever-project.org/
• Nanopublicationhttp://Nanopub.org/
• ISA-toolshttp://www.isa-tools.org/
• Research Objects Community Group at W3Chttp://w3.org/community/rosc
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Conclusions (1/2)
• Applications of RO and Nanopublication data models to capture the bioinformatics research process ‘beyond the PDF’
• Data models:ISA, Research Objects, Nanopublications
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Conclusions (2/2)
• Reference implementations / first to adopt:myExperiment, DLibra, Checklist service, Curation/monitoring, Landmark tool
• Private partners developing stable nanopublication applications
• Prevent perfectionism of the developers:get involved now!
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THANK YOU FOR YOUR ATTENTION
http://researchobject.org/ http://nanopub.org/ http://isa-tools.org/ Research Object Community group at W3C: http://w3.org/community/rosc