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).
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Data models for preserving and publishing digital research material beyond the PDF
1. 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)
2. 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/
4. 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
5. 5
Components to understand an experiment
Is a workflow enough?
Workflow:
Which biological
pathways explain the
associations?
Interpret results
(Interaction
pathways in the
cell)
Research Question
Genome 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.
6. 6
Components to understand an experiment
Is a workflow enough?
Workflow:
Which biological
pathways explain the
associations?
Interpret results
(Interaction
pathways in the
cell)
Research Question
Genome 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.
8. Research Object Model
Preservation for understanding
Preserve at least the:
– Hypothesis
– A workflow-like sketch
– One or more workflows
– Input data
– Workflow runs
– Results
– Conclusion
My Research Book
9. 9
Fame and Glory
It was
me, me,
me!
What I
found
How I
found
it
HDAC1 interacts with Parvb
Discovered by: me
Nanopublication
Assertion
Provenance of Assertion
Metadata of
nanopublication
10. 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
50. Research Object Model at a glance
50
Research
Object
Resource
Resource
Resource
Annotation
Annotation
Annotation
oa:hasTarget
Resource
Resource
Annotation graph
oa:hasBody
ore:aggregates
Manifest
For more information and extensions (Evolution model, MINIM) see
http://wf4ever-project.org/
52. Wf4Ever architecture
52
Semantic REST API
RDF triple store
(RO structure,
Annotations)
RO index
Uploaded files
PortalChecklist
service
Command
line
Workflow
runner
...
53. Nanopublication Data Model
Assertion
Nanopublication URL
Provenance PublicationInfo
assertio
n
opm:
was
Derived
From
opm:
wasGene-
ratedBy
this
nanopub
dcterms:
created
pav:
authored-
By
associa-
tion
a
sio:statis-
ticalAssociation
sio:has-
measurem
entValue
Association_1_
p_value
a
Sio:probability-
value
sio:has-value
6.56e-5
^^xsd:float
sio:
refers-to
dcterms:
DOI
…
Integrity Key
An Individual association
between concepts:
• statement or declaration
• measurement
• hypothetical inference
• quantitative or qalitative
Guarantee immutability
after 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
58. Community effort
• Research Objects
http://researchobjects.org/
http://wf4ever-project.org/
• Nanopublication
http://Nanopub.org/
• ISA-tools
http://www.isa-tools.org/
• Research Objects Community Group at W3C
http://w3.org/community/rosc
60. 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
61. 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!
62. 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
Hinweis der Redaktion
Attribution is part of the RO model and myExperiment, but we are also developing something specifically to address this aspect of digital preservation and publishing… Nanopublications
expected (based on previous knowledge) or serendipitous result/finding?
So let’s have a look at what a Research Object looks like. The core is the concept of the Research Object itself, which you may also known as an ORE aggregation. This is described by the manifest, which is simply an RDF file. The RO aggregates a series of resources – in Linked Data these could be anywhere in the world. Additionally it aggregates a set of annotations, which we know is the link between a target resource (here aggregated in the RO), and an body resource. In Wf4Ever we typically provide the body as a separate RDF Graph, so that we can use existing vocabularies to describe and relate the resources.
new schemalandmark screenshotworkflow hypothese sketch
new schemalandmark screenshotworkflow hypothese sketch
new schemalandmark screenshotworkflow hypothese sketch
new schemalandmark screenshotworkflow hypothese sketch
So we have recently formed a W3C Community Group for Research Object, which has gathered significant interest, 75 participant. As you see, I am one of the chairs, and so is Rob which you already know from OA group. We are just starting up, and our focus in the RO community group is rather how to practically use Research Objects as a concept than to specify a new model – we’ll refer to existing models where it’s appropriate, but also explore other models which could be described as research objects.