research objects, seek and fairdom
TRANSCRIPT
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Research Objects,
SEEK4Science and
FAIRDOMProfessor Carole Goble CBE FREng FBCSThe University of Manchester, UKThe Software Sustainability Institute, [email protected]
researchobject.org
Schloss Dagstuhl Seminar 16041 Reproducibility of Data-Oriented Experiments in e-Science, 25-29 January 2016
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Metadata objects – not necessarily encapsulated!Platform Independent framework to Bundle, Port and Link(scattered) resources, related experiments, and hold context
ContainerPackaging: Zip files, Docker images, BagIt, …
Catalogues & Commons Platforms: FAIRDOM SEEK, STELAR eLab
ManifestMetadataDescribes the aggregated resources, theirannotations and their provenance
Manifest
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Manifest Metadata
Manifest Construction• Identification – id, title, creator, status….• Aggregates – list of ids/links to resources• Annotations – list of annotations about resources
Manifest
Manifest Description• Checklists – what should be there• Provenance – where it came from• Versioning – its evolution• Dependencies – what else is needed
Manifest
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Manifest Construction
Unique identifiers as
names for things.
doi, epic, orcid, purl, RII,
Identifiers.org
Mechanism of
aggregation to group
things together.
OAI-ORE
Metadata about those
things & how they relate
to each other.
W3C OADM
http://w3id.org/ro/
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FAIR Manifest Descriptions: RO typesContent Annotation Profiles
Checklist
Pro
ven
ance
Versio
nin
g
Dependencies
NISO-JATS
Dublin Core
EFO ISA
SBML
JERM
Gamble, Goble, Klyne, ZhaoMIM: A Minimum Information Model vocabulary and framework for Scientific Linked Data,IEEE 8th Intl Conf on eScience , 2012
SED-ML
SBOLMIAPE
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FAIRDOMHub Sys Bio Commons
https://doi.org/10.15490/seek.1.investigation.56
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Aggregating Commons
Links into public resources
Integration with public
resources
Integration with
modelling tools
FAIRDOM Repositories
SOPs
models
dataLaunch local
executables
Integration with lab tools
Integration with lab
management systems
and local file stores
Direct Upload
BiVes
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RO Unzip
• Reproducibility• Versioning• Systematic and
extensible meta-data collection
• Cross platform exchange
• Publishing
Living Snapshot
https://doi.org/10.15490/seek.1.investigation.56
https://dx.doi.org/10.1111/febs.13237
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SEEK Demo
Video
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Other Implementations
• COMBINE Archive +RO
• Workflows RO Bundle
• STELAR Asthma eLabs
• Data Publishing
• ATLAS LHC Experiments
using CDE, Docker, improved manifests for
people
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Links
• Researchobject.org
• Fair-dom.org
• Seek4science.org