OMEX Combine Archives as example of Research Object in the wild - how converting it to RO Bundles using http://dx.doi.org/10.5281/zenodo.10439
Source pptx:
https://onedrive.live.com/view.aspx?cid=37935FEEE4DF1087&resid=37935FEEE4DF1087!788&app=PowerPoint%20f
Assure Ecommerce and Retail Operations Uptime with ThousandEyes
2014-06-13 Research objects in the wild
1. Research Objects
in the wild
Stian Soiland-Reyes, University of Manchester
@soilandreyes http://orcid.org/0000-0001-9842-9718
2014-06-13
This work is licensed under a
Creative Commons Attribution 3.0 Unported License
2. Research Objects in the wild:
COMBINE archives (.omex)
Open Modelling Exchange Format for tools used in System Biology
Specializations: SED-ML, SBML, CellML, NeuroML, PharmML
Reusable representation of biological model and its dependency
resources
All bundled within archive
Format specified per resource
Graceful degradation – applications can open the sub-models
which format they support
Master file – indicate a top-level model
Includes provenance/metadata (who made each sub-model)
Java API: https://sems.uni-rostock.de/trac/combinearchive
http://co.mbine.org/documents/archive
3. Research Object Bundle
(.bundle.zip)
Downloadable research object, transfer & publish
Citable DOI, publish at http://zenodo.org/ straight from GitHub
ZIP file, can be unpacked with regular tools
Reserved folders: .ro/ and META-INF/
Programmatic access
JSON manifest also interpretable as Linked Data
Provenance of bundle and resources (W3C PROV-O and PAV)
Annotations using Open Annotation Model (W3C Community Group)
RO Bundle API
Works offline and in desktop applications
Basis for more specific file formats, e.g. Taverna run bundle
Exchanged with myExperiment and Research Object tools
https://w3id.org/bundle/ https://github.com/wf4ever/robundle
doi:10.5281/zenodo.10440
4. Combining COMBINE and RO:
ro-combine-archive
Parsing COMBINE manifest.xml, adding RO Bundle
.ro/manifest.json
Manifests can co-exist:
File is both COMBINE archive and RO Bundle
Extracts provenance metadata to enrich RO Bundle
RO Bundle standardizes provenance relations like:
authoredBy, createdOn, curatedBy, aggregatedBy
Future:
Embed into RO Bundle API – any RO Bundle could become
COMBINE
Joining effort with COMBINE API developer
https://github.com/stain/ro-combine-archive
doi:10.5281/zenodo.10439
Notes de l'éditeur
So not everyone have access to set up a RESTful semantic web servers, in particular we’ve run into this with desktop applications – users just want to save files and then they decide where they are stored. So we decided to write a serialization format for Research Object, which we call the RO Bundle.
We wanted this to be accessible for applicaton developers, so we’ve adopted ZIP and JSON, and in a way this would let you create research objects and make annotations without ever seing any RDF.