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