Research Objects

in the wildStian 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

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

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/robundledoi:10.5281/zenodo.10440

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-archivedoi:10.5281/zenodo.10439