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2014-06-13 Research objects in the wild
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2014-06-13 Research objects in the wild

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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 …

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

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  • 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.
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    • 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