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 Source pptx: https://onedrive.live.com/view.aspx?cid=37935FEEE4DF1087&resid=37935FEEE4DF1087!788&app=PowerPoint%20f
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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
Editor's Notes
- 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.