BagIt for transferring and archiving Research Objects

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BagIt is an Internet Draft that specifies a file system structure for transferring and archiving a collection of files, including their checksums and brief metadata. BagIt is commonly used by digital library communities for archival purposes, and is mandated by the Library of Congress for digital preservation.

Research Object bundles are structured ZIP-files for serializes a Research Objects, embedding some or all of its resources within the ZIP file, and list the RO content in a manifest, in addition to embedding and referencing annotations and provenance.

While BagIt and RO Bundle might at first seem to provide similar functionalies, the two approaches are complementary in the sense that BagIt focuses on the transfer and consistency checks, recording checksums for resources and their file sizes, while RO Bundles focus on the metadata, provenance and annotations about the resources, relating them to each other.

Research Object BagIt archive defines a profile for a BagIt bag to also be a Research Object. This approach builds on the RO Bundle structure, but modifies it to also be compliant with BagIt.


Research Objects at BOSC

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Norman Morrison presented Research Objects at BOSC including work on ‘Research Objects in the wild’, where Research Objects supported a reproducibility case study that was recently publish in PLOS One. This work was also presented at BOSC by Alejandra González-Beltrán from the ISA-team and you can get the slides here.

You can read more about the BOSC conference in Scott Edmunds excellent blog post ‘Open Bioinformatics in The Irish Free Software State‘.


Why publish and be so damned hard to find?

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Chris Parr from Times Higher Education Interviewed Prof Carole Goble at JISC Digifest. You can read and listen to Carole’s views on the lack of transparency about academic research methods by clicking on the links below.

“Outdated practices and lack of simplicity result in ‘unfindable’ work, Carole Goble tells Jisc Digital Festival”

JISC Digifest Keynote

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Carole Goble gave a thought provoking keynote presentation at the JISC Digital Festival where she talked about It was great to see that the TARDIS (Time and Relative Dimensions in Scholarship) analogy was picked up by Chris Parr from Times Higher Education. You can find the talk live on the JISC website here.

Example of Encoding an RO using RDF-a

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rdf-a example screenshot

As an example of encoding a Research Object using RDF-a is now available to the community, see the “Parameter Optimization of an Ecological Niche Modeling Workflow”. The page represents a Research Object representing the optimizations made on the AUC output parameter of the ENM workflow using Support Vector Machines (SVM). The optimizations are performed using genetic algorithms and have been represented with the Research Object Optimization Ontology.



Our Workshop on “What Bioinformaticians need to know about digital publishing beyond the PDF2″ has been accepted for ISMB2014

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Following our very successful workshop on “What Bioinformaticians need to know about digital publishing beyond the PDF” last year in ISMB 2013 (see our blog post), we are thrilled to announce that our workshop series will be continued in ISMB2014, Boston, USA (tentative dates July 13, 14 or 15). This year, we will join force with BioMed Central, to expand our discussion on new ways of digital publishing by a new topic, i.e., new ways of peer review and their impact on bioinformatics. The workshop is organized by the managing board of Research Object, representatives of ISA community, and participation of BioMed Central and their journals Biology Direct and GigaScience. The workshop web site will be announced shortly! Mark your date, and join us in Boston!

The Launch of Research Object Creator Tool (Give it a try!)

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ro creator example screenshot

 Research Object Creator Tool is a very lightweight RO creation tool built by Daniel Garijo of UPM. The tool takes as input a LaTeX file and extracts its title and abstract to create an annotated page in RDF-a. It also produces a structure of the contents to reference, so users only have to fill in (and annotate if you want) the resources to point to. A sample can be seen in the image to the left and more details can be found in Daniel’s blog page.