[ome-devel] Updates on Data Publication

[Ilan Davis]

Hi Jason

This is great and thanks for the update. Also congrats on your very nice paper in open bio. 

I wonder whether you considered ways to include Figure as an option within the publication process. My lab now has a general system in place that people use Figure very effectively as a device to summarise “typical” data from each data set. This is an important shortcut to browse your own data and that of others and be able to record what people think is a correct summary of a data set. 

In other words, publishing the original data transparently should be part of the publication process and your example in the open bio paper is great. It would also be good to be able to publish the figures in a paper as OMERO Figures that map each panel to the exact original data - as it does anyway at the moment. 

Can that be achieved already with the existing omero server infrastructure? Can figure be integrated in some way within the IDR infrustructure so IDR can be used to publish data from individual low throughout papers as well as high throughout studies with the figures providing a high level Quick view and guide to the data?

Thanks
Regards
Ilan




Sent from my iPhone

> On 1 Feb 2018, at 01:46, Jason Swedlow (Staff) <j.r.swedlow at dundee.ac.uk> wrote:
> 
> Dear All
>  
> Just a quick update on our recent activities in data publication.
>  
> IDR continues to receive datasets, and we have several exciting new datasets upcoming.  Keep an eye on the announcements and let us know if you have a reference dataset that should be in IDR.  See https://idr.openmicroscopy.org/about/submission.html.
>  
> OME, as it always has, wants to make data publication from individual laboratories routine. That’s one of the big reasons to use OMERO in a lab or research institute.  We’ve worked hard to make the process for publishing data easier in OMERO 5.4, and also better documented.  We used OMERO 5.4’s features to publish data associated with a paper from our lab (some of you will correctly recognize this as a dogfooding exercise).  The paper is at http://doi.org/10.1098/rsob.170099, and the original image data is at http://dx.doi.org/10.17867/10000109.  For more info, see our recent entry on the OME Blog (http://blog.openmicroscopy.org/community/2018/01/25/fair/).
>  
> And finally, we’ve contributed to a white paper that discusses the resources the community must (at least we think it must) build to make image data publication routine and universal. This is now on arxiv at https://arxiv.org/abs/1801.10189  (it’s on arxiv because bioRxiv doesn't publish proposals and white papers; yes we did try to put it there first!).
>  
> As always, we welcome your thoughts, comments, critiques, and ideas.
>  
> Cheers,
>  
> Jason
>  
>  
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
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