[ome-devel] Updates on Data Publication

Wed May 16 15:59:07 BST 2018

Hi Jason

Now I have to plead fatigue or organisational incompetence. I finally clicked on the linked below from your email from Feb 1st. 
This is a good demonstration of using figure for a specific study. 

However, I would regard this as a vanilla use of FIGURE.  What we are doing is to scale this up to the level of hundreds or thousands of figures. 
In otherwords, Figure is the default method of summarising the typical data of any data set you acquire. 

Once you reach this scale, it becomes difficult to manage so many figures. The way we are dong so is through using Zegami, as it allows slicing and dicing the figures according to a rich n-dimensional metadata landscape. That way you can explore all the images produced by a group in an instance. 

At the moment we have only done this for our smFISH screen in a systematic manner. And we have achieved this through using a strict naming convention for each figure name. Ideally we would like to see better integration into OMERO - so that we for example can export collections of Figures that are themselves tagged in a similar way to the Autotag tool. At the moment we are importing figures through a script that imports all figures with a suffix that constitute a collection (e.g. ending in _zegami1). Not ideal but works. 

I hope we can progress these discussions without me or Steve being there. 

Regards
Ilan

____________________________________________________________________________
Prof. Ilan Davis   ilan.davis at bioch.ox.ac.uk   http://www.ilandavis.com
https://twitter.com/ilandavis
Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK
Direct Office No: (44) (0)1865 613265  Office Fax: (44) (0)1865 613340
Lab manager: Dr Darragh Ennis darragh.ennis at bioch.ox.ac.uk (44) (0)1865 613271 / 613272 
PA:  jolanta.parkinson at bioch.ox.ac.uk  (44) (0)1865 613218 
____________________________________________________________________________

> On 1 Feb 2018, at 09:23, Jason Swedlow (Staff) <j.r.swedlow at dundee.ac.uk> wrote:
> 
> 
> More to the point-- I definitely should have mentioned OMERO.figure. I was remiss (I plead fatigue and jetlag-- too many meetings in too many timezones). I should have pointed out that all the imaging figures in the Schleicher et al paper were made in OMERO.figure and all of them them are available in the public resource-- go to http://dx.doi.org/10.17867/10000109 <http://dx.doi.org/10.17867/10000109>, click on the "Figure" tab, Open File, and under owner select Katharina Schleicher.  Not a perfect workflow yet, but getting there.  It's critically important that we get your (and others) ideas and use cases for this. So far, the funding panels have not been convinced by OMERO.figure-- we need your help to convince them!
> 
> 
> Cheers,
> 
> Jason
> 
> ----------------------
> Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee 
> 
> Phone:  +44 (0) 1382 385819 
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>  
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> 
> From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of Ilan Davis <ilandavis at mac.com>
> Sent: 01 February 2018 07:33:27
> To: OME External Developer List; King Charles House; darragh.ennis at bioch.ox.ac.uk; Richard Parton; David Pinto
> Subject: Re: [ome-devel] Updates on Data Publication
>  
> 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 <mailto: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 <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 athttp://doi.org/10.1098/rsob.170099 <http://doi.org/10.1098/rsob.170099>, and the original image data is at http://dx.doi.org/10.17867/10000109 <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/ <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 <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
>>  
>>  
>> 
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