[ome-devel] Updates on Data Publication

Wed May 16 15:45:58 BST 2018

Hi Jason and Steve

I am trawling through old emails trying to work out where to post the OMERO FIGURE requests, now we have Zegami working reasonably well from Figure through an important script (but still needs work on the metadata and important more data). 

Jason - I cannot find your description for the life of me of where best to post my suggestions.  Was it best on the mailing list?

Steve and Jason - I found an old reply from Jason in February that was not followed up. 
I wonder whether it would be possible to write a grant to work on developing ML capabilities for Zegami (open source python plugins) and OMERO working together with OMERO FIGURE and or IDR?
Not sure who to. Perhaps MRC MCMB (molecular cellular medicine board).  

Regards
Ilan

Hi Ilan

Thanks for your comments.  Lots to think about, as always.

Regarding the workflow your lab is using-- it would be great if you or someone from the lab would share it here, or maybe even on the OME blog. If by workflow you mean a real script, is it anywhere athttps://github.com/MicronOxford <https://github.com/MicronOxford>?  Could it be?  We've so far failed to get funding for OMERO.figure and cool use cases we haven't thought of would help.  It would be great to see what you are doing, understand your workflow, and get ideas how we might improve things-- the spirit and practice of open source, and so on...

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!

There is nothing to stop a journal including a link to an OMERO resource (e.g., https://omero.lifesci.dundee.ac.uk/figure/file/364219 <https://omero.lifesci.dundee.ac.uk/figure/file/364219>) in a paper.  They just need to do it!  Maybe help us convince the journals that this would be a useful idea to consider??

Integrating OMERO.figure into IDR?  Interesting suggestion-- we should look at the workflow and presentation carefully. As is often the case, it's less about the technical capability and more about the ease and accessibility of the tool and workflow.  

Thanks again for your thoughts!  Keep them coming!

Cheers,

Jason

____________________________________________________________________________
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:
> 
> Hi Ilan
> 
> Thanks for your comments.  Lots to think about, as always.
> 
> Regarding the workflow your lab is using-- it would be great if you or someone from the lab would share it here, or maybe even on the OME blog. If by workflow you mean a real script, is it anywhere athttps://github.com/MicronOxford <https://github.com/MicronOxford>?  Could it be?  We've so far failed to get funding for OMERO.figure and cool use cases we haven't thought of would help.  It would be great to see what you are doing, understand your workflow, and get ideas how we might improve things-- the spirit and practice of open source, and so on...
> 
> 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!
> 
> There is nothing to stop a journal including a link to an OMERO resource (e.g., https://omero.lifesci.dundee.ac.uk/figure/file/364219 <https://omero.lifesci.dundee.ac.uk/figure/file/364219>) in a paper.  They just need to do it!  Maybe help us convince the journals that this would be a useful idea to consider??
> 
> Integrating OMERO.figure into IDR?  Interesting suggestion-- we should look at the workflow and presentation carefully. As is often the case, it's less about the technical capability and more about the ease and accessibility of the tool and workflow.  
> 
> Thanks again for your thoughts!  Keep them coming!
> 
> 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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> 
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