[ome-users] Metadata editability in OMERO

[Jason Swedlow]

Dear All-

As we move towards release of OMERO-Beta4, we have a number of issues  
coming up we'd like feedback on.

The first is metadata editability.  In Beta4, we've gone for something  
we call "metadata completion".  This means that, for a given image  
file format, we capture and find a home for all of the metadata in  
that format which fits into OMERO.  For some formats, that's easy,  
because there is so little metadata.  But many are quite rich, and  
this project has been a huge effort by the Bio-Formats (Melissa  
Linkert) and OMERO (Brian Loranger, Chris Allan, Jean-Marie Burel)  
teams.

The result is that we will support 5 rich file formats in Beta4  
"completely".  Note that we have to make decision about what each  
piece of metadata means-- we certify that it has been imported into  
OMERO, although there are a few edge cases where we've had to make  
decisions about where each piece of metadata goes.

This raises a critical question, that we have debated within OME for  
years (some of you might recall emails on this a few years ago), namely:

What image metadata should be editable? Imagine that some value was  
either unset or wrongly set on the microscope, a user may want to  
correct the situation after import. Then, if we allow editing, how  
much info about that editing should we track?

Some technical points:

-- in OMERO, we store every write to the DB as an Event.  So we know  
every change, who did it and when.

-- we really do NOT want to store every metadata change made.  Doing  
this properly means making multiple copies of every database entry  
every time one thing changes-- so things get bloated very rapidly.

A compromise we are considering seriously-- keep only the last  
metadata value, but log all the changes.  If a user has changed any  
metadata that came with an image fille, we can add functionality to  
the client applications to let the user find this out.  You'll know  
that the data has changed, by whom, and when, you just wont know what  
the previous data was.

If necessary, we could implement an audit database, which stores  
previous metadata versions, or maybe just the first version-- the one  
that was acquired with the original .  This would be optional-- if  
needed it could be turned on.  We won't get that done for the first  
Beta4.0 release, but if it's a priority, it could come later this year.

Thanks for your ideas and comments.

Cheers,

Jason

**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
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FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
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The University of Dundee is a Scottish Registered Charity, No. SC015096.



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