[ome-users] Custom annotations absent in exported metadata

[Graham Klyne]

Ilya Goldberg wrote:
> 
> On Aug 4, 2005, at 6:52 AM, Graham Klyne wrote:
> 
>> I've been examining an exported OME/XML file (after stripping out the
>> raw binary data), and am rather surpised to see that the custom  Semantic
>> Type annotations created for our data (which show up in the online view
>> of the image information) do not appear in the exported OME/XML data.
>>
>> I had expected to see the custom semantic type data appear in the
>> <CustomAttributes> element inside the <Image> element, but I see the
>> <CustomAttributes> element is empty.
>>
>> I attach a copy of the exported OME/XML for one such image, with
>> newlines inserted before each '<', and the content of <BinData>  elements
>> stripped out.
> 
> 
> 
> A problem with XML export is that you can literally dump the entire  
> database into a single XML document.  The problem is to decide what to  
> export and to expose this to the user in some logical, easy-to-use way.  
>  The "solution" we came up with was to export the image objects that  
> got imported during image import.  Its obviously not ideal, but it  
> would always work and would be minimally useful.  Exporting everything  
> associated with an image may work OK in some uses of OME, but in others  
> would result in exporting way, way more than you want.
> The interface to the XML export is very easy to use (for a developer) -  
> its just a list of OME objects, which can be practically anything  
> (anything supported by the various XML schemas).  The big question is  
> how do you build an interface to let the user specify what they want to  
> export?
> 
> One possibility is to (again) use templates.  A special XML Export  
> template would specify the object types desired during export.  At  
> least this way the list of object types would be configurable  
> relatively easily.  Another option that was kicked around, but somewhat  
> difficult to implement, was basically a shopping basket.  You can pick  
> and choose certain objects to export as you browse around your data.   
> Exposing search criteria for inclusion of objects in an XML export to  
> an HTTP interface may be useful also.  Any other ideas would be most  
> welcome.

Although I've been trying to avoid getting into the OME code so far, 
this is an area where I feel that it would be reasonable to dig in to 
get the output we want.  For our purposes, a one-off specification of 
what needs to be exported would be fine (even best), and I don't think 
we really need a UI to control the details.

I assume I can create a new perl module in the appropriate CGI 
directory, and subsequently access the required data simply by using an 
appropriately constructed URI?

The following information would help:
- is there a sample module that does something close to this?  The 
current export module described in your other message sounds as if it 
could be copied and adapted.
- what would I need to tweak to get a link to this external export 
format placed on the image information page?  (Maybe HTML templates will 
be the best answer for this?)

#g

-- 
Graham Klyne
Image Bioinformatics Research Group (http://www.bioimage.org/)
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, UK
E-mail: <Graham.Klyne at zoo.ox.ac.uk>
Direct phone: +44-(0)1865-281991
Departmental fax: +44-(0)1865-310447