[ome-users] Custom annotations absent in exported metadata

[Ilya Goldberg]

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.

-Ilya


>
> #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
> <OME xmlns = "http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd"  
> xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance"  
> xsi:schemaLocation =  
> "http://www.openmicroscopy.org/XMLschemas/CA/RC1/CA.xsd  
> http://www.openmicroscopy.org/XMLschemas/CA/RC1/CA.xsd" >
>
> <Experimenter ID = "urn:lsid:ome.dtged.org:Experimenter:1-1dYUKt" >
> <FirstName >Graham
> </FirstName>
> <LastName >Klyne
> </LastName>
> <Email >graham.klyne at zoo.ox.ac.uk
> </Email>
> <Institution />
> <GroupRef ID = "urn:lsid:ome.dtged.org:Group:4-1dYUKt" />
> </Experimenter>
>
> <Experimenter ID = "urn:lsid:ome.dtged.org:Experimenter:6-1dYUKt" >
> <FirstName >OME
> </FirstName>
> <LastName >test
> </LastName>
> <Email />
> <Institution />
> <GroupRef ID = "urn:lsid:ome.dtged.org:Group:4-1dYUKt" />
> </Experimenter>
>
> <Group ID = "urn:lsid:ome.dtged.org:Group:4-1dYUKt" Name = "OME" >
> <Leader ID = "urn:lsid:ome.dtged.org:Experimenter:1-1dYUKt" />
> <Contact ID = "urn:lsid:ome.dtged.org:Experimenter:1-1dYUKt" />
> </Group>
>
> <Image Name = "rfx5" ID = "urn:lsid:ome.dtged.org:Image:3-1dYUKt"  
> DefaultPixels = "urn:lsid:ome.dtged.org:Pixels:32-1dYUKt" >
> <CreationDate >2005-08-03T16:13:33.052501
> </CreationDate>
> <ExperimenterRef ID = "urn:lsid:ome.dtged.org:Experimenter:6-1dYUKt" />
> <Description >2 testes plus genital tract.
> </Description>
> <GroupRef ID = "urn:lsid:ome.dtged.org:Group:4-1dYUKt" />
> <ChannelInfo ID = "urn:lsid:ome.dtged.org:LogicalChannel:34-1dYUKt"  
> PhotometricInterpretation = "RGB" >
> <ChannelComponent Pixels = "urn:lsid:ome.dtged.org:Pixels:32-1dYUKt"  
> Index = "0" ColorDomain = "" />
> <ChannelComponent Pixels = "urn:lsid:ome.dtged.org:Pixels:32-1dYUKt"  
> Index = "1" ColorDomain = "" />
> <ChannelComponent Pixels = "urn:lsid:ome.dtged.org:Pixels:32-1dYUKt"  
> Index = "2" ColorDomain = "" />
> </ChannelInfo>
> <DisplayOptions ID = "urn:lsid:ome.dtged.org:DisplayOptions:41-1dYUKt"  
> Display = "RGB" >
> <RedChannel ChannelNumber = "0" BlackLevel = "0" WhiteLevel = "255"  
> Gamma = "1" isOn = "true" />
> <GreenChannel ChannelNumber = "1" BlackLevel = "0" WhiteLevel = "255"  
> Gamma = "1" isOn = "true" />
> <BlueChannel ChannelNumber = "2" BlackLevel = "0" WhiteLevel = "255"  
> Gamma = "1" isOn = "true" />
> <GreyChannel ChannelNumber = "0" BlackLevel = "0" WhiteLevel = "255"  
> Gamma = "1" />
> <Projection Zstart = "0" Zstop = "0" />
> <Time Tstart = "0" Tstop = "0" />
> </DisplayOptions>
> <Pixels ID = "urn:lsid:ome.dtged.org:Pixels:32-1dYUKt" SizeX = "1280"  
> SizeY = "820" SizeZ = "1" SizeC = "3" SizeT = "1" PixelType = "Uint8"  
> DimensionOrder="XYZCT" BigEndian="t">
> <BinData  
> xmlns="http://www.openmicroscopy.org/XMLschemas/BinaryFile/RC1/ 
> BinaryFile.xsd" Compression="zlib">
> </BinData>
>
> <BinData  
> xmlns="http://www.openmicroscopy.org/XMLschemas/BinaryFile/RC1/ 
> BinaryFile.xsd" Compression="zlib">
> </BinData>
>
> <BinData  
> xmlns="http://www.openmicroscopy.org/XMLschemas/BinaryFile/RC1/ 
> BinaryFile.xsd" Compression="zlib">
> </BinData>
>
> </Pixels>
> <CustomAttributes />
> </Image>
>
> <CustomAttributes />
> </OME>
>
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