[ome-users] Storing gene information as annotation data with a well in a screen

[Melissa Linkert]

Hi Jürgen,

> I am working on a system that allows users to combine image data
> from an Andor as well as an metaXpress system with gene annotation
> data, like gene name, different database IDs and such.
> 
> What is the best way to add this gene annotation data to an OME-XML
> structure?
> 
> I could use the Reagents tag and the Reagents external identifier.
> That wouls all ow any one to get the annotation data from my
> external database but I can only store a Reagent name and would have
> to skip all the other information...

Someone else might have a better idea, but one option would be to use a
Reagent in combination with a StructuredAnnotation, so you would end up
with something like:

<Reagent ID="Reagent:0">
  <Name>reagent name</Name>
  <Description>reagent description</Description>
  <ReagentIdentifier>12345</ReagentIdentifier>
  <AnnotationRef ID="Annotation:0"/>
  <AnnotationRef ID="Annotation:1"/>
</Reagent>
<StructuredAnnotations>
  <TextAnnotation ID="Annotation:0">
    <Value>more information</Value>
  </TextAnnotation>
  <TextAnnotation ID="Annotation:1">
    <Value>even more information</Value>
  </TextAnnotation>
</StructuredAnnotation>


...the important point being that StructuredAnnotations can store whatever
information you like.

(Note that there are other Annotation types besides TextAnnotation;
please consult the OME-XML schema for a list of the remaining types.)

> I found a screen-cast about adding annotation data from a CSV file
> to Omero.tables but neither do I find documentation on this nor do I
> have access to the python script used to do that. In addition the
> annotation would not be with the image file and only exist inside of
> Omero.

I don't know which movie that is, but the relevant documentation should
be here:

http://trac.openmicroscopy.org.uk/ome/wiki/OmeroTables
http://trac.openmicroscopy.org.uk/ome/wiki/OmeroPy#OMEROtables
http://trac.openmicroscopy.org.uk/ome/wiki/OmeroJava#HowtouseOMEROtables

...and there are a few examples here:

https://github.com/openmicroscopy/openmicroscopy/tree/develop/examples/OmeroTables

Regards,
-Melissa

On Wed, May 09, 2012 at 11:55:52AM +0200, Dr. Juergen helmers wrote:
> Hi,
> 
> I am working on a system that allows users to combine image data
> from an Andor as well as an metaXpress system with gene annotation
> data, like gene name, different database IDs and such.
> 
> What is the best way to add this gene annotation data to an OME-XML
> structure?
> 
> I could use the Reagents tag and the Reagents external identifier.
> That wouls all ow any one to get the annotation data from my
> external database but I can only store a Reagent name and would have
> to skip all the other information...
> 
> I found a screen-cast about adding annotation data from a CSV file
> to Omero.tables but neither do I find documentation on this nor do I
> have access to the python script used to do that. In addition the
> annotation would not be with the image file and only exist inside of
> Omero.
> 
> I could simply write my own XML structure to store my information
> which would be in every files header but would not be imported into
> Omero.
> 
> Any suggestions to do this? Quick and dirty is better than cool and
> complicated as I have a rather looming deadline approaching...
> 
> Thanks for any suggestions.
> 
> Juergen
> 
> 
> 
> 
> -- 
> *Dr. Jürgen Helmers*
> /Chief Developer/ | webnow | http://www.web-now.de
> *email:*juergen.helmers at gmail.com | *tel:*+49 30 37301306 | *skype:*
> helmerj

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