[ome-users] What did OME ever do for us?

[Graham Klyne]

(with apologies to Monty Python and others for the subject line...)

Now that I have OME up and running and able to import microscope images, I 
am exploring the extent to which it can help us with our image+annotation 
requirements.  I have some specific questions, but first I'll try and 
outline what we're trying to do, in case we're trying to do something that 
isn't reasonable to expect OME to handle.

...

The research project I'm supporting aims to create a database of images of 
in situ gene expression in drosophila testes.  To create these images, the 
researchers go through a fairly involved process of gene selection, gene 
expression analysis and in situ gene expression image creation. Image 
acquisition is very much toward the end of the overall experimental 
procedure, and the resulting images are not (in the current procedure) 
subjected to subsequent computer analysis.  What we do want to do is to 
cross-refer the images to details of genetic and other information from 
preparatory steps, and also to capture researcher annotations at the time 
of image acquisition (noting that researchers can often see more through 
the microscope than they can see in the resulting computer images).

At the present time, we're not trying to use OME for capturing the 
preparatory information.  What I am trying to do is use OME to capture 
researchers' observations and annotations in a structured form at the point 
of image acquisition and importation to OME, with the possibility of adding 
additional annotations later.  These will later be combined with the 
genetic information and researchers conclusions to create a database for 
final publication.

 From this, I hope it's clear that what is important to us is capturing 
researchers' observations and annotations about images, rather than 
automated image analysis, which appears to be OME's primary target.  The 
incorporation of annotation as an OME "module execution" seems to support 
this kind of use, but I'm not sure how the annotation features are intended 
to be used.

...

So to my specific questions:

1. How are custom annotations intended to be used?

2. How to create new annotation metadata structures?

Details follow.  If these questions are answered in existing documentation, 
please just provide pointers.


1. How are custom annotations intended to be used?  I have tried to use 
custom annotations as follows, using the web browser interface:
- create a dataset and import an image into that dataset
- I have successfully created "DatasetAnnotation" and 
"DatasetTestSignature" annotations for the dataset by selecting the 
corresponding listbox entries and clicking on "Create a custom 
annotation".  (I don't know if the values I entered make sense, but they 
have been stored and are retrievable as part of the dataset metadata.)
- I then tried to use a similar procedure to create a custom annotation for 
the image.Selecting "ImageExperiment" as the type of custom annotation, I 
am asked to create an "Experiment" and an "Experimenter", which I duly do, 
filling in all the proffered fields and clicking the corresponding "Create 
..." buttons.
- The "Image experiment" dialog ends up with an experiment identified by a 
number ("38" in my case) and an image (the one I am annotating), but 
nothing that seems to reflect the information just entered.  Clicking on 
"Create image experiment" returns me to the original screen, but it's not 
obvious that the annotation has been added.  (I now notice that it appears 
in the "Module execution" list, but not at the top or bottom of the 
list.  The first time I tried something like this, the new information 
appears to have been lost.)

My question is:  the above procedures seem non-obvious and error prone; are 
they consonant with how the annotation feature is intended to be used, or 
am I overlooking something?


2. How to create new annotation metadata structures?  A simpler question 
with, I suspect, a more complex answer, but hopefully one that can be 
addressed by a pointer to relevant documentation.

We aim to capture data in a semi-structured form that can be exported to a 
semantic web database for further cross-referencing with other information 
sources.  The built-in custom annotations seem to support the right kind of 
general structures for this purpose.  Are the form displays linked directly 
to the XML metadata schema, or is there an additional 
presentation-description component?  How do I go about adding additional 
metadata to OME?  Can the metadata format be dynamically updated, or does 
this require a re-build of the database?

...

Thanks for any insights or pointers that anyone can offer.

#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