[ome-users] Correct use of annotations in OME

[Tom Kazimiers]

Hi all,

to manage the image and meta data in our lab, I try to get OMERO to
annotate data sets in a certain way, but am unsure about the correct way
to do so. Hence this mail :-).

Up to now we used a small tool I wrote to find and look at the data set
of interest. This is just a prototype and works as a Fiji plugin. I now
planned to do a rewrite and figured that maybe OMERO.server could be
used as a back-end. This would have many advantages for me, e.g. no need
for own data management. I will either extend one of the existing
clients or build a new one for my purpose. Now I want to find out how I
describe my current data model with OME. Therefore I'll briefly describe
what this simple date model is.

This data viewer tool opens a project which can have many experiments.
Each experiment has a name, some linked data (file paths, not only
images, also text, xls, pdf) and a set experiment conditions. Based on
that the tool provides a user interface that allows one to filter
certain experiments based on selectable conditions. Such conditions can
e.g. be a marker, type of experiment (e.g, a position in the tisuse
(e.g. posterior), etc.. In the user interface I now can select all the
conditions I want to filter experiments. These experiments can then be
opened in the actual data viewer. The data viewer is a separate topic,
for now I want to find a good way to define this model (projects,
experiments, structured conditions) in OME.

I thought one of my experiments would be a Dataset in OME, then I could
link images and other data like xls end pdf (as file annotations?) to
it. The conditions could probably be annotations, too. Based on the
samples from structured annotation wiki page, these would just be string
annotations. Now does this make sense to organize my data that way?
Would this data then somehow be editable in OMERO.insight?

Thanks in advance,
Tom

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