[ome-users] Questions about OME-XML and Java OME-XML library

[Ponti, Aaron]

Dear all

 

This was initially a direct mail to Curtis and Jason, and Jason
suggested posting it on the ome-users list.

 

(...)

 

In house we handle our data and associated metadata with a commercial
package, and we are now interested in storing the metadata (only) in the
OME-XML format. Each of our experiments has a quite large set of
metadata associated to it, but the core information that we would like
(at least initially) to store in XML is the following:

 

Project = { Project name, Start date, Owner, Description, User } 

Experiment = { Experiment name, Start date, Organism, User, Experiment
ID } 

Image = { x, y, z, Filename, AQ Date, Microscope, Objective, NA, Image
File Name, Image file size, Image file date, User }

 

This list is simply to give you an idea on what kind of information is
relevant to us. Some basic information on the dataset structure (level
0?), plus some more on the experiment and project to which the dataset
belongs. We have much more stuff stored in the database, but this does
not need to end up in the XML file, at least in an initial stage.

 

Now a couple of questions for you:

 

( 1 ) How far/completely have the different levels of the OME-XML
specifications been defined?

( 2 ) Are they supported in your Java OME-XML library?

( 3 ) Can you store "arbitrary fields" (meaning without sticking to a
specific OME-XML level) into a valid OME-XML file using your Java
OME-XML library?

Assuming that all fields are defined in the XML schema, can you just add
them, without sticking to a specific set of entries (e.g. a defined
level)?

( 4 ) Can you use custom-made XSLT stylesheets to map some XML scheme to
OME-XML? (Our software already exports all entries from the database
into a tailor-made XML file, and we would like to map it into OME-XML
via XSLT). Can you also do the opposite (OME-XML -> some other XML)?

 

The idea is of course to be able to create valid and portable OME-XML
files.

 

Thank you for any info you can give me.

Aaron Ponti

 

 ----------------------------------------------------------------------

| Dr. Aaron C. Ponti

| Friedrich Miescher Institute

| Facility for Advanced Microscopy and Imaging 

| Software development 

| Maulbeerstrasse 66 CH-4058, Basel

| WRO-1066.2.32

| Tel: +41 61 697 3012

| Fax: +41 61 697 3976

| http://www.fmi.ch/faim

 ----------------------------------------------------------------------

 

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