Open Microscopy Environment

Hi,
I am discussing with research teams of our institute to elaborate a unique vocabulary to be used when annotating projects, datasets and images.
We will probably use tag-set and tags for modalities.
the question is how to make such list of tags visible and accessible for all teams and their members? for example, we want to centralise the tags creation and description by the omero data manager and make it visible for all teams without need to create a new ones?

PS: teams are with groups of read/annot levels.

best wishes

Nabila

nabila.elarouci wrote:Hi,

Hi Nabila,

the question is how to make such list of tags visible and accessible for all teams and their members? for example, we want to centralise the tags creation and description by the omero data manager and make it visible for all teams without need to create a new ones?

At the moment, there's no ready solution to do what you're looking for. On the one hand, it's technically possible to make tags public, but the dialogs for attaching tags, etc. don't show them as expected. Another possibility would be to keep a copy of the tags in each group, and teach the server how to keep them synchronized.

Neither is ideal at the moment.

Can you perhaps tell us more about which client (insight or web, etc) you are using and what steps you think your users are looking to perform? Maybe we can help come up with a workaround.

All the best,
~Josh

Dear Josh,

Dear Josh, dear all,
thank you for you answer and interest on our workflow. to be clearer, I am the data manager and groups/users admin from the omero insight and web, but not admin on the server (IT department is responsible).
So, I have tested the proof of the concept of the omero on our institution, with few research teams and 3 microscopy (and HCS) platforms. Here, we generate about 130 TO of images data per year.
We want to make thinks properly and with best practices for all users, without making tasks difficult and time consuming for every one. otherwise, people will not follow our procedure.... and omero will be used as repository of data only!!
We would like to use Omero with maximum features to annotate and orgnize our data. this is our priority.
our general procedure would be:
1 -all groups would be read/annot and PIs/managers as groups owner.
2- importing images directly from the facility plateform to Omero, using the insight, by the researcher.
3- researchers should annotate their projects/datasets as soon as data orgnised in omero. several levels of meta-data (study description, assay or experience protocols, samples preparations/types ....), samples phenotyping post analysis or observations.
I have used the Omero-form apps to prepare a pre-formatted k/v form, and compared the same task with list of tag-sets and tags.
We hope to find the easiest way to implement collaboratively a set of variables/values and make them available for all users in order to use the same. for example k/v: variable=organism with 2 values (Humain, mouse) or tagset=organism and tags (human, mouse). the creation of tagset is possible with insight only, but we can use them with omero.web.

please, let me know about your experience and what do you think about such a choice?

best wihses

Nabila

nabila.elarouci wrote:We want to make things properly and with best practices for all users, without making tasks difficult and time consuming for every one. otherwise, people will not follow our procedure.... and omero will be used as repository of data only!!

We definitely understand that sentiment!

I have used the Omero-form apps to prepare a pre-formatted k/v form, and compared the same task with list of tag-sets and tags. the advantage of the tag-list is that is easy for any member to add new ones, but with the form, they have to ask me for changes.

Ah, interesting to hear that you've tried OMERO.forms. As far as I know, there hasn't been any development on it recently, but perhaps either someone in the community has tried something similar, or we could imagine a way to make the modification of the forms easier, if that otherwise suits your needs.

We hope to find the easiest way to implement collaboratively a set of variables/values and make them available for all users in order to use the same. for example k/v: variable=organism with 2 values (Humain, mouse)

This is similar to what we do in the IDR, but the definition of valid values is done outside of OMERO, e.g. in ontologies. That wouldn't give you any tools for editing the list of terms or validating user input.

or tagset=organism and tags (human, mouse). the creation of tagset is possible with insight only, but we can use them with omero.web.

All understood, and definitely a use-case that others have brought up, like Douglas who eventually created OMERO.forms.

Unfortunately, at the moment, there isn't a way to do precisely what you want without modifying OMERO somehow. If you have someone who would like to try, for example, a database trigger that would key tags in sync between groups, we're more than happy to help her or him do that.

All the best,
~Josh

Dear Josh,

many thanks for your answer. I have asked access to the data base to visualize and understand the underlying schema. Yes, The solution of triggers and synchronization between groups could be a solution for our need.

However, It is really difficult for Omero developpers consortia to implement such a feature in the next future? (any group can visualize any tags from any other group.... it seems for me as a logical situation and can not be conflictual between them)!

regards

Nabila

Hi Nabila,

nabila.elarouci wrote:However, It is really difficult for Omero developpers consortia to implement such a feature in the next future? (any group can visualize any tags from any other group.... it seems for me as a logical situation and can not be conflictual between them)!

We agree that it makes sense, and we certainly would love to have such a feature ready to go. Unfortunately, like probably every other group, there's only so much we can do with the funding we have. But by all means, if there is anyone who is interested in making progress on a solution for shared tag hierarchies, we would be ecstatic to help them!

If not, we'll certainly get to it as soon as we can.

All the best,
~Josh