Dear openBIS team,
I have several questions concerning the integration and use of controlled vocabularies in openBIS:
- Is there a maximum recommended length for a controlled vocabulary in openBIS or are there any known issues for the integration of very long vocabularies? We would, e.g., like to include the “DFG Gerätegruppenschlüssel” for instruments which is a list of ~4400 terms and associated numbers.
- Does the option to allow for the inclusion of unofficial/ad hoc vocabulary terms by power users still exist? If yes, in which UI can the suggestions for new terms be made?
- Where do I define the term-specific part of the URL (e.g., the ENSEMBL Gene ID) after defining the general URL Template for the complete controlled vocabulary (e.g., http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=)? It would also be great if users could click on the URL of a term in the Vocabulary Browser in the ELN-LIMS UI.
- No limit, sizes don’t affect performance whatsoever.
- We are not actively supporting this feature on new interfaces.
- Missing features:
- Edition Vocabulary, the edit button is missing on the view on the admin UI.
- Vocabulary URLs support on ELN.
I add this two to our backlog, hopefully if not for the next minor release, for the one after we should solve these.
Hope this helps,
I was testing with larger vocabularies and noticed a huge slowdown in the ELN.
When creating or editing objects that contain properties with ~5000 vocabulary entries the browser shows the edit form with a delay of several seconds.
After adding another property with 10000 entries the delay extended to ~1 minute. In the meantime the browser even reported “website not responding”.
Any idea what we are doing wrong? Or was “sizes don’t affect performance whatsoever” just meant for the core system, and not for the ELN?
My guess is that the ELN is trying to load the whole vocabulary before showing the editing form. Maybe it would be better to load the entries delayed or even on-demand when selecting the drop-down box?
I did just retest using a vocabulary with 10000 entries.
This is what I observed:
- The vocabulary took 2 seconds to create.
- On the ELN-LIMS the loading icon gets stuck for 3.4 seconds when entering edit mode.
- On the ELN-LIMS no loading when entering the same entity in view mode.
As far as I remember the ELN-LIMS load all types including vocabularies when the app starts.
That said, the main thread getting stuck indicates to me that the browser is having trouble loading the elements of the form.
I tested both Firefox and Safari. Can you tell me what browser are you using?
I can acknowledge that there is an effect on having large vocabularies that I honestly didn’t expect, but not to the point of being unusable, in my opinion.
thank you very much! It really looks like a browser-related problem. I did some tests with the same object in different browsers. The object has a property with 5000 entries and another property with 10000 entries in the vocabulary.
Time between hitting the Edit-button and the display of the edit form:
Edge @ Windows: 1min (with warning)
Chrome @ Windows: 50s (with warning)
Chromium @ Linux: 30s
Firefox portable @ Windows: <1s
Firefox @ Linux: <1s
Firefox works perfect, but Chrome-related browsers seem to have a problem here. Unfortunately the standard clients of our institution only ship with Edge and Chrome.
are you able to reproduce the problem with Chromium-based browsers and large vocabularies?
If yes, is there a chance for a fix or a workaround?
I can confirm that Chromium-based browsers suffer from a great slowdown when a page with object containing vocabulary of a huge size.
We have pinpointed the bottleneck and the fix for it will be included in the newest release.
If you wish to incorporate the fix into your installation right now, please apply this change:
to the file:
I’d like to come back to my earlier question concerning the correct use of the URL Template for Controlled Vocabularies:
I can define a general URL Template in the Admin UI (e.g., https://ethz.ch). When using a term of the vocabulary in an Entity in the ELN-LIMS UI, I get a hyperlink which is identical to the URL Template entered in the Admin UI. However, it is not clear to me where I can define the term-specific part of the URL.
Does anyone have a solution for this?
I would like to acknowledge the issue, the older core ui shown an example but the new admin ui does not. See screenshots attached.
I hope we add an example on the field for next minor version.