Controlled Vocabularies : Integrate Ontoportal as a new supported third-party vocabulary service

[Dimitri Szabo]

Hi everyone,

We started to work on  integrating a new third-party vocabulary service after SKOSMOS for ontologies, namely Ontoportal.
This can be found in this issue https://github.com/IQSS/dataverse/issues/9276 and this PR https://github.com/IQSS/dataverse/pull/10145 ,though they are not yet fully up to date with our latest approach.

We are now at a stage where we would like to organize a meeting with the community to share our vision, make sure we are not forgetting important elements and maybe get more ideas into the mix :D.

It'd be great to have at least Jim M, Philip D and Slava T due to your interest and expertise over the topic.

Here are some propositions for a date & time, we'll add more later if needed :

- Wed 01/17 4PM UTC
- Mon 01/29 4PM UTC
- Tue 01/30 4PM UTC

Cheers,

Dimitri

[Philipp Conzett]

Hi Dimitri,

Thanks for initiating this work. Sounds exciting. I'd be interested in joining a call about this. Maybe you initially could give a brief overview of the rationale for the PR and what Ontoportal is.

I'd be available at these times:

- Mon 01/29 4PM UTC
- Tue 01/30 4PM UTC

Best, Philipp

[Vyacheslav Tikhonov]

Hi Dimitri,

I'll be definitely interested to join the meeting. Monday and Wednesday suggested times should work for me.

Best,

Slava

[James Myers]

Dimitri ,

I can meet any of the times suggested.

 

Re: discussion before/at the meeting: FWIW: I left one comment in the PR for the one change I wasn’t sure was needed. Otherwise, I think adding the params needed to interact with other services is fine, and the ones you want to add seem generic, i.e. I expect other services may have a different URL for human readable entries and may need headers. The one thought I had is to ask whether switching to have a cvoc-other-params for anything that the scripts don’t need to use as selectors might be a better approach for the long term versus one cvoc-* per param (my fault – I started us having one entry per param). Also - are you also planning a PR to https://github.com/gdcc/dataverse-external-vocab-support for the OntoPortal script? At a minimum it would be useful if you could update the schema there to match any additions. And last – thinking about how this design might change for the SPA would be a good idea. AFAIK, there hasn’t been much discussion there beyond our initial docs that said we should think about it. (I don’t know that we have to address the SPA now, but if there’s an obvious design, we might be able to work to make the change easier rather than harder with any updates we make.)

 

-- Jim

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[Dimitri Szabo]

Hello again and thanks for your replies,

It seems that the best time so far is the Monday 01/29 4PM UTC.

Here are the details for the webconference :
- Web and application link:
https://rendez-vous.renater.fr/dataverse-cvoc-ontoportal_be5c56-9ca90c-5e411b

- Phone access:
Conference code: 7110921526
Tel: 09 88 83 00 10
From mobile: tel:0988830010,,7110921526#

- Access from a SIP video conferencing equipment:
Conference code: 7110921526
Direct access:sip:71109...@194.57.7.21
Video menu:sip:0...@194.57.7.21
Room connector documentation:https://services.renater.fr/rendez-vous/rsip_pp/index
Screen Sharing link (all audio muted):https://rendez-vous.renater.fr/dataverse-cvoc-ontoportal_be5c56-9ca90c-5e411b#config.startSilent=true

As per a short recontextualization of the use case, the point is to allow autocompletion of Dataverse metadata fields using concepts from semantic artefacts stored in Ontoportal platform.
This allows Dataverse to retrieve the URI of the terms for the metadata, as well as providing searches on translations and related concepts to the selected one.
Ontoportal (https://ontoportal.org) is a platform to host and serve ontologies and semantic artefacts both for machines and via browsing user interface.
The pull request (https://github.com/IQSS/dataverse/pull/10145) deals with the prerequisites to support Ontoportal for this use case, as has been already done for SKOSMOS.

Dimitri

[Philipp Conzett]

Thanks for the informative call yesterday. At the end of the call, an alternative approach was briefly touched upon, namely adding a fourth field to the Keyword section. I think this might be a more sustainable approach as it would allow us to store the necessary information also when deploying other controlled vocabulary services than OntoPortal.

Best, Philipp

[Ludovic DANIEL]

Hello Jim Myers, where can I contact or meet with you ? I would like to exchange on the splitting of developments and idea of code implementation. 

[Dimitri Szabo]

Hello everyone and thanks again to everyone that attended,

A bit late, but here is the presentation.

Following the meeting, the first actions taken :

- adding the 4th metadata field in keywords for Term URIs : #10288

- splitting the "central" issue/PR #9276 into smaller chunks ( e.g. #10316)

- discussion needed about the issue of URI + Ontology acronym needed with Ontoportal in FAIR-IMPACT project meeting

Dimitri

[felix engel]

Dear all,
Unfortunately, I have only just come across this conversation, but it correlates very well with some of our future plans. In line with Dimitri's suggestion, we would like to contribute to the integration of the Ontology Lookup Service (EBI OLS). Like Ontoportal, OLS is a terminology service. Both services are long established and provide biomedical terminologies in their original installation.    
In Germany, we are working on the long-term establishment of research data management infrastructures (National Research Data Infrastructures, NFDI). This includes the provision of terminology services that are not only focussed on biomedicine, but are much more broadly based. This includes engineering, cultural sciences and more.
I would be delighted if we could contribute here in some form.

Please let me know if you are interested.

All the best
Felix

[Philip Durbin]

The Dataverse Project has a fair amount of funding from the NIH* right now so we're definitely interested in better supporting biomedicine, including better metadata.

* https://www.iq.harvard.edu/news/dataverse-joins-nih-data-repository-initiative

To view this discussion on the web visit https://groups.google.com/d/msgid/dataverse-community/48051973-9ec4-4c13-a729-7bc19a3cece8n%40googlegroups.com.

--

Philip Durbin
Software Developer for http://dataverse.org
http://www.iq.harvard.edu/people/philip-durbin

[James Myers]

FWIW: Right now, the support within Dataverse for external vocabulary services is not intended to be specific to any particular service(s), but there may be limits to what the current mechanism can handle that need to be added for a new service (e.g. Ontoportal expects a header with the calls being made, so the generic ability to send headers is being added). We also have a separate community repository - https://github.com/gdcc/dataverse-external-vocab-support where scripts and examples for any service are welcome. If OLS needs something new in Dataverse, please create an issue (minimal) or issue and PR. If the mechanism in Dataverse is sufficient, just go ahead and make a PR in the dataverse-external-vocabulary-support repo and, if you’re interested in maintaining your code there, we can give you the relevant permissions in that repository. (Also happy to have general help in maintaining that repository.)

 

I/we would also be happy to discuss any challenges you see – we had/have an external vocabulary working group that designed the existing mechanism and might be able to suggest approaches if the existing examples/scripts don’t match what you need.

 

Hope that helps.

-- Jim

To view this discussion on the web visit https://groups.google.com/d/msgid/dataverse-community/CABbxx8H_1yHU7CyJ%2BPTpWKKoRDbN80N3TDFUGhnAWXrpy7eFUw%40mail.gmail.com.

[felix engel]

Hey,

Thank you for your quick replies. We will have a look at the community repository and see how far we get.
I will keep you posted on our progress. If you have any questions, please drop me a line

Many thanks,

Felix

[Vyacheslav Tikhonov]

Hi Felix,

I did presentation of the external controlled vocabularies support together with Jim during Dataverse Community Meeting 2021, we've covered the most of CV related issues. 

There are a lot of not solved issues like concept caching mechanism, sustainability etc: https://youtu.be/mWMPxCwB2ys?si=Z7NRO1KFk1flJTxm&t=1821

Proposal: https://zenodo.org/records/5845540

Paper: https://zenodo.org/records/8133723

I'm really happy the importance of this functionality finally is being recognised by the Dataverse community and things are hopefully it can help us to improve it. 

Best,

Slava Tykhonov

DANS-KNAW

[felix engel]

Hey Slava

super, thanks a lot for these valuable resources. We are very interested in making a contribution here.
We'll be in touch again ...

All the best,

Felix