Onboarding our ontologies as an EOSC service

[servansod]

The techniques ontology developed by ExPaNDS needs to be made available as an EOSC service.

Timeline up to now (from the e-mail threads to keep the record):

• June 2020: decision to use BioPortal to host our ontologies
• March 2021: two possibilities to have our ontologies as an EOSC service:
  • a: asking NCBO (Stanford) if they are willing to register as an EOSC service provider and add BioPortal as a service in their portfolio
  • b: deploy and run the BioPortal appliance at one of our sites, register the ontology there and then onboard the service ourselves
    ➡️ Stanford agrees to register and onboard BioPortal, CEDAR and Protégé/WebProtégé 🥳
• May 2021: BioPortal not registered yet as an EOSC service (low priority for Stanford people)
• June 2021: EGI starts preparing plan b, setting up BioPortal in EGI Cloud

[andrea-manzi]

We managed to setup the Ontoportal ( which is the name of the Bioportal service generic distribution ) at http://ontoportal.fedcloud-tf.fedcloud.eu/

we will find a better domain name then.

I have submitted a request to get a license, which should be not a problem given that the service is used for research.

In the meantime we are doing some tests

[andrea-manzi]

@dfq16044 we have a valid licence now for that server, can you please try to create an account ( http://ontoportal.fedcloud-tf.fedcloud.eu/accounts/new) and submit the Expands ontology ?
(we are still on http but we are planning to enable https soon)

[servansod]

Sylvie onboarded PaNET as a public repository in EGI's OntoPortal: ontoportal.egi.eu/ontologies/PANET
Andrea is starting the onboarding of ontoportal.egi.eu on EOSC 👍

[servansod]

Last update from @andrea-manzi :

At the beginning of summer we have been contacted again by Bioportal admins with the intent to register Bioportal to EOSC
So we decided to wait for them as that is the preferred way to have the ontologies on EOSC

[servansod]

Last update from @andrea-manzi :

I have asked for a meeting to Bioportal to understand what are their issues in continuing with the onboarding

The registration of the EGI instance turned out to be even more difficult unfortunately. The EOSC Portal accepts services with TLR7 at minimum and in our case this is a service which is in status at least Beta.

In order to reach status Beta in our portfolio for ontoportal.egi.eu we need to go to a series of stages which I would like to avoid for a service hosting a single ontology ( we don’t have at the moment exploitation plans for this kind of services in EGI)

[servansod]

Plan C: look for alternative ontology repositories in Europe and contact the people to talk about EOSC onboarding.
@spc93 gave the example of the Linked Open Vocabularies.
I asked Gerry from FAIRsFAIR.
Also worth having a look in FAIRsharing.org, for example this ontology lookup service (OLS) from EBI.

[paulmillar]

I know I'm late to the party, but was Zenodo considered a possible solution for hosting PaNET?

OpenAIRE and ROR both use Zenodo to host their ontologies.

[agbeltran]

We can indeed use the Zenodo/Github link so that each PaNET release is also associated with a Zenodo DOI and persisted in Zenodo.

[RKrahl]

We can indeed use the Zenodo/Github link so that each PaNET release is also associated with a Zenodo DOI and persisted in Zenodo.

I agree. That might give us the best from both worlds: the ability to have a well structured code repository together with the stability and persistence of a publication archive.

[paulmillar]

At the risk of mentioning what's already known, Zenodo has some help on integrating with github.

[agbeltran]

thanks @paulmillar, that's exactly what I was referring to as the Zenodo/Github link - here there is more documentation too: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content

it is a very easy process and I have used it for both software repositories and GitHub repositories containing specifications (e.g. https://github.com/CellMigStandOrg/MIACME)

[servansod]

I agree it's agood idea to use Zenodo/Github feature for the releases of the ontology (this is something that Alejandra had already encouraged as a good practice in our project's data management plan) BUT careful, to me this is more linked to issue #21 and proper version management. Putting our ontology in Zenodo doesn't make it available "as an EOSC service".

[marauskajul]

Discussed in PEB (27/09/2022):
→ Paul is going to take this topic into the PaNET group meeting
→ our goal is to make the ontologies available as an EOSC service

[paulmillar]

Current discussion is centred on Carlo's offer to provide ("on-board") an "PaN ontology API" service.

The PaN ontology API is a software product that, when deployed, allows clients to expand a PaN search API query that includes (one or more) PaNET terms into an equivalent search query that includes all PaNET sub-term: those that are more specific research techniques.

The result is that datasets may be "tagged" with very specific PaNET terms, but would still be found when a user makes a query that includes more general PaNET terms. This is provided the query takes advantage of the PaN Search API service, which may require some configuration at the front-end (web interface).

I believe this would tick the boxes: it would be an EOSC on-boarded service that makes PaNET (an ExPaNDS ontology) available to clients.

This approach is not yet confirmed: there is still some discussion underway.

[minottic]

After discussing this internally, PSI has agreed to register the aforementioned service in EOSC.

For that to happen, I need to expose the URL publicly (it's enough to register its domain name in the PSI DNS) and fill out the form in EOSC. I am currently addressing the first need, namely making the URL publicly reachable

[minottic]

The service is currently registered here: https://marketplace.eosc-portal.eu/services/photon-and-neutron-techniques-ontology-service

[marauskajul]

See comment above from Carlo, service is registered in the marketplace.