[bioontology-support] BioPortal web+API request

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[bioontology-support] BioPortal web+API request

Bryce Mecum
Hey BioPortal folks, 

Mark Schildhauer and I were talking today about some of the tools we're building on top of BioPortal and its APIs and we had a feature request. We'd love to hear your thoughts:

For some of our ontologies, we redirect requests for our term URIs to BioPortal like so:


This has been super helpful to us because we think BioPortal's view of our ontology is super user-friendly and easy to use.

However, in the most recent ontology we've published to BioPortal (ARCRC), we used Named Individuals in a few places to express what we wanted to express. The issue we ran into is that we couldn't find a way to resolve those in a manner similar to how we resolve our classes. See what happens here with an instance:


Generally, this makes sense to us: BioPortal doesn't provide an Instances/Individuals view so it has nothing to redirect to. Would adding something like this be something BioPortal might consider? As a reference, OntoBee has a way to see instances, e.g., http://www.ontobee.org/ontology/GAZ.

The second thing is that we use the Term Search API at the moment to suggest classes for users in some of our user interfaces. We'd love to see instances listed right alongside classes in the same UI. It looks like the only way we could do this now is issue two API requests (the term search and instances APIs) and handle the rest on our end. Would something like a flag on the term search API to include instances be of interest to BioPortal?

Thanks for taking a look!

Cheers,
Bryce


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] BioPortal web+API request

John Graybeal-2
Hi Bryce (and Mark S), good to hear from you on all counts.

We really like your email and both suggestions. We have been thinking about instances for a while now, so in that sense we will definitely consider it! Instances have not been first-class objects in BioPortal for way too long, in my opinion. 

We also use it for term search in some of our tools, particularly CEDAR. And I have thought it would be great to support instances with term search also, I didn't think of something as simple as what you suggest, though. 

I'm struggling to think it through—it seems to me that instances would behave a bit different than classes, for example instances have no inherent hierarchy, do they? Well, they follow the hierarchy of their class type, I suppose. The point being, we'd have to be thoughtful about how to offer users the appropriate instances (e.g., within a 'branch equivalent', and not every instance in the ontology.)

Let me share one way we deal with this at the moment, which is not a great answer but might suggest a way meet some of your needs. BioPortal can process appropriately formatted SKOS files (see https://www.bioontology.org/wiki/SKOSSupport for details). The way it does this is to pun the individuals as classes, which makes them available on the classes API used by CEDAR's search terminology server. I wonder if direct punning of terms as classes might be an effective way to make these terms visible?  Of course, this only works if you have control over the ontology.

The ideal way to make this work is to have an instance representation in the UI.  We have proposed doing this in the past, but it has not caused any money to flow our way. It's something we'd love to have funded.

Adding a flag to the Term search, on the other hand, seems even more obviously a good idea, and I think less expensive too, and I don't think we've discussed it previously. I'll bring that up with the team anyway, it's issue https://github.com/ncbo/bioportal-project/issues/197

The main challenge for us at this point is funding, we are working with very thin resources at the moment. If you see a funding opportunity to help make this happen, be sure to let us know!)

Thanks again for the input!

John

On Dec 10, 2020, at 6:49 PM, Bryce Mecum <[hidden email]> wrote:

Hey BioPortal folks, 

Mark Schildhauer and I were talking today about some of the tools we're building on top of BioPortal and its APIs and we had a feature request. We'd love to hear your thoughts:

For some of our ontologies, we redirect requests for our term URIs to BioPortal like so:


This has been super helpful to us because we think BioPortal's view of our ontology is super user-friendly and easy to use.

However, in the most recent ontology we've published to BioPortal (ARCRC), we used Named Individuals in a few places to express what we wanted to express. The issue we ran into is that we couldn't find a way to resolve those in a manner similar to how we resolve our classes. See what happens here with an instance:


Generally, this makes sense to us: BioPortal doesn't provide an Instances/Individuals view so it has nothing to redirect to. Would adding something like this be something BioPortal might consider? As a reference, OntoBee has a way to see instances, e.g., http://www.ontobee.org/ontology/GAZ.

The second thing is that we use the Term Search API at the moment to suggest classes for users in some of our user interfaces. We'd love to see instances listed right alongside classes in the same UI. It looks like the only way we could do this now is issue two API requests (the term search and instances APIs) and handle the rest on our end. Would something like a flag on the term search API to include instances be of interest to BioPortal?

Thanks for taking a look!

Cheers,
Bryce

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] BioPortal web+API request

Bryce Mecum
Hey John, thanks for getting back so quickly. To some of your points:

> for example instances have no inherent hierarchy, do they?

Surely in some senses, but for us really a flat listing is both what we're used to and what would work. Similar to how Protégé does things.

> I wonder if direct punning of terms as classes might be an effective way to make these terms visible?  Of course, this only works if you have control over the ontology.

Sounds like this could work for us. I'll take a look and try it out.

We totally understand on the funding front and will certainly reach out if we see any good funding opportunities.

Thanks again.


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support