Provide Web APIs to access ontologies in WebProtege

[tudorache]

Provide Web APIs (REST, ideally) to:

• download an ontology
• get the list of available ontologies
• upload an ontology
• replace an ontology

[ejwinter]

A rich API would be so powerful. I don't see any indication that there is one.

This has been a great tool for play but an API will make it a truly useful backbone.

Thank you!

A way to get autocompletion suggestions
GET /api/#projects/GUID/suggest?query=Prostate

A way to get info about a term including HATEOES to parents and children, synonyms, related terms.
GET /api/#projects/GUID/{term/synoym}

[rodriguesk]

is this ever going to be in the works?

[matuskalas]

We from https://github.com/edamontology rely heavily on WebProtégé. An API to

• create an ontology
• update an ontology (returning list of changes)

would be extreeemely useful. Otherwise our life is made very difficult, with no CI and CD possible (Continuous Integration and Deployment).

The WebProtégé web frontend has to somehow communicate with the backend. Could that channel be used by 3rd-party applications as some kind of an API?

[BreeAnn7]

I can see that WebProtege 3.0.0 tag was removed. Does this mean there is still no API access?? We'd really like to see this happen!! If it did happen is there developer documentation on how to access available?

[ronniebrito]

looks like there is an API in current code version, but couldnt find any documentation about it
an API, or another method to download and ontology would be very usefull

[matuskalas]

I can see that WebProtege 3.0.0 tag was removed. Does this mean there is still no API access?? We'd really like to see this happen!! If it did happen is there developer documentation on how to access available?

We really need it too! WebProtégé is so amazing and important for us, we just need an API in addition to what it provides (even a very simple API would help)

[joakimsod]

Any progress on this?

[boris-horner]

Just being able to export / import an ontology throughh an API would be extremely helpful (and I think for others in this thread, too). Wouldn't it be possible to expose that as a first step, and add more functionality later? I am working on a better integration to convert an existing ontology to graphml to visualize it in yEd...

[matthewhorridge]

This is in the works now. We have a project that is funded by BASF to provide a proper Web API and to make WebProtege more extensible.

[boris-horner]

Great to hear, thanks for the quick reply. I'll keep an eye on new WebProtégé versions then.

[matuskalas]

Just being able to export / import an ontology throughh an API would be extremely helpful (and I think for others in this thread, too). Wouldn't it be possible to expose that as a first step, and add more functionality later?

Exactly that! 👆🏽 Pretty please 😊

[matthewhorridge]

@matuskalas are you using your own installation of WebProtege?

[matuskalas]

This is in the works now. We have a project that is funded by BASF to provide a proper Web API and to make WebProtege more extensible.

Really awesome to hear! 🎉🎆

If you would like to have more folks to test or help shape or specifiy the needs, we the EDAM ontology maintainers would be very happy to help. 🙌🏽

[matuskalas]

@matuskalas are you using your own installation of WebProtege?

Nope, the public server. Which is important for us, as we don't have the capacity to maintain our own.

[etiennecl]

This is in the works now. We have a project that is funded by BASF to provide a proper Web API and to make WebProtege more extensible.

I will second @matuskalas! I would be happy to help on shaping out the needs or writing some features of the API.

[Gorogora]

happy to hear that a Web API. @matthewhorridge is there a planned release date?

[matthewhorridge]

Some time early next year for deployment on webprotege.stanford.edu @Gorogora

[Komposten]

Any update on this?

[rodriguesk]

@matthewhorridge is the API available in any capacity? If not, is there any idea of an updated timeline? Thanks!

[volodymyrss]

We also have the same use case: need to use CI/CD to generate ontology doc and publish the validation reference.

By looking in the code I found that it would should be possible to make a key and then use it to download. Then I also found this discussion https://mailman.stanford.edu/pipermail/protege-dev/2020-May/001873.html which seems to confirm this usage.

In my case the key could not be recognized, not sure why. It should be possible to understand - the code is all there.

More importantly, I found that by letting the guest account read a particular project (also done with webprotege-cli), I can download the ontology with a simple GET request and integrate it as I need to. In our case the server is in private network and I do not mind this being unrestricted. Could be some hidden security implications of course due to increased attack surface.

Anyway, the use case is largely solved for us, maybe this approach helps other people too!

[asideras]

"Are there any updates on this?
Following @volodymyrss's suggestion, I generated an API key using the CLI and associated it with a user. Then, I used this API key to retrieve the project using the code snippet below:

session = requests.Session()
headers = {'Authorization': f'ApiKey {API_KEY}'}
project_url = f"{BASE_URL}/download?project={PROJECT_ID}&format=ttl"
response = session.get(project_url, headers=headers)

However, I got a 403 response and in the WebProtege logs I see the following message:

INFO Received download request from UserId{**guest**} at X for project ProjectId{Y}
INFO Denied download request as the user does not have permission to download this project.

Notice that it says "guest" and not the username that I created the API key for.

Thanks in advance.

[volodymyrss]

Notice that it says "guest" and not the username that I created the API key for.

Yes, well, I had to let guest account read a particular project (see I explained in my message).
It's not completely ideal, for good for our purposes at least.

[aweissen1]

Any news concerning the API? I am wondering if there is a description of the API - how to use it?