Add OWL query restful API server

[Robbie1977]

Take manchester syntax query via JSON and return results as JSON

[dosumis]

Here's a more fleshed out version of the draft script I posted on the last ticket. https://gist.github.com/dosumis/ce57643890d331930aee

Should be pretty straightforward to rewrite in Java and to hook it up to an http server allowing queries to be passed as post requests + JSON. Also needs better error handling - returning something useful when the OWL-API throws an error due to a bad query. Typically, this would be an unrecognised entity in a manchester syntax query. In this case the query should return an error message in the status field that includes the ID of the unrecognised entity.

We might want to fold this into a more general API for VFB, with OWL queries returning data from SOLR.

[dosumis]

This service is provided by Aber-OWL:

Example query http://aber-owl.net/service/api/runQuery.groovy?type=subeq&query=overlaps%20some%20%27adult%20antennal%20lobe%27&ontology=FB-BT&labels=true

No support for individuals right now, but have requested. Can point people to this as a way of getting JSON lists of terms relveant for annotation.

We might want to re-use their code locally to run our reasoner. We could ditch all of the Nestor Code for OWL queries in favour of some very compact Groovy scripts.

[dosumis]

https://github.com/bio-ontology-research-group/AberOWL/tree/master/src

[dosumis]

@Robbie1977: We still urgently need an OWL server. Either:

• a simple OWL server based on Brain (see example code here: https://gist.github.com/dosumis/ce57643890d331930aee - Note, if no need to support synonyms, we can drop the owltools call. I don't care what language. Obvious choices are Java or Groovy.
• Aber-OWL: I haven't played with setting this up yet. Aber-OWL devs happy to help if we run into setup problems.

As well as being needed for queries on VFB, this would be extremely useful for back-end scripting, much of which could be switched from Jython to Python 3.

[Robbie1977]

Got a local Aber-OWL server running - waiting for a query on the sync setup.

running on test machine (via VPN): 129.215.164.244 :3000 is web server :31337 AberOWL server :6379 Redis DB

Once sync is running then you can in theory run the same querys as you showed above here: http://129.215.164.244:31337/api/runQuery.groovy

Would we be looking to sync their ontology copies (as they have fbbt) of load our own directly?

[dosumis]

Would we be looking to sync their ontology copies (as they have fbbt) of load our own directly?

Best to configure just to run ours. Can get their help to do that if not obvious.

[dosumis]

Attempting to load full VFB KB into AberOWL: http://aber-owl.net/ontology/VFB

Ticket claiming support for individuals is here: https://github.com/bio-ontology-research-group/AberOWL/issues/18

[dosumis]

Smaller test KB uploaded here: http://aber-owl.net/ontology/VFB_test

[dosumis]

Some test queries - for once this loaded (taking an age) http://aber-owl.net/service/api/runQuery.groovy?type=realize&query=%3Chttp://purl.obolibrary.org/obo/FBbt_00007683%3E&ontology=VFB_test http://aber-owl.net/service/api/runQuery.groovy?type=realize&direct=false&query=%3Chttp://purl.obolibrary.org/obo/FBbt_00007683%3E&ontology=VFB_test

[Robbie1977]

behaving the same as the full sized one did for me. time didn't seem to help: http://129.215.164.244:8080/ontology (via ed VPN) http://129.215.164.244:8080/service/api/runQuery.groovy?type=realize&direct=false&query=%3Chttp://purl.obolibrary.org/obo/FBbt_00007683%3E&ontology=VFB Although API is giving no response rather than

java.lang.IllegalArgumentException: URI is not absolute

[dosumis]

Is ontology name as specified during load?

[Robbie1977]

Fixed http://aber-owl.net/ontology/VFB See https://github.com/bio-ontology-research-group/AberOWL/issues/38