OMERO Virtual Knowledge Graph

This repository contains the code to create a virtual knowledge graph for OMERO using ontop-vkg mappings.

Install the Ontop command line client

The utility script in utils/install_ontop.sh can be used to install the ontop cli into ontop-cli. We will assume the binary ontop is located in that directory. The script also installs the postgresql jdbc driver into ontop-cli/jdbc/.

Deployment

To deploy your own OMERO-VKG, follow these steps:

Generate site configuration directory

In the top level directory, run the command

bash deploy.sh PREFIX URI

Replace PREFIX AND URI with the prefix name and URL for your OMERO instance, respectively. E.g. for the (hypothetical ) Institute of Bioimaging, running OMERO at https://ome.iob.net, a sensible choice could be bash deploy.sh iob https://ome.iob.net/. This would create a new deployment directory named iob/ (in the example above), containing these files:

1. iob.ttl: The mapping ontology
2. iob.obda: The mappings with adjusted site prefix and URL.
3. iob.properties: Properties file containing the database connection parameters.
4. core.owl.ttl: A patched version of the OME core ontology originally obtained form https://joshmoore.github.io/ome-ld/core .
5. catalog-v001.xml: 3rd party ontologies imported into iob.ttl, in particular the OME core ontology.

Edit properties file

In the properties file, you need to change the values for jdbc.user, jdbc.password, and jdbc.url. Consider setting up a read-only database user (role) with SELECT rights on the public database tables (see below). The jdbc.url should be configured according to your OMERO DB host's hostname and port on which the postgresql daemon accepts requests. Leave the jdbc.driver value as it is.

Create read-only OMERO DB user

Consult utils/setup_ontop_dbuser.sh and queries/sql/ontop_user.sql to setup the read-only DB user.

Test setup

Run

ontop-cli/ontop validate -m PREFIX/PREFIX.obda -t PREFIX/PREFIX.ttl -p PREFIX/PREFIX.properties -x PREFIX/catalog-v001.xml

to validate your deployment.

Launch OMERO-VKG

Change into the deployment directory

cd PREFIX

and run the omero-ontop.sh script

bash omero-ontop.sh

This will launch the OMERO Virtual Knowledge Graph SPARQL endpoint at http://localhost:8080. You may wish to configure a different port and/or hostname. Consult the ontop-cli user manual to this effect (ontop-cli/ontop help endpoint).

Development

For development, the omero-test-infra docker-compose file can be used. Follow these step to set it up:

Get omero-test-infra

In the root of this repository:

git clone https://github.com/ome/omero-test-infra .omero

Patch the port mapping configuration

We need to access omero's postgresql database. Inside the container, it runs on port 5432 but is not mapped to the host. We patch the docker-compose file to have the database served on postgresql://localhost:15432.

cp utils/portmapping.patch .omero
cd .omero
patch -p1 < portmapping.patch
cd ..

Add ontop database user

This step must be redone every time after resetting the test infrastructure.

utils/setup_ontop_dbuser.sh

Get omero-py

Install omero-py via pip or from conda-forge. The script /utils/install_omero-py.sh/ downloads and installs miniconda to the user's home directory and install omero-py as well as pytest and rdflib into the base environment.

source utils/install_omero-py.sh

Launch omero-test-infra

.omero/docker dev start_up

Populate omero with test data.

We need something to play with, so let's create some projects and datasets, import a few images and annotate with key-value pairs (map annotations) and tags.

utils/insert_data.sh

Launch ontop endpoint

Assuming ontop is in your path:

omero-ontop-mappings endpoint --mapping omero-ontop-mappings/omero-ontop-mappings.obda \
               --ontology omero-ontop-mappings/omero-ontop-mappings.ttl \
               --properties omero-ontop-mappings/omero-ontop-mappings.properties \
               --xml-catalog omero-ontop-mappings/catalog-v001.xml \
               --dev

The commandline arguments point to the mappings file, mapping ontology, database connection details (properties), ontology import catalog, respectively. The --dev flag starts ontop int development mode. Edits to the mappings or ontology will trigger a restart of the endpoint. By default, the ontop endpoint is served at http://localhost:8080/sparql , the query editor is at http://localhost:8080 . Use the --port option to configure a different port.

Run tests

Finally,

pytest

will run the python test suite.

Reset database

To restart from a blank omero-test-infra (without images, datasets, projects, or annotations), run

.omero/docker srv

Don't forget to restart it according to above.

Acknowledgments

This project was developed with support from the Biohackathon 2024.