Ontoserver

https://ontoserver.csiro.au/docs/
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Ontoserver is a CSIRO-developed ontology server for managing and syndicating SNOMED CT terminology...
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### Start Ontoserver

Source: https://ontoserver.csiro.au/docs

Start the Ontoserver service in detached mode using Docker Compose. Ontoserver may take up to 60 seconds to fully initialize.

```bash
docker-compose up -d
```

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### Get index.sh Help

Source: https://ontoserver.csiro.au/docs

Display help information for the `index.sh` script within the Ontoserver container.

```bash
docker exec ontoserver /index.sh -h
```

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### Get Latest SNOMED CT-AU Version

Source: https://ontoserver.csiro.au/docs

Execute the index script within the Ontoserver container to retrieve the latest SNOMED CT-AU version.

```bash
docker exec ontoserver /index.sh
```

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### Get Specific SNOMED CT-AU Version

Source: https://ontoserver.csiro.au/docs

Retrieve a specific SNOMED CT-AU version by providing the version date. This operation involves a large download and may take time.

```bash
docker exec ontoserver /index.sh -v 20250831
```

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### Minimal Ontoserver Docker Compose Configuration

Source: https://ontoserver.csiro.au/docs

This docker-compose.yml file sets up a minimal Ontoserver instance with a PostgreSQL database. Adjust JAVA_OPTS for memory requirements and consider ONTOSERVER_INSECURE for disabling SSL/TLS.

```yaml
version: '3'
volumes:
  onto:
    driver: local
  pgdata:
    driver: local
services:
  db:
    image: postgres:12
    volumes:
      - pgdata:/var/lib/postgresql/data
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U postgres"]
      interval: 10s
      timeout: 5s
      retries: 5
    environment:
      - POSTGRES_HOST_AUTH_METHOD=trust
  ontoserver:
    image: quay.io/aehrc/ontoserver:ctsa-6
    container_name: ontoserver
    read_only: true
    security_opt:
      - no-new-privileges
    depends_on:
      - db
    ports:
      - "8443:8443"
      - "8080:8080"
    environment:
      - spring.datasource.url=jdbc:postgresql://db/postgres
# These two lines are specific to deployment in Australia only
      - authentication.oauth.endpoint.client_id.0=NCTS_CLIENT_ID
      - authentication.oauth.endpoint.client_secret.0=NCTS_CLIENT_SECRET
      - JAVA_OPTS=-Xmx2G        # Minimum
#      - JAVA_OPTS=-Xmx8G      # Preferred
    volumes:
      - onto:/var/onto
      - /tmp
      - /var/log

```

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### Inspect Ontoserver Logs

Source: https://ontoserver.csiro.au/docs

View the logs for the Ontoserver container. Use the `-f` flag to follow live log updates.

```bash
docker logs ontoserver
```

```bash
docker logs -f ontoserver
```

--------------------------------

### Log in to quay.io

Source: https://ontoserver.csiro.au/docs

Use this command to log in to your quay.io account, which is necessary for pulling Ontoserver images.

```bash
docker login quay.io
```

--------------------------------

### Configure MLDS Credentials

Source: https://ontoserver.csiro.au/docs

Provide your MLDS credentials for authentication. Replace `<username>` and `<password>` with your actual credentials.

```properties
authentication.basic.endpoint.0=https://mlds.ihtsdotools.org/api
authentication.basic.endpoint.user.0=<username>
authentication.basic.endpoint.password.0=<password>
```

--------------------------------

### Stop Ontoserver

Source: https://ontoserver.csiro.au/docs

Stop the Ontoserver service using Docker Compose.

```bash
docker-compose stop
```

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### Configure Default SNOMED CT Edition

Source: https://ontoserver.csiro.au/docs

Set the default SNOMED CT Edition for Ontoserver. This is useful when working with international editions.

```properties
snomed.default.edition=45991000052106
```

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### Configure SNOMED International MLDS Feed

Source: https://ontoserver.csiro.au/docs

Include SNOMED International's MLDS syndication feed. Filter conditions can be applied to include specific extensions like the Swedish Extension or the International Edition.

```properties
atom.syndication.feedLocation=https://mlds.ihtsdotools.org/api/feed?canonical=http://snomed.info/sct/900000000000207008,https://mlds.ihtsdotools.org/api/feed?canonical=http://snomed.info/sct/45991000052106
```
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