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OBASK Advanced Settings

Configuring Ontology Files in collectdata

The OBASK pipeline allows you to configure both remote and local ontology files that will be used in your project. These files are configured as part of the collectdata module within the config/collectdata folder, specifically in the vfb_fullontologies.txt file, and are processed as follows:

Remote Ontology Files

To configure remote ontology files, add the URLs of the ontology files you want to download directly to the config/collectdata/vfb_fullontologies.txt file. Each URL should be on a new line.

http://purl.obolibrary.org/obo/go.owl
http://purl.obolibrary.org/obo/cl.owl

When the pipeline runs, it will download these ontology files from the specified remote sources and process them accordingly.

Local Ontology Files

For local ontology files that you want to include in the pipeline, you should follow these steps:

  1. Place the Files: Copy the local ontology files into the config/collectdata/local_ontologies directory. The files should have a .owl extension.

  2. No Need to List in vfb_fullontologies.txt: Unlike remote files, you do not need to add the local files to the vfb_fullontologies.txt file. The pipeline automatically detects any .owl files in the local_ontologies directory.

  3. Pipeline Processing: During the pipeline execution, any .owl files found in the local_ontologies directory will be copied to the VFB_DOWNLOAD_DIR. After this, the pipeline will proceed to download and process any remote ontology files listed in vfb_fullontologies.txt.

Example Configuration

If your project requires both remote and local ontology files, your setup might look like this:

  1. Remote Files in vfb_fullontologies.txt:

  2. Local Files in config/collectdata/local_ontologies:

    Place files like my_local_ontology.owl and custom_terms.owl directly in the local_ontologies directory.

This configuration ensures that your project uses a combination of remote and local ontology files, processed in a seamless and automated way during the pipeline run.