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Tools

This directory contains a number of tools that can be used to work with local .owl files and directories for organizing temporary intermediate release artifacts. Note: each tool has dependencies. Please look under the each header for more details.

Release Process

The root directory is structured loosely based on the Ontology Development Kit (ODK). However, full testing and continuous integration have not been set up to release ICO per ODK (as this is not needed at the time of this writing). The reason this process is labeled temporary is that a simple shell script performs the necessary tasks using ROBOT, the OBO Foundry tool set. This process assumes that the current release of ROBOT is installed on the machine that is releasing ICO. Please visit http://robot.obolibrary.org/ for more information.

Running the Release Script

The script can be invoked as follows:

./release_process.sh

The script performs the following actions:

  1. Merge ico-edit.owl in the src/ontology/ directory.
  2. Create version IRI using the current date.
  3. Reason (lightweight), include inferred axioms.
  4. Generate reporting.

Intermediate OWL artifacts

This directory contains intermediate owl files produced by the release process. The products can be removed during the

Mass Update Tools

This is a set of command line tools designed to extract terms and definitions from an .owl file into a .csv using Python. The .csv file can be imported into a common application such as MS Excel in order to make changes to the content. Once changes have been made the OWL file can be updated for all terms that were changed. This is helpful for teams that want to make significant content changes to terms and definitions at once. The primary reason for including these is that they were used to revise content in ico.owl during the summer of 2018.

extract_classes.py

This tool takes one .owl file command line argument. It produces a .csv file with terms and definitions in the following format:

PURL,Term Label,Definition

insert_new_definitions.py

This tool takes one .owl file and one .csv command line argument. It is expected that the .csv file is in exactly the same format as the output from extract_classes.py. It compares the 'PURLS' in the .csv to the existing content in the .owl file and creates an updated .owl file and and revisions file to compare and document the changes.