ontodev-gizmos 0.1.2

Gizmos for ontology development

gizmos

Utilities for ontology development

Testing

For development, we recommend installing and testing using:

python3 -m pip install -e .
python3 setup.py pytest

There are some dependencies that are test-only (e.g., will not be listed in the project requirements). If you try and run pytest alone, it may fail due to missing dependencies.

Modules

gizmos.tree

The tree module produces a CGI tree browser for a given term contained in a SQL database. The SQL database should be created from OWL using rdftab to ensure it is in the right format.

Usage in the command line:

python3 -m gizmos.tree [path-to-database] [term] > [output-html]

The term should be a CURIE with a prefix already defined in the prefix table of the database. If the term is not included, the output will show a tree starting at owl:Thing.

The links in the tree return query strings with the ID of the term:

?id=FOO:123

If you provide the -i/--include-db flag, you will also get the db parameter in the query string. The value of this parameter is the base name of the database file.

?db=bar&id=FOO:123

This can be useful when writing scripts that return trees from different databases.