ROBOT Template Adapter

Warning

This is experimental and incomplete.

This is an extension of the abstract TabularInterface adapter that provides access to a collection of ROBOT templates.

Note that it does NOT use the ROBOT tool itself to access these, it uses custom code that only implements a portion of the spec.

One of the main driving use cases here is to enable KGCL commands with ontologies that use ROBOT templates.

For example, the OBI templates folder on GitHub contains a collection of ROBOT templates.

  • assays.tsv

  • biobank-specimens.tsv

  • …

Assuming these are in a local path my/path/templates, you can use a selector:

runoak -i robottemplate:my/path/templates COMMAND ...

Or in python:

from oaklib import get_adapter
adapter = get_adapter('robottemplate:my/path/templatestemplates')

Note that this does NOT trigger compilation of the templates into OWL - this implementation works on the templates as a collection of TSVs, facilitating update operations.

Command Line Examples

From here we assume your templates are in a local folder ./templates.

Basic operations

Currently very few operations are supported, but you can do basic things like:

runoak -i robottemplate:templates info OBI:0002516

Returns:

  • OBI:0002516 ! brain specimen

Or limited search:

runoak -i robottemplate:templates info l~brain

Returns:

  • OBI:0002516 ! brain specimen

  • OBI:0003357 ! brain region atlas image data set

  • …

Applying KGCL commands

You can also apply KGCL commands:

runoak -i robottemplate:templates apply \
  "rename OBI:0002516 from 'brain specimen' to 'brain sample'" -o new_templates

This will create a new copy of all templates in new_templates, with the label column modified in biobank-specimens.tsv

Warning

only a small subset of KGCL is implemented so far.