v0.5.32
Robot Template Adapter (EXPERIMENTAL)
see https://incatools.github.io/ontology-access-kit/packages/implementations/robot-template.html
This is experimental and incomplete.
This is an extension of the 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
only a small subset of KGCL is implemented so far
What's Changed
- Added mock tests by @hrshdhgd in #721
- Partial robot template implementation. by @cmungall in #722
Full Changelog: v0.5.31...v0.5.32
