Releases: INCATools/ontology-access-kit
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
Contributors
Assets 2
v0.5.31
v0.5.30
v0.5.29
0.5.28
v0.5.27
What's Changed
- Add link to llm how-to by @cmungall in #709
- value_set_names is None rather than () by @hrshdhgd in #707
- llm exception handling by @cmungall in #711
- Autoadding current year to footer, fixes #710 by @cmungall in #712
- Adding pantherdb adapter by @cmungall in #713
- Extending amigo and llm adapters by @cmungall in #714
Full Changelog: v0.5.26...v0.5.27
Contributors
Assets 2
v0.5.26
What's Changed
- Update Validator Interface link in howto guide by @anitacaron in #694
- Add codespell support: config, action (to detect new) + get some typos fixed by @yarikoptic in #671
- Implementing search using translator endpoint. by @cmungall in #695
- d3viz writer by @cmungall in #700
- Adding a validate_mappings implementations for LLMImplementation by @cmungall in #705
New Contributors
- @anitacaron made their first contribution in #694
Full Changelog: v0.5.25...v0.5.26
Contributors
Assets 2
v0.5.25
What's Changed
- Fix broken md hyperlink by @yarikoptic in #672
- Update README.md by @azankl in #668
- VSKit Permissible Value Label Fix by @plbremer in #689
- VSKit - description newline replacement by @plbremer in #691
- Enhanced implementations for remote endpoints. by @cmungall in #682
- Expanded enrichment notebook by @cmungall in #692
New Contributors
- @yarikoptic made their first contribution in #672
- @azankl made their first contribution in #668
- @plbremer made their first contribution in #689
Full Changelog: v0.5.24...v0.5.25
