Partial robot template implementation.

docs/packages/implementations/index.rst

@@ -23,4 +23,5 @@ Implementations (also known as *adapters*) implement one or more :ref:`interface
    gilda
    aggregator
    pantherdb
+   robot-template
    llm

docs/packages/implementations/robot-template.rst

@@ -0,0 +1,85 @@
+.. _robot_template_implementation:
+
+ROBOT Template Adapter
+=============
+
+.. warning::
+
+    This is experimental and incomplete.
+
+This is an extension of the abstract :ref:`TabularInterface` adapter that provides
+access to a collection of `ROBOT templates <http://robot.obolibrary.org/template>`_.
+
+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 <https://github.com/obi-ontology/obi/tree/016ca67c7e6f31a048780cee56afde24d4af7125/src/ontology/templates>`_
+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:
+
+.. code-block:: bash
+
+    runoak -i robottemplate:my/path/templates COMMAND ...
+
+Or in python:
+
+.. code-block:: 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:
+
+.. code-block:: bash
+
+    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:
+
+.. code-block:: bash
+
+    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.

src/oaklib/datamodels/vocabulary.py

@@ -23,12 +23,14 @@
 HAS_NARROW_SYNONYM = omd.slots.has_narrow_synonym.curie
 HAS_RELATED_SYNONYM = omd.slots.has_related_synonym.curie
 SKOS_ALT_LABEL = "skos:altLabel"
+IAO_ALTERNATIVE_LABEL = "IAO:0000118"
 SYNONYM_PREDICATES = [
     HAS_RELATED_SYNONYM,
     HAS_NARROW_SYNONYM,
     HAS_EXACT_SYNONYM,
     HAS_BROAD_SYNONYM,
     SKOS_ALT_LABEL,
+    IAO_ALTERNATIVE_LABEL,
 ]
 
 SCOPE_TO_SYNONYM_PRED_MAP = {

src/oaklib/implementations/__init__.py

@@ -56,6 +56,7 @@
 )
 from oaklib.implementations.sparql.sparql_implementation import SparqlImplementation
 from oaklib.implementations.sqldb.sql_implementation import SqlImplementation
+from oaklib.implementations.tabular.robot_template_implementation import RobotTemplateImplementation
 from oaklib.implementations.translator.translator_implementation import (
     TranslatorImplementation,
 )
@@ -97,6 +98,7 @@
     "GildaImplementation",
     "LLMImplementation",
     "KGXImplementation",
+    "RobotTemplateImplementation",
     "UniprotImplementation",
     "TranslatorImplementation",
     "OakMetaModelImplementation",