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Add info that pipe is internal separator to biobank-specimens.tsv #1776

Merged
merged 2 commits into from
Mar 21, 2024
Merged

Add info that pipe is internal separator to biobank-specimens.tsv #1776

merged 2 commits into from
Mar 21, 2024

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cmungall
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Fixes #1775

cmungall added a commit to INCATools/ontology-access-kit that referenced this pull request Mar 20, 2024
@cmungall
Syncing test files with proposed changes in obi-ontology/obi#1776
252861b
cmungall added a commit to INCATools/ontology-access-kit that referenced this pull request Mar 21, 2024
@cmungall
Partial robot template implementation. (#722)
8da76e1 
* Partial robot template implementation.

Simple ROBOT-template backed implementation.

    .. note::

        Highly incomplete!

    This provides a minimal implementation of some interfaces using a collection of ROBOT tenplates as
    a backend.

    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 ``templates``, you can use a selector:

    .. code-block:: bash

        runoak -i robottemplate:templates COMMAND ...

    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.

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

    .. code-block:: bash

        runoak -i robottemplate:templates info OBI:0002516

        OBI:0002516 ! brain specimen

    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.

* add missing

* Syncing test files with proposed changes in obi-ontology/obi#1776

* Adding functionality for aliases

* Additional docs and tests

Skipping patcher test until INCATools/kgcl#64 is fixed

* Explicit dumping (should not be necessary?)

* Adding metadata to asserts

* Ensure cache is cleared after modifications

* docs
@jamesaoverton jamesaoverton merged commit 8cf5481 into obi-ontology:master Mar 21, 2024
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@jamesaoverton
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Thanks!

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Successfully merging this pull request may close these issues.

OBI has synonyms like nasal wash specimen|nasopharyngeal aspirate
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@cmungall @jamesaoverton