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Update readme #42

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Complete philosophy
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14 changes: 6 additions & 8 deletions docs/README.md
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## Overview

`pyiron_ontology` is a new pyiron project built on top of `owlready2` for ontologically-guided workflow design.
This project is currently in alpha-stage and subject to rapid change.
`pyiron_ontology` is a pyiron project built on top of `owlready2` to leverage ontologies for guided workflow design and dynamic (use-based) typing.

Philosophically, `pyiron_ontology` breaks the construction of ontologies down into two parts: a set of classes that are "universal" to all `pyiron_ontology` ontologies, which describe the core elements of a workflow, and a set of "domain specific" declarations (most or all of which) define
Philosophically, `pyiron_ontology` breaks the construction of ontologies down into two parts: a set of classes that are "universal" to all `pyiron_ontology` ontologies, which describe the core elements of a workflow, and a set of "domain specific" instance declarations (most or all of which) define relationships between different pieces of code.

## Installation and setup

For the bleeding-edge, clone this repo.
`pyiron_ontology` is also available from Conda Forge via `conda install -c conda-forge pyiron_ontology`.
`pyiron_ontology` available to clone, pip-install, or on conda (recommended) from Conda Forge via `conda install -c conda-forge pyiron_ontology`.

`pyiron_ontology` uses `owlready2`, which requires java.
In case you try to run and get an `owlready2` error about not finding java, you may need to set the java path (cf. [owlready2 docs](https://owlready2.readthedocs.io/en/latest/reasoning.html#configuration)): `import owlready2; owlready2.JAVA_EXE = "C:\\path\\to\\java.exe"`.
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## Reasoning on existing `pyiron_atomistics` data

`pyiron_ontology` also comes with an ontology defined for (a small sub-set of) `pyiron_atomistics`.
`pyiron_ontology` also comes with an ontology defined for (a small sub-set of) `pyiron_atomistics` (an optional dependency).

For example, if you have `Murnaghan` jobs in your pyiron project, the snippet below will return a nice little dataframe of results:

```python
>>> import pyiron_ontology as po
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Index(['Chemical Formula', 'atomistics.BulkModulus', 'unit', 'Engine'], dtype='object')

```

If you have `Murnaghan` jobs in your project, this will return a nice little dataframe.
2 changes: 1 addition & 1 deletion setup.py
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license='BSD',

classifiers=[
'Development Status :: 3 - Alpha',
'Development Status :: 5 - Production/Stable',
'Topic :: Scientific/Engineering :: Physics',
'License :: OSI Approved :: BSD License',
'Intended Audience :: Science/Research',
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