Metadata-Version: 2.1
Name: pyobo
Version: 0.2.8
Summary: Handling and writing OBO
Home-page: https://github.com/pyobo/pyobo
Author: Charles Tapley Hoyt
Author-email: cthoyt@gmail.com
Maintainer: Charles Tapley Hoyt
Maintainer-email: cthoyt@gmail.com
License: MIT
Download-URL: https://github.com/pyobo/pyobo/releases
Project-URL: Bug Tracker, https://github.com/pyobo/pyobo/issues
Project-URL: Source Code, https://github.com/pyobo/pyobo
Keywords: Open Biomedical Ontologies,OBO
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.7
Requires-Dist: obonet
Requires-Dist: click
Requires-Dist: tqdm
Requires-Dist: pyyaml
Requires-Dist: pandas
Requires-Dist: requests
Requires-Dist: protmapper
Requires-Dist: more-itertools
Requires-Dist: humanize
Requires-Dist: tabulate
Requires-Dist: scrapy
Requires-Dist: sqlalchemy
Requires-Dist: psycopg2-binary
Requires-Dist: flask
Requires-Dist: flask-bootstrap
Requires-Dist: flask-admin
Requires-Dist: flasgger
Requires-Dist: psutil
Provides-Extra: docs
Requires-Dist: sphinx ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
Requires-Dist: sphinx-click ; extra == 'docs'
Requires-Dist: sphinx-autodoc-typehints ; extra == 'docs'

PyOBO |build|
=============
Tools for biological identifiers, names, synonyms, xrefs, hierarchies, relations, and properties through the
perspective of OBO.

Example Usage
-------------
Note! PyOBO is no-nonsense. This means that there's no repetitive
prefixes in identifiers. It also means all identifiers are strings,
no exceptions.

Note! The first time you run these, they have to download and cache
all resources. We're not in the business of redistributing data,
so all scripts should be completely reproducible. There's some
AWS tools for hosting/downloading pre-compiled versions in
``pyobo.aws`` if you don't have time for that.

Note! PyOBO can perform grounding in a limited number of cases, but
it is *not* a general solution for named entity recognition (NER) or grounding.
It's suggested to check `Gilda <https://github.com/indralab/gilda>`_
for a no-nonsense solution.

Mapping Identifiers and CURIEs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Get mapping of ChEBI identifiers to names.

.. code-block:: python

   import pyobo

   chebi_id_to_name = pyobo.get_id_name_mapping('chebi')

   name = chebi_id_to_name['132964']
   assert name == 'fluazifop-P-butyl'

Or, you don't have time for two lines

.. code-block:: python

    import pyobo

    name = pyobo.get_name('chebi', '132964')
    assert name == 'fluazifop-P-butyl'

Get reverse mapping of ChEBI names to identifiers

.. code-block:: python

    import pyobo

    chebi_name_to_id = pyobo.get_name_id_mapping('chebi')

    identifier = chebi_name_to_id['fluazifop-P-butyl']
    assert identifier == '132964'

Maybe you live in CURIE world and just want to normalize something like
`CHEBI:132964`:

.. code-block:: python

    import pyobo

    name = pyobo.get_name_by_curie('CHEBI:132964')
    assert name == 'fluazifop-P-butyl'

Sometimes you accidentally got an old CURIE. It can be mapped to the more recent
one using alternative identifiers listed in the underlying OBO with:

.. code-block:: python

    import pyobo

    # Look up DNA-binding transcription factor activity (go:0003700)
    # based on an old id
    primary_curie = pyobo.get_primary_curie('go:0001071')
    assert primary_curie == 'go:0003700'

    # If it's already the primary, it just gets returned
    assert 'go:0003700' == pyobo.get_priority_curie('go:0003700')

Grounding
~~~~~~~~~
Maybe you've got names/synonyms you want to try and map back to ChEBI synonyms.
Given the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look
it up and its preferred label.

.. code-block:: python

    import pyobo

    prefix, identifier, name = pyobo.ground('chebi', 'Fusilade II')
    assert prefix == 'chebi'
    assert identifier == '132964'
    assert name == 'fluazifop-P-butyl'

    # When failure happens...
    prefix, identifier, name = pyobo.ground('chebi', 'Definitely not a real name')
    assert prefix is None
    assert identifier is None
    assert name is None

If you're not really sure which namespace a name might belong to, you
can try a few in a row (prioritize by ones that cover the appropriate
entity type to avoid false positives in case of conflicts):

.. code-block:: python

    import pyobo

    # looking for phenotypes/pathways
    prefix, identifier, name = pyobo.ground(['efo', 'go'], 'ERAD')
    assert prefix == 'go'
    assert identifier == '0030433'
    assert name == 'ubiquitin-dependent ERAD pathway'

Cross-referencing
~~~~~~~~~~~~~~~~~
Get xrefs from ChEBI to PubChem

.. code-block:: python

    import pyobo

    chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs('chebi', 'pubchem.compound')

    pubchem_compound_id = chebi_id_to_pubchem_compound_id['132964']
    assert pubchem_compound_id == '3033674'

Get xrefs from Entrez to HGNC, but they're only available through HGNC
so you need to flip them

.. code-block:: python

    import pyobo

    hgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene')
    ncbigene_id_to_hgnc_id = {
        ncbigene_id: hgnc_id
        for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()
    }
    mapt_hgnc = ncbigene_id_to_hgnc_id['4137']
    assert mapt_hgnc == '6893'

Since this is a common pattern, there's a keyword argument `flip`
that does this for you:

.. code-block:: python

    import pyobo

    ncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene', flip=True)
    mapt_hgnc = ncbigene_id_to_hgnc_id['4137']
    assert mapt_hgnc == '6893'

Remap a CURIE based on pre-defined priority list and `Inspector Javert's Xref
Database <https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html>`_:

.. code-block:: python

    import pyobo

    # Map to the best source possible
    mapt_ncbigene = pyobo.get_priority_curie('hgnc:6893')
    assert mapt_ncbigene == 'ncbigene:4137'

    # Sometimes you know you're the best. Own it.
    assert 'ncbigene:4137' == pyobo.get_priority_curie('ncbigene:4137')

Find all CURIEs mapped to a given one using Inspector Javert's Xref Database:

.. code-block:: python

    import pyobo

    # Get a set of all CURIEs mapped to MAPT
    mapt_curies = pyobo.get_equivalent('hgnc:6893')
    assert 'ncbigene:4137' in mapt_curies
    assert 'ensembl:ENSG00000186868' in mapt_curies

If you don't want to wait to build the database locally for the ``pyobo.get_priority_curie`` and
``pyobo.get_equivalent``, you can use the following code to download a release from
`Zenodo <https://zenodo.org/record/3757266>`_:

.. code-block:: python

    import pyobo.resource_utils

    pyobo.resource_utils.ensure_inspector_javert()

Properties and Relations
~~~~~~~~~~~~~~~~~~~~~~~~
Get properties, like SMILES. The semantics of these are defined on an OBO-OBO basis.

.. code-block:: python

    import pyobo

    # I dont make the rules. I wouldn't have chosen this as the key for this property. It could be any string
    chebi_smiles_property = 'http://purl.obolibrary.org/obo/chebi/smiles'
    chebi_id_to_smiles = pyobo.get_filtered_properties_mapping('chebi', chebi_smiles_property)

    smiles = chebi_id_to_smiles['132964']
    assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'

Check if an entity is in the hierarchy:

.. code-block:: python

    import networkx as nx
    import pyobo

    # check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
    assert 'go:0008219' in pyobo.get_ancestors('go', '0006915')

    # check that go:0070246 ! natural killer cell apoptotic process is a
    # descendant of go:0006915 ! apoptotic process
    apopototic_process_descendants = pyobo.get_descendants('go', '0006915')
    assert 'go:0070246' in apopototic_process_descendants

Get the subhierarchy below a given node:

.. code-block:: python

    # get the descendant graph of go:0006915 ! apoptotic process
    apopototic_process_subhierarchy = pyobo.get_subhierarchy('go', '0006915')

    # check that go:0070246 ! natural killer cell apoptotic process is a
    # descendant of go:0006915 ! apoptotic process through the subhierarchy
    assert 'go:0070246' in apopototic_process_subhierarchy

Get a hierarchy with properties pre-loaded in the node data dictionaries:

.. code-block:: python

    import pyobo

    prop = 'http://purl.obolibrary.org/obo/chebi/smiles'
    chebi_hierarchy = pyobo.get_hierarchy('chebi', properties=[prop])

    assert 'chebi:132964' in chebi_hierarchy
    assert prop in chebi_hierarchy.nodes['chebi:132964']
    assert chebi_hierarchy.nodes['chebi:132964'][prop] == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'

Installation |pypi_version| |python_versions| |pypi_license|
------------------------------------------------------------
PyOBO can be installed from `PyPI <https://pypi.org/project/pyobo/>`_ with:

.. code-block:: sh

    $ pip install pyobo

It can be installed in development mode from `GitHub <https://github.com/pyobo/pyobo>`_
with:

.. code-block:: sh

    $ git clone https://github.com/pyobo/pyobo.git
    $ cd pyobo
    $ pip install -e .

Curation of the Metaregistry
----------------------------
At src/pyobo/registries/metaregistry.json is the curated registry. This is a source of information that contains
all sorts of fixes for missing/wrong information in MIRIAM, OLS, and OBO Foundry; entries that don't appear in
any of them; additional synonym information for each namespace/prefix; rules for normalizing xrefs and CURIEs, etc.

Most users will be interested in the ``"database"`` subdictionary.
Each entry has a key that was chosen first by preference for MIRIAM, then OBO Foundry,
then OLS, or assigned based on what felt right/was how they appeared in xrefs in other OBO files.
Their corresponding entries can have some combination of these keys:

- ``title``
- ``pattern``, a regex string for identifiers
- ``url``, a url pattern to resolve identifiers. Uses $1 to represent the identifier.
- ``synonyms``, a list of alternative prefixes that should point to this
- ``download``, a URL to the OBO file in case OBO Foundry doesn't list it or has a mistake
- ``not_available_as_obo``, a boolean telling you exactly what it sounds like
- ``no_own_terms``, a boolean telling you if it is completely derived from external sources
- ``wikidata_property``, a string pointing to the wikidata property that connects item in WikiData
  to identifers in this namespace
- ``miriam``: a dictionary containing "id" and "prefix" to point to MIRIAM
- ``obofoundry``: a dictionary containing "prefix" to point to OBO Foundry
- ``ols``, a dictionary containing "ontologyId" to point to OLS

Other entries in the metaregistry:

- The ``"remappings"->"full"`` entry is a dictionary from strings that might follow ``xref:``
  in a given OBO file that need to be completely replaced, due to incorrect formatting
- The ``"remappings"->"prefix"`` entry contains a dictionary of prefixes for xrefs that need
  to be remapped. Several rules, for example, remove superfluous spaces that occur inside
  CURIEs or and others address instances of the GOGO issue.
- The ``"obsolete"`` entry maps prefixes that have been changed.
- The ``"blacklists"`` entry contains rules for throwing out malformed xrefs based on
  full string, just prefix, or just suffix.


Troubleshoting
--------------
The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO resources. If you get an error like:

.. code-block::

   pyobo.getters.MissingOboBuild: OBO Foundry is missing a build for: mondo

Then you should check the corresponding page on the OBO Foundry (in this case, http://www.obofoundry.org/ontology/mondo.html)
and make an update to the ``url`` entry for that namespace in the metaregistry.

Development
-----------
Update the registries with the following commands. These external resources get updated all the
time, so don't forget about this.

.. code-block:: bash

    $ python -m pyobo.registries.obofoundry
    $ python -m pyobo.registries.ols
    $ python -m pyobo.registries.miriam


.. |build| image:: https://travis-ci.com/pyobo/pyobo.svg?branch=master
    :target: https://travis-ci.com/pyobo/pyobo
    :alt: Build Status

.. |coverage| image:: https://codecov.io/gh/pyobo/pyobo/coverage.svg?branch=master
    :target: https://codecov.io/gh/pyobo/pyobo?branch=master
    :alt: Coverage Status

.. |docs| image:: http://readthedocs.org/projects/pyobo/badge/?version=latest
    :target: http://pyobo.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

.. |python_versions| image:: https://img.shields.io/pypi/pyversions/pyobo.svg
    :alt: Stable Supported Python Versions

.. |pypi_version| image:: https://img.shields.io/pypi/v/pyobo.svg
    :alt: Current version on PyPI

.. |pypi_license| image:: https://img.shields.io/pypi/l/pyobo.svg
    :alt: MIT License


