pyobo 0.10.12__py3-none-any.whl → 0.11.1__py3-none-any.whl

pyobo-0.10.12.dist-info/METADATA

@@ -1,499 +0,0 @@
-Metadata-Version: 2.1
-Name: pyobo
-Version: 0.10.12
-Summary: Handling and writing OBO
-Home-page: https://github.com/pyobo/pyobo
-Download-URL: https://github.com/pyobo/pyobo/releases
-Author: Charles Tapley Hoyt
-Author-email: cthoyt@gmail.com
-Maintainer: Charles Tapley Hoyt
-Maintainer-email: cthoyt@gmail.com
-License: MIT
-Project-URL: Bug Tracker, https://github.com/pyobo/pyobo/issues
-Project-URL: Source Code, https://github.com/pyobo/pyobo
-Keywords: Open Biomedical Ontologies,OBO
-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 :: 3.12
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.9
-License-File: LICENSE
-Requires-Dist: obonet>=0.3.0
-Requires-Dist: click
-Requires-Dist: tqdm
-Requires-Dist: pyyaml
-Requires-Dist: pandas
-Requires-Dist: requests
-Requires-Dist: protmapper
-Requires-Dist: more-itertools
-Requires-Dist: more-click>=0.0.2
-Requires-Dist: humanize
-Requires-Dist: tabulate
-Requires-Dist: cachier
-Requires-Dist: pystow>=0.2.7
-Requires-Dist: bioversions>=0.5.202
-Requires-Dist: bioregistry>=0.10.20
-Requires-Dist: bioontologies>=0.4.0
-Requires-Dist: zenodo-client>=0.0.5
-Requires-Dist: class-resolver
-Requires-Dist: psycopg2-binary
-Requires-Dist: drugbank-downloader
-Requires-Dist: chembl-downloader
-Requires-Dist: umls-downloader>=0.1.3
-Requires-Dist: typing-extensions
-Provides-Extra: agrovoc
-Requires-Dist: rdflib; extra == "agrovoc"
-Provides-Extra: docs
-Requires-Dist: sphinx<8.0; extra == "docs"
-Requires-Dist: sphinx-rtd-theme; extra == "docs"
-Requires-Dist: sphinx-click; extra == "docs"
-Requires-Dist: sphinx-automodapi; extra == "docs"
-Provides-Extra: tests
-Requires-Dist: coverage; extra == "tests"
-Requires-Dist: pytest; extra == "tests"
-Provides-Extra: web
-Requires-Dist: flask; extra == "web"
-Requires-Dist: bootstrap-flask; extra == "web"
-Requires-Dist: flask-admin; extra == "web"
-Requires-Dist: flasgger; extra == "web"
-Requires-Dist: psutil; extra == "web"
-
-PyOBO
-=====
-|build| |pypi_version| |python_versions| |pypi_license| |zenodo| |black| |bioregistry|
-
-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')
-
-Mapping Species
-~~~~~~~~~~~~~~~
-Some resources have species information for their term. Get a mapping of WikiPathway identifiers
-to species (as NCBI taxonomy identifiers):
-
-.. code-block:: python
-
-    import pyobo
-
-    wikipathways_id_to_species = pyobo.get_id_species_mapping('wikipathways')
-
-    # Apoptosis (Homo sapiens)
-    taxonomy_id = wikipathways_id_to_species['WP254']
-    assert taxonomy_id == '9606'
-
-Or, you don't have time for two lines:
-
-.. code-block:: python
-
-    import pyobo
-
-    # Apoptosis (Homo sapiens)
-    taxonomy_id = pyobo.get_species('wikipathways', 'WP254')
-    assert taxonomy_id == '9606'
-
-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'
-
-If you don't have time for two lines:
-
-.. code-block:: python
-
-    import pyobo
-
-    pubchem_compound_id = pyobo.get_xref('chebi', '132964', 'pubchem.compound')
-    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_id = ncbigene_id_to_hgnc_id['4137']
-    assert mapt_hgnc_id == '6893'
-
-If you don't have time for two lines (I admit this one is a bit confusing) and
-need to flip it:
-
-.. code-block:: python
-
-    import pyobo
-
-    hgnc_id = pyobo.get_xref('hgnc', '4137', 'ncbigene', flip=True)
-    assert hgnc_id == '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
-~~~~~~~~~~
-Get properties, like SMILES. The semantics of these are defined on an OBO-OBO basis.
-
-.. code-block:: python
-
-    import pyobo
-
-    # I don't 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'
-
-If you don't have time for two lines:
-
-.. code-block:: python
-
-    import pyobo
-
-    smiles = pyobo.get_property('chebi', '132964', 'http://purl.obolibrary.org/obo/chebi/smiles')
-    assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
-
-Hierarchy
-~~~~~~~~~
-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'
-
-Relations
-~~~~~~~~~
-Get all orthologies (``ro:HOM0000017``) between HGNC and MGI (note: this is one way)
-
-.. code-block:: python
-
-    >>> import pyobo
-    >>> human_mapt_hgnc_id = '6893'
-    >>> mouse_mapt_mgi_id = '97180'
-    >>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')
-    >>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]
-
-If you want to do it in one line, use:
-
-.. code-block:: python
-
-    >>> import pyobo
-    >>> human_mapt_hgnc_id = '6893'
-    >>> mouse_mapt_mgi_id = '97180'
-    >>> assert mouse_mapt_mgi_id == pyobo.get_relation('hgnc', 'ro:HOM0000017', 'mgi', human_mapt_hgnc_id)
-
-Writings Tests that Use PyOBO
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-If you're writing your own code that relies on PyOBO, and unit
-testing it (as you should) in a continuous integration setting,
-you've probably realized that loading all of the resources on each
-build is not so fast. In those scenarios, you can use some of the
-pre-build patches like in the following:
-
-.. code-block:: python
-
-    import unittest
-    import pyobo
-    from pyobo.mocks import get_mock_id_name_mapping
-
-    mock_id_name_mapping = get_mock_id_name_mapping({
-        'chebi': {
-            '132964': 'fluazifop-P-butyl',
-        },
-    })
-
-    class MyTestCase(unittest.TestCase):
-        def my_test(self):
-            with mock_id_name_mapping:
-                # use functions directly, or use your functions that wrap them
-                pyobo.get_name('chebi', '1234')
-
-
-Installation
-------------
-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 Bioregistry
----------------------------
-In order to normalize references and identify resources, PyOBO uses the
-`Bioregistry <https://github.com/bioregistry/bioregistry>`_. It used to be a part of PyOBO, but has since
-been externalized for more general reuse.
-
-At `src/pyobo/registries/metaregistry.json <https://github.com/pyobo/pyobo/blob/master/src/pyobo/registries/metaregistry.json>`_
-is the curated "metaregistry". 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.
-
-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 ``"blacklists"`` entry contains rules for throwing out malformed xrefs based on
-  full string, just prefix, or just suffix.
-
-Troubleshooting
----------------
-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 update to the ``url`` entry for that namespace in the Bioregistry.
-
-.. |build| image:: https://github.com/pyobo/pyobo/workflows/Tests/badge.svg
-    :target: https://github.com/pyobo/pyobo/actions?query=workflow%3ATests
-    :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
-
-.. |zenodo| image:: https://zenodo.org/badge/203449095.svg
-    :target: https://zenodo.org/badge/latestdoi/203449095
-    :alt: Zenodo
-
-.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-    :target: https://github.com/psf/black
-    :alt: Black Code Style
-
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