Metadata-Version: 2.1
Name: pyobo
Version: 0.3.0
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
Description: PyOBO
        =====
        |build| |pypi_version| |python_versions| |pypi_license| |zenodo|
        
        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'
        
        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/cthoyt/bioregistry>`_. It used to be a part of PyOBO, but has since
        been externalized for more general reuse. The following text is out of date, and will be updated with
        the next PyOBO release to better reflect how to contribute.
        
        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
        - ``references``, a list of URLs to web pages and articles describing the resource. Often
          used for NCBI resources that can't actually be accessed, but seem to keep popping up
        
        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.
        
        
        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 an 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
        
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 :: 3.6
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.6
Provides-Extra: docs
Provides-Extra: web
Provides-Extra: database
