Metadata-Version: 2.1
Name: pyobo
Version: 0.2.3
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|
        =============
        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.
        
        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'
        
        
        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
        
        
        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()
            }
        
        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'
        
        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.
        
        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
        
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
Provides-Extra: docs
