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Typing and minor updates (#496)
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‎docs/source/cli.rst‎

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Command Line Interface
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======================
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########################
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Command Line Interface
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########################
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pyobo automatically installs the command ``pyobo``. See ``pyobo --help`` for usage
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details.

‎docs/source/functional.rst‎

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Functional OWL
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==============
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################
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Functional OWL
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################
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.. automodapi:: pyobo.struct.functional.dsl
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‎docs/source/index.rst‎

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PyOBO |release| Documentation
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=============================
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###############################
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PyOBO |release| Documentation
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###############################
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.. toctree::
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:maxdepth: 2
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ner
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scispacy
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Indices and Tables
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------------------
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********************
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Indices and Tables
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********************
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- :ref:`genindex`
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- :ref:`modindex`

‎docs/source/installation.rst‎

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Installation
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============
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##############
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Installation
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##############
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The most recent release can be installed from `PyPI <https://pypi.org/project/pyobo>`_
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with uv:
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$ python3 -m pip install pyobo
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Installing from git
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-------------------
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*********************
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Installing from git
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*********************
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The most recent code and data can be installed directly from GitHub with uv:
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$ python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
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Installing for development
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--------------------------
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****************************
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Installing for development
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****************************
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To install in development mode with uv:
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‎docs/source/ner.rst‎

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Named Entity Recognition
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========================
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##########################
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Named Entity Recognition
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##########################
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PyOBO has high-level wrappers to construct literal mapping objects defined by
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:mod:`ssslm.LiteralMapping`, which can be used to construct generic named entity

‎docs/source/scispacy.rst‎

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ScispaCy Integration
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====================
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######################
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ScispaCy Integration
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######################
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.. automodapi:: pyobo.ner.scispacy_utils
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:no-heading:

‎docs/source/usage.rst‎

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Reference
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=========
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###########
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Reference
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###########
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.. automodapi:: pyobo
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:no-heading:

‎pyproject.toml‎

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"cachier",
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"pystow>=0.8.11",
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"bioversions>=0.10.0",
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"bioregistry>=0.13.44",
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"ssslm>=0.1.3",
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"bioregistry>=0.13.48",
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"ssslm>=0.2.0",
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"zenodo-client>=0.4.1",
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"class_resolver>=0.7.1",
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"pydantic>=2.0",
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#
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"typing_extensions",
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"rdflib",
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"obographs>=0.0.10",
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"obographs>=0.0.11",
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"sssom_pydantic>=0.5.5",
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"pytz",
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"robot-obo-tool",
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"pyperclip",
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"lxml",
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]
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# see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups

‎src/pyobo/__init__.py‎

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get_relation,
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get_relation_mapping,
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get_relations_df,
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get_semantic_mapping_metadata,
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get_semantic_mappings,
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get_species,
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get_sssom_df,
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"get_scispacy_entities",
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"get_scispacy_entity_linker",
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"get_scispacy_knowledgebase",
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"get_semantic_mapping_metadata",
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"get_semantic_mappings",
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"get_species",
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"get_sssom_df",

‎src/pyobo/api/__init__.py‎

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from .xrefs import (
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get_filtered_xrefs,
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get_mappings_df,
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get_semantic_mapping_metadata,
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get_semantic_mappings,
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get_sssom_df,
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get_xref,
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"get_relation",
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"get_relation_mapping",
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"get_relations_df",
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"get_semantic_mapping_metadata",
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"get_semantic_mappings",
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"get_species",
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"get_sssom_df",

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