From 11f9318a0ae242f35edb45d60a005de6d28e9456 Mon Sep 17 00:00:00 2001
From: Sunny Sun <38218185+sunnyosun@users.noreply.github.com>
Date: Fri, 12 Jan 2024 04:57:25 -0500
Subject: [PATCH] =?UTF-8?q?=F0=9F=9A=9A=20Rename=20`Bionty`=20to=20`Public?=
 =?UTF-8?q?Ontology`=20class=20(#536)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* 🚚 Rename Bionty to PublicOntology class

* 💚 Use 3.10

* 💚 Fix import

* 💚 Fix import

* 💚 Fix

* 💚 Add quotes
---
 .github/workflows/build.yml                |   8 +-
 bionty/__init__.py                         |  15 ++-
 bionty/_display_sources.py                 |   2 +-
 bionty/{_bionty.py => _public_ontology.py} | 141 +++++++++++----------
 bionty/entities/_bfxpipeline.py            |   4 +-
 bionty/entities/_biosample.py              |   4 +-
 bionty/entities/_cellline.py               |   4 +-
 bionty/entities/_cellmarker.py             |   4 +-
 bionty/entities/_celltype.py               |   4 +-
 bionty/entities/_developmentalstage.py     |   4 +-
 bionty/entities/_disease.py                |   4 +-
 bionty/entities/_drug.py                   |   4 +-
 bionty/entities/_ethnicity.py              |   4 +-
 bionty/entities/_experimentalfactor.py     |   9 +-
 bionty/entities/_gene.py                   |   4 +-
 bionty/entities/_organism.py               |   4 +-
 bionty/entities/_pathway.py                |   4 +-
 bionty/entities/_phenotype.py              |   4 +-
 bionty/entities/_protein.py                |   4 +-
 bionty/entities/_tissue.py                 |   4 +-
 docs/developer/updating_source.md          |   4 +-
 docs/guide/concepts.md                     |   6 +-
 docs/guide/extend.md                       |  14 +-
 docs/guide/ontology.ipynb                  |  36 ++----
 docs/guide/sources.ipynb                   |  18 +--
 scripts/upload_new_ontologies.py           |   6 +-
 tests/entities/test_experimentalfactor.py  |   2 +-
 tests/test_bionty.py                       |   2 +-
 28 files changed, 158 insertions(+), 165 deletions(-)
 rename bionty/{_bionty.py => _public_ontology.py} (85%)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 01e9e34e..958fd0a2 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
         group: ["bionty-unit", "bionty-docs"]
     timeout-minutes: 25
 
@@ -61,7 +61,7 @@ jobs:
           aws-region: eu-central-1
 
       - name: Lint
-        if: matrix.python-version == '3.9' && matrix.group == 'bionty-unit'
+        if: matrix.python-version == '3.10' && matrix.group == 'bionty-unit'
         run: |
           nox -s lint
       - name: Build
@@ -75,7 +75,7 @@ jobs:
           path: .coverage
 
       - name: Deploy docs
-        if: ${{ matrix.python-version == '3.9' && matrix.group == 'bionty-docs' }}
+        if: ${{ matrix.python-version == '3.10' && matrix.group == 'bionty-docs' }}
         id: netlify
         uses: nwtgck/actions-netlify@v1.2
         with:
@@ -94,7 +94,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
           cache: "pip"
           cache-dependency-path: ".github/workflows/build.yml"
       - run: |
diff --git a/bionty/__init__.py b/bionty/__init__.py
index 7e2ff7dd..98e73d7c 100644
--- a/bionty/__init__.py
+++ b/bionty/__init__.py
@@ -31,10 +31,10 @@
 .. autosummary::
    :toctree: .
 
-   Bionty
-   BiontyField
+   PublicOntology
+   PublicOntologyField
 
-Bionty sources:
+PublicOntology sources:
 
 .. autosummary::
    :toctree: .
@@ -65,11 +65,11 @@
 
 # dynamic classes
 from . import dev
-
-# tools
-from ._bionty import Bionty, BiontyField
 from ._display_sources import display_available_sources, display_currently_used_sources
 from ._ontology import Ontology
+
+# tools
+from ._public_ontology import PublicOntology, PublicOntologyField
 from ._settings import settings
 
 # sources
@@ -92,6 +92,7 @@
 from .entities._tissue import Tissue
 
 # backward compat
-Entity = Bionty
+Entity = PublicOntology
+Bionty = PublicOntology
 Readout = ExperimentalFactor
 Species = Organism
diff --git a/bionty/_display_sources.py b/bionty/_display_sources.py
index 64106db5..accbe5f0 100644
--- a/bionty/_display_sources.py
+++ b/bionty/_display_sources.py
@@ -18,7 +18,7 @@ def display_available_sources() -> pd.DataFrame:
     return parse_sources_yaml(settings.local_sources).set_index("entity")  # type: ignore
 
 
-# This function naming is consistent with the `currently_used` field in BiontySource SQL table
+# This function naming is consistent with the `currently_used` field in PublicSource SQL table
 # Do not rename!
 def display_currently_used_sources() -> pd.DataFrame:
     """Displays all currently used sources.
diff --git a/bionty/_bionty.py b/bionty/_public_ontology.py
similarity index 85%
rename from bionty/_bionty.py
rename to bionty/_public_ontology.py
index 80387dc6..2fdff126 100644
--- a/bionty/_bionty.py
+++ b/bionty/_public_ontology.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-from functools import cached_property
 from typing import (
     TYPE_CHECKING,
     Iterable,
@@ -26,10 +25,10 @@
 
 
 def encode_filenames(
-    organism: str, source: str, version: str, entity: Bionty | str
+    organism: str, source: str, version: str, entity: PublicOntology | str
 ) -> tuple[str, str]:
     """Encode names of the cached files."""
-    if isinstance(entity, Bionty):
+    if isinstance(entity, PublicOntology):
         entity_name = entity.__class__.__name__
     else:
         entity_name = entity
@@ -41,8 +40,8 @@ def encode_filenames(
     return parquet_filename, ontology_filename
 
 
-class Bionty:
-    """Bionty base model."""
+class PublicOntology:
+    """PublicOntology object."""
 
     def __init__(
         self,
@@ -76,7 +75,7 @@ def __init__(
                     f"please consider:\n"
                     f"    close your instance via `lamin close` and use Bionty stand alone\n"
                     f"    OR\n"
-                    f"    modify currently_used {self.__class__.__name__} source in `lnschema_bionty.BiontySource`"
+                    f"    modify currently_used {self.__class__.__name__} source in `lnschema_bionty.PublicSource`"
                 )
                 # fmt: on
 
@@ -105,33 +104,34 @@ def __init__(
         # set column names/fields as attributes
         for col_name in self._df.columns:
             try:
-                setattr(self, col_name, BiontyField(self, col_name))
-            # Some fields of an ontology (e.g. Gene) are not Bionty class attributes and must be skipped.
+                setattr(self, col_name, PublicOntologyField(self, col_name))
+            # Some fields of an ontology (e.g. Gene) are not PublicOntology class attributes and must be skipped.
             except AttributeError:
                 pass
 
     def __repr__(self) -> str:
         # fmt: off
         representation = (
-            f"{self.__class__.__name__}\n"
+            f"PublicOntology\n"
+            f"Entity: {self.__class__.__name__}\n"
             f"Organism: {self.organism}\n"
             f"Source: {self.source}, {self.version}\n"
             f"#terms: {self._df.shape[0] if hasattr(self, '_df') else ''}\n\n"
-            f"📖 {self.__class__.__name__}.df(): ontology reference table\n"
-            f"🔎 {self.__class__.__name__}.lookup(): autocompletion of terms\n"
-            f"🎯 {self.__class__.__name__}.search(): free text search of terms\n"
-            f"✅ {self.__class__.__name__}.validate(): strictly validate values\n"
-            f"🧐 {self.__class__.__name__}.inspect(): full inspection of values\n"
-            f"👽 {self.__class__.__name__}.standardize(): convert to standardized names\n"
-            f"🪜 {self.__class__.__name__}.diff(): difference between two versions\n"
-            f"🔗 {self.__class__.__name__}.ontology: Pronto.Ontology object"
+            f"📖 .df(): ontology reference table\n"
+            f"🔎 .lookup(): autocompletion of terms\n"
+            f"🎯 .search(): free text search of terms\n"
+            f"✅ .validate(): strictly validate values\n"
+            f"🧐 .inspect(): full inspection of values\n"
+            f"👽 .standardize(): convert to standardized names\n"
+            f"🪜 .diff(): difference between two versions\n"
+            f"🔗 .to_pronto(): Pronto.Ontology object"
         )
         # fmt: on
         return representation
 
     @property
     def organism(self):
-        """The `name` of `Organism` Bionty."""
+        """The `name` of `Organism`."""
         return self._organism
 
     @property
@@ -141,12 +141,12 @@ def source(self):
 
     @property
     def version(self):
-        """The `name` of `version` entity Bionty."""
+        """Version of the source."""
         return self._version
 
     @property
     def fields(self) -> set:
-        """All Bionty entity fields."""
+        """All PublicOntology entity fields."""
         blacklist = {"include_id_prefixes"}
         fields = {
             field
@@ -155,23 +155,6 @@ def fields(self) -> set:
         }
         return fields - blacklist
 
-    @cached_property
-    def ontology(self):
-        """The Pronto Ontology object.
-
-        See: https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html
-        """
-        if self._local_ontology_path is None:
-            logger.error(f"{self.__class__.__name__} has no Pronto Ontology object!")
-            return
-        else:
-            self._download_ontology_file(
-                localpath=self._local_ontology_path,
-                url=self._url,
-                md5=self._md5,
-            )
-            return Ontology(handle=self._local_ontology_path)
-
     def _download_ontology_file(self, localpath: Path, url: str, md5: str = "") -> None:
         """Download ontology source file to _local_ontology_path."""
         if not localpath.exists():
@@ -299,7 +282,7 @@ def _set_file_paths(self) -> None:
         else:
             self._local_ontology_path = settings.dynamicdir / self._ontology_filename
 
-    def _get_default_field(self, field: BiontyField | str | None = None) -> str:
+    def _get_default_field(self, field: PublicOntologyField | str | None = None) -> str:
         """Default to name field."""
         if field is None:
             if "name" in self._df.columns:
@@ -325,7 +308,7 @@ def _load_df(self) -> pd.DataFrame:
         # If download is not possible, write a parquet file of the ontology df
         if not self._url.endswith("parquet"):
             if not self._local_parquet_path.exists():
-                df = self.ontology.to_df(
+                df = self.to_pronto().to_df(
                     source=self.source, include_id_prefixes=self.include_id_prefixes
                 )
                 df.to_parquet(self._local_parquet_path)
@@ -334,6 +317,22 @@ def _load_df(self) -> pd.DataFrame:
         df = pd.read_parquet(self._local_parquet_path)
         return df
 
+    def to_pronto(self):
+        """The Pronto Ontology object.
+
+        See: https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html
+        """
+        if self._local_ontology_path is None:
+            logger.error(f"{self.__class__.__name__} has no Pronto Ontology object!")
+            return
+        else:
+            self._download_ontology_file(
+                localpath=self._local_ontology_path,
+                url=self._url,
+                md5=self._md5,
+            )
+            return Ontology(handle=self._local_ontology_path)
+
     def df(self) -> pd.DataFrame:
         """Pandas DataFrame of the ontology.
 
@@ -352,7 +351,7 @@ def df(self) -> pd.DataFrame:
     def validate(
         self,
         values: Iterable,
-        field: BiontyField,
+        field: PublicOntologyField,
         *,
         mute: bool = False,
         **kwargs,
@@ -375,7 +374,7 @@ def validate(
     def inspect(
         self,
         values: Iterable,
-        field: BiontyField,
+        field: PublicOntologyField,
         *,
         mute: bool = False,
         **kwargs,
@@ -384,7 +383,7 @@ def inspect(
 
         Args:
             values: Identifiers that will be checked against the field.
-            field: The BiontyField of the ontology to compare against.
+            field: The PublicOntologyField of the ontology to compare against.
                    Examples are 'ontology_id' to map against the source ID
                    or 'name' to map against the ontologies field names.
             return_df: Whether to return a Pandas DataFrame.
@@ -398,9 +397,9 @@ def inspect(
 
         Examples:
             >>> import bionty as bt
-            >>> gene_bt = bt.Gene()
+            >>> public = bt.Gene()
             >>> gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
-            >>> gene_bt.inspect(gene_symbols, field=gene_bt.symbol)
+            >>> public.inspect(gene_symbols, field=public.symbol)
         """
         from lamin_utils._inspect import inspect
 
@@ -419,14 +418,14 @@ def inspect(
     def standardize(
         self,
         values: Iterable,
-        field: BiontyField | str | None = None,
+        field: PublicOntologyField | str | None = None,
         *,
         return_field: str = None,
         return_mapper: bool = False,
         case_sensitive: bool = False,
         mute: bool = False,
         keep: Literal["first", "last", False] = "first",
-        synonyms_field: BiontyField | str = "synonyms",
+        synonyms_field: PublicOntologyField | str = "synonyms",
     ) -> dict[str, str] | list[str]:
         """Convert into standardized names.
 
@@ -454,9 +453,9 @@ def standardize(
 
         Examples:
             >>> import bionty as bt
-            >>> gene_bt = bt.Gene()
+            >>> public = bt.Gene()
             >>> gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
-            >>> standardized_symbols = gene_bt.standardize(gene_symbols, gene_bt.symbol)
+            >>> standardized_symbols = public.standardize(gene_symbols, public.symbol)
         """
         from lamin_utils._standardize import standardize as map_synonyms
 
@@ -482,8 +481,8 @@ def map_synonyms(
         return_mapper: bool = False,
         case_sensitive: bool = False,
         keep: Literal["first", "last", False] = "first",
-        synonyms_field: BiontyField | str = "synonyms",
-        field: BiontyField | str | None = None,
+        synonyms_field: PublicOntologyField | str = "synonyms",
+        field: PublicOntologyField | str | None = None,
     ) -> dict[str, str] | list[str]:
         """Maps input synonyms to standardized names."""
         logger.warning("`map_synonyms()` is deprecated, use `.standardize()`!'")
@@ -496,8 +495,8 @@ def map_synonyms(
             field=field,
         )
 
-    def lookup(self, field: BiontyField | str | None = None) -> tuple:
-        """An auto-complete object for a Bionty field.
+    def lookup(self, field: PublicOntologyField | str | None = None) -> tuple:
+        """An auto-complete object for a PublicOntology field.
 
         Args:
             field: The field to lookup the values for.
@@ -524,16 +523,16 @@ def search(
         self,
         string: str,
         *,
-        field: BiontyField | str | None = None,
+        field: PublicOntologyField | str | None = None,
         limit: int | None = None,
         case_sensitive: bool = False,
-        synonyms_field: BiontyField | str | None = "synonyms",
+        synonyms_field: PublicOntologyField | str | None = "synonyms",
     ):
-        """Search a given string against a Bionty field.
+        """Search a given string against a PublicOntology field.
 
         Args:
             string: The input string to match against the field values.
-            field: The BiontyField of the ontology the input string is matching against.
+            field: The PublicOntologyField of the ontology the input string is matching against.
             top_hit: Return all entries ranked by matching ratios.
                 If True, only return the top match.
                 Defaults to False.
@@ -548,8 +547,8 @@ def search(
 
         Examples:
             >>> import bionty as bt
-            >>> celltype_bt = bt.CellType()
-            >>> celltype_bt.search("gamma delta T cell")
+            >>> public = bt.CellType()
+            >>> public.search("gamma delta T cell")
         """
         from lamin_utils._search import search
 
@@ -562,11 +561,13 @@ def search(
             synonyms_field=str(synonyms_field),
         )
 
-    def diff(self, compare_to: Bionty, **kwargs) -> tuple[pd.DataFrame, pd.DataFrame]:
-        """Determines a diff between two Bionty objects' ontologies.
+    def diff(
+        self, compare_to: PublicOntology, **kwargs
+    ) -> tuple[pd.DataFrame, pd.DataFrame]:
+        """Determines a diff between two PublicOntology objects' ontologies.
 
         Args:
-            compare_to: Bionty object that must be of the same class as the calling object.
+            compare_to: PublicOntology object that must be of the same class as the calling object.
             kwargs: Are passed to pd.DataFrame.compare()
 
         Returns:
@@ -576,20 +577,20 @@ def diff(self, compare_to: Bionty, **kwargs) -> tuple[pd.DataFrame, pd.DataFrame
 
         Examples:
             >>> import bionty as bt
-            >>> disease_bt_1 = bt.Disease(source="mondo", version="2023-04-04")
-            >>> disease_bt_2 = bt.Disease(source="mondo", version="2023-04-04")
-            >>> new_entries, modified_entries = disease_bt_1.diff(disease_bt_2)
+            >>> public_1 = bt.Disease(source="mondo", version="2023-04-04")
+            >>> public_2 = bt.Disease(source="mondo", version="2023-04-04")
+            >>> new_entries, modified_entries = public_1.diff(public_2)
             >>> print(new_entries.head())
             >>> print(modified_entries.head())
         """
         if type(self) is not type(compare_to):
-            raise ValueError("Both Bionty objects must be of the same class.")
+            raise ValueError("Both PublicOntology objects must be of the same class.")
 
         if not self.source == compare_to.source:
-            raise ValueError("Both Bionty objects must use the same source.")
+            raise ValueError("Both PublicOntology objects must use the same source.")
 
         if self.version == compare_to.version:
-            raise ValueError("The versions of the Bionty objects must differ.")
+            raise ValueError("The versions of the PublicOntology objects must differ.")
 
         # The 'parents' column (among potentially others) contain Numpy array values.
         # We transform them to tuples to determine the diff.
@@ -623,10 +624,10 @@ def _convert_arrays_to_tuples(arr):  # pragma: no cover
         return new_entries, modified_entries
 
 
-class BiontyField:
-    """Field of a Bionty model."""
+class PublicOntologyField:
+    """Field of a PublicOntology model."""
 
-    def __init__(self, parent: Bionty, name: str):
+    def __init__(self, parent: PublicOntology, name: str):
         self.parent = parent
         self.name = name
 
diff --git a/bionty/entities/_bfxpipeline.py b/bionty/entities/_bfxpipeline.py
index 8f73f438..00345318 100644
--- a/bionty/entities/_bfxpipeline.py
+++ b/bionty/entities/_bfxpipeline.py
@@ -4,14 +4,14 @@
 
 import pandas as pd
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 from bionty.dev._io import s3_bionty_assets
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class BFXPipeline(Bionty):
+class BFXPipeline(PublicOntology):
     """Bioinformatics pipelines.
 
     Args:
diff --git a/bionty/entities/_biosample.py b/bionty/entities/_biosample.py
index 930579e1..2145418d 100644
--- a/bionty/entities/_biosample.py
+++ b/bionty/entities/_biosample.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class BioSample(Bionty):
+class BioSample(PublicOntology):
     """BioSample attributes.
 
     1. NCBI BioSample Attributes
diff --git a/bionty/entities/_cellline.py b/bionty/entities/_cellline.py
index b5e0cc78..8e95c963 100644
--- a/bionty/entities/_cellline.py
+++ b/bionty/entities/_cellline.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class CellLine(Bionty):
+class CellLine(PublicOntology):
     """Cell line.
 
     1. Cell Line Ontology
diff --git a/bionty/entities/_cellmarker.py b/bionty/entities/_cellmarker.py
index 83b7029e..6eb6a6e1 100644
--- a/bionty/entities/_cellmarker.py
+++ b/bionty/entities/_cellmarker.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class CellMarker(Bionty):
+class CellMarker(PublicOntology):
     """Cell markers.
 
     1. Cell Marker Ontology
diff --git a/bionty/entities/_celltype.py b/bionty/entities/_celltype.py
index b8eb6319..b609e2d4 100644
--- a/bionty/entities/_celltype.py
+++ b/bionty/entities/_celltype.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class CellType(Bionty):
+class CellType(PublicOntology):
     """Cell type ontologies.
 
     1. Cell ontology
diff --git a/bionty/entities/_developmentalstage.py b/bionty/entities/_developmentalstage.py
index a2dfa24c..d2a4062b 100644
--- a/bionty/entities/_developmentalstage.py
+++ b/bionty/entities/_developmentalstage.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class DevelopmentalStage(Bionty):
+class DevelopmentalStage(PublicOntology):
     """Developmental Stage.
 
     1. Developmental Stage Ontology
diff --git a/bionty/entities/_disease.py b/bionty/entities/_disease.py
index a0780989..8cb4aad8 100644
--- a/bionty/entities/_disease.py
+++ b/bionty/entities/_disease.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class Disease(Bionty):
+class Disease(PublicOntology):
     """Disease ontologies.
 
     1. Mondo
diff --git a/bionty/entities/_drug.py b/bionty/entities/_drug.py
index 178367b6..7249d7e7 100644
--- a/bionty/entities/_drug.py
+++ b/bionty/entities/_drug.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class Drug(Bionty):
+class Drug(PublicOntology):
     """Drug ontologies.
 
     1. DRON
diff --git a/bionty/entities/_ethnicity.py b/bionty/entities/_ethnicity.py
index eb3caa74..e5eb06f9 100644
--- a/bionty/entities/_ethnicity.py
+++ b/bionty/entities/_ethnicity.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class Ethnicity(Bionty):
+class Ethnicity(PublicOntology):
     """Ethnicity.
 
     1. Human Ancestry Ontology
diff --git a/bionty/entities/_experimentalfactor.py b/bionty/entities/_experimentalfactor.py
index 172973e6..a1c3d35c 100644
--- a/bionty/entities/_experimentalfactor.py
+++ b/bionty/entities/_experimentalfactor.py
@@ -4,13 +4,13 @@
 import pandas as pd
 from lamin_utils import logger
 
-from bionty._bionty import Bionty
 from bionty._ontology import Ontology
+from bionty._public_ontology import PublicOntology
 from bionty.entities._shared_docstrings import _doc_params, organism_removed
 
 
 @_doc_params(doc_entities=organism_removed)
-class ExperimentalFactor(Bionty):
+class ExperimentalFactor(PublicOntology):
     """Experimental Factor.
 
     1. Experimental Factor Ontology
@@ -20,7 +20,7 @@ class ExperimentalFactor(Bionty):
     Args:
         {doc_entities}
 
-    Also see: `bionty.Bionty <https://lamin.ai/docs/bionty/bionty.entity>`__
+    Also see: `bionty.PublicOntology <https://lamin.ai/docs/bionty/bionty.entity>`__
     """
 
     def __init__(
@@ -38,8 +38,7 @@ def __init__(
             **kwargs,
         )
 
-    @cached_property
-    def ontology(self) -> Ontology:  # type:ignore
+    def to_pronto(self) -> Ontology:  # type:ignore
         """The Pronto Ontology object.
 
         See: https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html
diff --git a/bionty/entities/_gene.py b/bionty/entities/_gene.py
index cf91868b..a722ebcc 100644
--- a/bionty/entities/_gene.py
+++ b/bionty/entities/_gene.py
@@ -3,7 +3,7 @@
 import pandas as pd
 from lamin_utils import logger
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 from bionty._settings import settings
 from bionty.dev._io import s3_bionty_assets
 
@@ -12,7 +12,7 @@
 
 
 @_doc_params(doc_entities=doc_entites)
-class Gene(Bionty):
+class Gene(PublicOntology):
     """Gene.
 
     1. Ensembl
diff --git a/bionty/entities/_organism.py b/bionty/entities/_organism.py
index f3532434..d4c7d5ba 100644
--- a/bionty/entities/_organism.py
+++ b/bionty/entities/_organism.py
@@ -2,13 +2,13 @@
 
 import pandas as pd
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 from bionty.dev._io import s3_bionty_assets
 from bionty.entities._shared_docstrings import _doc_params, organism_removed
 
 
 @_doc_params(doc_entities=organism_removed)
-class Organism(Bionty):
+class Organism(PublicOntology):
     """Organism.
 
     1. Organism ontology
diff --git a/bionty/entities/_pathway.py b/bionty/entities/_pathway.py
index 302b8a57..7d090f45 100644
--- a/bionty/entities/_pathway.py
+++ b/bionty/entities/_pathway.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class Pathway(Bionty):
+class Pathway(PublicOntology):
     """Pathway.
 
     1. Gene Ontology
diff --git a/bionty/entities/_phenotype.py b/bionty/entities/_phenotype.py
index 5ff04fb5..ba7d502a 100644
--- a/bionty/entities/_phenotype.py
+++ b/bionty/entities/_phenotype.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class Phenotype(Bionty):
+class Phenotype(PublicOntology):
     """Phenotype.
 
     1. Human Phenotype Ontology
diff --git a/bionty/entities/_protein.py b/bionty/entities/_protein.py
index b4a25fb0..e8b91518 100644
--- a/bionty/entities/_protein.py
+++ b/bionty/entities/_protein.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class Protein(Bionty):
+class Protein(PublicOntology):
     """Protein.
 
     1. Uniprot
diff --git a/bionty/entities/_tissue.py b/bionty/entities/_tissue.py
index 66ed8867..58a40958 100644
--- a/bionty/entities/_tissue.py
+++ b/bionty/entities/_tissue.py
@@ -1,12 +1,12 @@
 from typing import Literal, Optional
 
-from bionty._bionty import Bionty
+from bionty._public_ontology import PublicOntology
 
 from ._shared_docstrings import _doc_params, doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)
-class Tissue(Bionty):
+class Tissue(PublicOntology):
     """Tissue.
 
     1. Uberon
diff --git a/docs/developer/updating_source.md b/docs/developer/updating_source.md
index a2bd66c3..877d3afb 100644
--- a/docs/developer/updating_source.md
+++ b/docs/developer/updating_source.md
@@ -9,8 +9,8 @@ Here we document the steps to required steps to take when updating the `source.y
 ## Steps
 
 1. Adapt the `sources.yaml` file as required.
-   Add a new top level entry if you've added a new Bionty entity or add a new source/version while confirming to the yaml structure.
-2. If you've added a new source or version, use Bionty's `diff` function to determine whether any terms were deleted.
+   Add a new top level entry if you've added a new PublicOntology entity or add a new source/version while confirming to the yaml structure.
+2. If you've added a new source or version, use PublicOntology's `diff` function to determine whether any terms were deleted.
    Consult the rest of the team if so.
    Ensure that your pull request contains a summary of the diff.
 3. Specify the new entity or the latest version in your local `.current_source.yaml`. Run the tests.
diff --git a/docs/guide/concepts.md b/docs/guide/concepts.md
index aa92fc99..82ac41cf 100644
--- a/docs/guide/concepts.md
+++ b/docs/guide/concepts.md
@@ -9,11 +9,11 @@ Let's define a biological entity (e.g., `Organism`) to be a variable that takes
 3. Terms in the vocabularies have different granularity, and are often hierarchical.
 4. Typically, vocabularies are based on a given version of a public reference ontology, but contain additional “custom” terms corresponding to "new knowledge" absent from reference ontologies. For example, new cell types or states, new synthetic genes, etc.
 
-## Bionty object
+## PublicOntology object
 
-The central class {class}`~bionty.Bionty` models 3 of the 4 above-mentioned properties of biological entities:
+The central class {class}`~bionty.PublicOntology` models 3 of the 4 above-mentioned properties of biological entities:
 
-1. Every `Bionty` object comes with a table of terms in which each column corresponds to an alternative vocabulary for the entity.
+1. Every `PublicOntology` object comes with a table of terms in which each column corresponds to an alternative vocabulary for the entity.
 2. Every table is versioned & has a tracked reference source (typically, a public ontology).
 3. Most tables have a children column that allows mapping hierarchies.
 4. Adding user-defined records amounts to managing bioregistries, and we recommend using Bionty's SQL extension ([lnschema_bionty](https://lamin.ai/docs/lnschema-bionty)).
diff --git a/docs/guide/extend.md b/docs/guide/extend.md
index dcdcc69d..44ec646c 100644
--- a/docs/guide/extend.md
+++ b/docs/guide/extend.md
@@ -67,9 +67,9 @@ If desired, the new ontology can be set as default. See {doc}`./config` for more
 
 ## New entities
 
-Adding new entities to Bionty requires subclassing the {class}`bionty.Bionty` and modifying the `sources_local.yaml` file.
+Adding new entities to Bionty requires subclassing the {class}`bionty.PublicOntology` and modifying the `sources_local.yaml` file.
 
-The {class}`bionty.Bionty` requires several properties to be defined:
+The {class}`bionty.PublicOntology` requires several properties to be defined:
 
 ```python
 organism: str,
@@ -77,15 +77,15 @@ source: str,
 version: str,
 ```
 
-These are automatically populated by either the currently used Bionty sources (see {doc}`./config`) or explicitly passed as parameters when initializing an Entity.
+These are automatically populated by either the currently used PublicOntology sources (see {doc}`./config`) or explicitly passed as parameters when initializing an Entity.
 
-Hence, a new Bionty class `MyEntity` would be defined as:
+Hence, a new PublicOntology class `MyEntity` would be defined as:
 
 ```python
-from bionty import Bionty
+from bionty import PublicOntology
 
 
-class MyEntity(Bionty):
+class MyEntity(PublicOntology):
     """MyEntity."""
 
     def __init__(
@@ -119,4 +119,4 @@ MyEntity:
         md5: "md5 if available or leave out this row"
 ```
 
-Great! Now we've added a new Bionty class, which can be used with all Bionty functions! 🎉
+Great! Now we've added a new PublicOntology class, which can be used with all PublicOntology functions! 🎉
diff --git a/docs/guide/ontology.ipynb b/docs/guide/ontology.ipynb
index de3f0cf0..567871de 100644
--- a/docs/guide/ontology.ipynb
+++ b/docs/guide/ontology.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "# Get Pronto ontology objects\n",
     "\n",
-    "When it comes to ontology defined vocabularies, such as cell type, tissue, disease, and phenotype, [Pronto Ontology object](https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html) can be accessed via `{entity}.ontology`\n",
+    "When it comes to ontology defined vocabularies, such as cell type, tissue, disease, and phenotype, [Pronto Ontology object](https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html) can be accessed via `{entity}.to_pronto()`\n",
     "\n"
    ]
   },
@@ -38,9 +38,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "disease_bt = bt.Disease()\n",
+    "public = bt.Disease()\n",
     "\n",
-    "disease_bt"
+    "public"
    ]
   },
   {
@@ -50,7 +50,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "disease_bt.df().head()"
+    "public.df().head()"
    ]
   },
   {
@@ -60,7 +60,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lookup = disease_bt.lookup()"
+    "lookup = public.lookup()"
    ]
   },
   {
@@ -126,7 +126,7 @@
    "id": "66ba4cba",
    "metadata": {},
    "source": [
-    "## `.pronto`: Pronto Ontology\n",
+    "## `.to_pronto()`: Pronto Ontology\n",
     "\n",
     "More hierarchical information can be accessed from the Pronto Ontology object:"
    ]
@@ -138,7 +138,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pronto_object = disease_bt.ontology"
+    "pronto_object = public.to_pronto()"
    ]
   },
   {
@@ -199,7 +199,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "readout_bt = bt.ExperimentalFactor()"
+    "public = bt.ExperimentalFactor()"
    ]
   },
   {
@@ -209,7 +209,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "readout_bt.df().head()"
+    "public.df().head()"
    ]
   },
   {
@@ -219,7 +219,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lookup = readout_bt.lookup()"
+    "lookup = public.lookup()"
    ]
   },
   {
@@ -301,7 +301,7 @@
    "id": "afa16569-5f98-41ec-981c-db1b81fbbe91",
    "metadata": {},
    "source": [
-    "Bionty provides {func}`bionty.Bionty.diff` to determine a diff between two ontology versions."
+    "Bionty provides {func}`bionty.PublicOntology.diff` to determine a diff between two ontology versions."
    ]
   },
   {
@@ -313,10 +313,10 @@
    },
    "outputs": [],
    "source": [
-    "disease_bt_old = bt.Disease(source=\"mondo\", version=\"2023-04-04\")\n",
-    "disease_bt_new = bt.Disease(source=\"mondo\", version=\"2023-02-06\")\n",
+    "disease_old = bt.Disease(source=\"mondo\", version=\"2023-04-04\")\n",
+    "disease_new = bt.Disease(source=\"mondo\", version=\"2023-02-06\")\n",
     "\n",
-    "new_entries, modified_entries = disease_bt_old.diff(disease_bt_new)"
+    "new_entries, modified_entries = disease_old.diff(disease_new)"
    ]
   },
   {
@@ -342,14 +342,6 @@
    "source": [
     "modified_entries.head()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8ff90ce1-d427-43f6-9c22-868878d59a35",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
diff --git a/docs/guide/sources.ipynb b/docs/guide/sources.ipynb
index 07469b6a..3772d575 100644
--- a/docs/guide/sources.ipynb
+++ b/docs/guide/sources.ipynb
@@ -57,7 +57,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When initializing a Bionty class, default source is used:"
+    "When initializing a PublicOntology class, default source is used:"
    ]
   },
   {
@@ -66,9 +66,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "celltype_bt = bt.CellType()\n",
+    "public = bt.CellType()\n",
     "\n",
-    "celltype_bt"
+    "public"
    ]
   },
   {
@@ -84,9 +84,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "celltype_bt = bt.CellType(source=\"cl\", version=\"2022-08-16\")\n",
+    "public = bt.CellType(source=\"cl\", version=\"2022-08-16\")\n",
     "\n",
-    "celltype_bt"
+    "public"
    ]
   },
   {
@@ -102,9 +102,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "gene_bt = bt.Gene()\n",
+    "public = bt.Gene()\n",
     "\n",
-    "gene_bt"
+    "public"
    ]
   },
   {
@@ -113,9 +113,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "gene_bt = bt.Gene(organism=\"mouse\")\n",
+    "public = bt.Gene(organism=\"mouse\")\n",
     "\n",
-    "gene_bt"
+    "public"
    ]
   },
   {
diff --git a/scripts/upload_new_ontologies.py b/scripts/upload_new_ontologies.py
index 4aebcf85..db08e5fa 100644
--- a/scripts/upload_new_ontologies.py
+++ b/scripts/upload_new_ontologies.py
@@ -1,7 +1,7 @@
 def _upload_ontology_artifacts(instance: str, lamindb_user: str, lamindb_password: str):
     import bionty as bt
     import lamindb as ln
-    from bionty._bionty import encode_filenames
+    from bionty._public_ontology import encode_filenames
     from bionty._settings import settings
 
     ln.setup.login(lamindb_user, password=lamindb_password)
@@ -32,9 +32,9 @@ def _upload_ontology_artifacts(instance: str, lamindb_user: str, lamindb_passwor
         if not queryset.filter(key=ontology_filename).exists():
             local_ontology_filename = settings.dynamicdir / ontology_filename
             if not local_ontology_filename.exists():
-                getattr(bt, entity)(  # noqa: B018
+                getattr(bt, entity)(
                     organism=row.organism, source=row.source, version=row.version
-                ).ontology
+                ).to_pronto()
             file = ln.File(local_ontology_filename, key=ontology_filename)
             files.append(file)
     if len(files) > 0:
diff --git a/tests/entities/test_experimentalfactor.py b/tests/entities/test_experimentalfactor.py
index f0c241c9..0e01150a 100644
--- a/tests/entities/test_experimentalfactor.py
+++ b/tests/entities/test_experimentalfactor.py
@@ -25,7 +25,7 @@ def test_efo_experimental_factor_inspect_ontology_id():
 
 def test_parse_efo_term():
     ro = bt.ExperimentalFactor(source="efo")
-    ontology = ro.ontology
+    ontology = ro.to_pronto()
     res = _parse_efo_term(term_id="EFO:0008913", ontology=ontology)
 
     assert res == {
diff --git a/tests/test_bionty.py b/tests/test_bionty.py
index b23b4509..c03129a1 100644
--- a/tests/test_bionty.py
+++ b/tests/test_bionty.py
@@ -33,7 +33,7 @@ def test_diff_successful():
 
 
 def test_diff_value_errors():
-    # Two different Bionty object types
+    # Two different PublicOntology object types
     disease_bt = bt.Disease()
     phenotype_bt = bt.Phenotype()
     with pytest.raises(ValueError):