pyobo 0.12.1__py3-none-any.whl → 0.12.2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pyobo/getters.py +2 -1
- pyobo/identifier_utils/__init__.py +2 -1
- pyobo/identifier_utils/api.py +1 -1
- pyobo/obographs.py +6 -1
- pyobo/sources/credit.py +17 -6
- pyobo/version.py +1 -1
- {pyobo-0.12.1.dist-info → pyobo-0.12.2.dist-info}/METADATA +3 -15
- {pyobo-0.12.1.dist-info → pyobo-0.12.2.dist-info}/RECORD +163 -167
- {pyobo-0.12.1.dist-info → pyobo-0.12.2.dist-info}/WHEEL +1 -1
- pyobo/identifier_utils/preprocessing.json +0 -873
- pyobo/identifier_utils/preprocessing.py +0 -27
- pyobo/resources/goc.py +0 -75
- pyobo/resources/goc.tsv +0 -188
- {pyobo-0.12.1.dist-info → pyobo-0.12.2.dist-info}/entry_points.txt +0 -0
- {pyobo-0.12.1.dist-info → pyobo-0.12.2.dist-info}/licenses/LICENSE +0 -0
pyobo/getters.py
CHANGED
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@@ -20,7 +20,6 @@ from typing import Any, TypeVar
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import bioregistry
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import click
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import pystow.utils
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from bioontologies import robot
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from tabulate import tabulate
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from tqdm.auto import tqdm
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from typing_extensions import Unpack
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@@ -160,6 +159,8 @@ def get_ontology(
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elif ontology_format == "obo":
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pass # all gucci
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elif ontology_format == "owl":
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from bioontologies import robot
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_converted_obo_path = path.with_suffix(".obo")
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if prefix in REQUIRES_NO_ROBOT_CHECK:
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robot_check = False
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"""Extract registry information."""
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from curies_processing import get_rules
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from .api import (
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DefaultCoercionError,
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EmptyStringError,
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@@ -13,7 +15,6 @@ from .api import (
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standardize_ec,
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wrap_norm_prefix,
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)
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from .preprocessing import get_rules
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from .relations import ground_relation
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__all__ = [
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pyobo/identifier_utils/api.py
CHANGED
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@@ -12,10 +12,10 @@ from bioregistry import NormalizedNamableReference as Reference
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from bioregistry.constants import FailureReturnType
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from curies import ReferenceTuple
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from curies.preprocessing import BlocklistError, PreprocessingConverter
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from curies_processing import get_rules
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from pydantic import ValidationError
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from typing_extensions import Doc
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from .preprocessing import get_rules
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from .relations import ground_relation
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__all__ = [
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pyobo/obographs.py
CHANGED
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@@ -4,6 +4,7 @@ from __future__ import annotations
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import logging
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from collections.abc import Iterable
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from typing import TYPE_CHECKING
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import bioregistry
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from bioontologies.obograph import (
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Synonym,
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Xref,
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)
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from bioontologies.robot import ParseResults
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from tqdm import tqdm
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from pyobo.struct import Obo, OBOLiteral, Reference, Term
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from pyobo.struct.typedef import definition_source, is_a
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if TYPE_CHECKING:
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from bioontologies.robot import ParseResults
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__all__ = [
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"graph_from_obo",
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"parse_results_from_obo",
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def parse_results_from_obo(obo: Obo) -> ParseResults:
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"""Get parse results from an OBO graph."""
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graph = graph_from_obo(obo)
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from bioontologies.robot import ParseResults
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return ParseResults(graph_document=GraphDocument(graphs=[graph]))
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pyobo/sources/credit.py
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from more_itertools import chunked
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from pyobo.struct import Obo, Term
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from pyobo.struct import CHARLIE_TERM, HUMAN_TERM, Obo, Reference, Term, default_reference
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from pyobo.utils.path import ensure_path
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__all__ = [
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url = "https://api.github.com/repos/CASRAI-CRedIT/Dictionary/contents/Picklists/Contributor%20Roles"
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PREFIX = "credit"
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ROOT = default_reference(prefix=PREFIX, identifier="contributor-role", name="contributor role")
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ROOT_TERM = (
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Term(reference=ROOT)
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.append_contributor(CHARLIE_TERM)
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.append_xref(Reference(prefix="cro", identifier="0000000"))
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)
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class CreditGetter(Obo):
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ontology = PREFIX
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static_version = "2022"
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root_terms = [ROOT]
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def iter_terms(self, force: bool = False) -> Iterable[Term]:
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"""Iterate over terms in the ontology."""
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path = ensure_path(PREFIX, url=url, name="picklist-api.json", force=force)
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with open(path) as f:
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data = json.load(f)
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terms = [
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terms = [
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CHARLIE_TERM,
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HUMAN_TERM,
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ROOT_TERM,
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]
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for x in data:
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name = x["name"].removesuffix(".md").lower()
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pp = ensure_path(PREFIX, "picklist", url=x["download_url"], backend="requests")
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with open(pp) as f:
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header, *rest = f.read().splitlines()
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name = header
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name = header.removeprefix("# Contributor Roles/")
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dd = {k.removeprefix("## "): v for k, v in chunked(rest, 2)}
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identifier = (
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dd["Canonical URL"]
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)
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desc = dd["Short definition"]
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terms.append(
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Term.from_triple(
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Term.from_triple(
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prefix=PREFIX, identifier=identifier, name=name, definition=desc
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).append_parent(ROOT)
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)
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return terms
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pyobo/version.py
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Metadata-Version: 2.4
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Name: pyobo
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Version: 0.12.
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Version: 0.12.2
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Summary: A python package for handling and generating OBO
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Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
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Author: Charles Tapley Hoyt
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Requires-Dist: pystow>=0.7.0
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Requires-Dist: bioversions>=0.8.0
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Requires-Dist: bioregistry>=0.12.7
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Requires-Dist: bioontologies>=0.7.
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Requires-Dist: bioontologies>=0.7.2
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Requires-Dist: ssslm>=0.0.13
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Requires-Dist: zenodo-client>=0.3.6
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Requires-Dist: class-resolver>=0.6.0
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Requires-Dist: psycopg2-binary
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Requires-Dist: pydantic>=2.0
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Requires-Dist: curies>=0.10.13
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Requires-Dist: curies-processing>=0.1.0
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Requires-Dist: python-dateutil
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Requires-Dist: networkx>=3.4
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Requires-Dist: drugbank-downloader
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pyobo.get_name("chebi", "1234")
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```
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## Preprocessing CURIEs, URIs, and unqualified identifiers
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In order to normalize references and identify resources, PyOBO uses the
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of PyOBO, but has since been externalized for more general reuse.
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is the curated set of pre-processing rules. These are used in combination with
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the `curies` package to do pre-processing steps on CURIEs, URIs, and unqualified
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identifiers beyond what is possible with the Bioregistry. See
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## Troubleshooting
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The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO
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pyobo/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
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pyobo/getters.py,sha256=68c8982ac868863e73d1428bcdb82dfdfd0d9397e25d9dc2e0eca05d9b9d566a,17366
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pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
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pyobo/.DS_Store,sha256=00b8c741cd5b001c03c1a582f55bfbcda0ad16f0e55019d64f93241b74991980,8196
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pyobo/version.py,sha256=dab7f9a58f271077f9eb69671bc8ff659ad64f36f418250a964fa030d634373d,926
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pyobo/ner/__init__.py,sha256=0199b704f1235184d521069034823c3d9960ff6756205c299649b87a4bbd4041,153
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pyobo/ner/api.py,sha256=b34309833eac8f5dea881d531323bf682f35d377e09d807066ba1183282964dc,2167
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pyobo/ner/normalizer.py,sha256=4e90d93801877f72f2fab8069db986e79cc749533a068a8b07a9d7c9e37cb9c2,954
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pyobo/obographs.py,sha256=f4d9904d939afd04b29b42aa40acbaf6ec9d4a8f2eb3e1dc714b051b1025c41e,4239
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pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
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pyobo/resources/goc.py,sha256=6b7e352d9a7e00e08c92588a65d283be09ab5dac9fc4e9780e14b130b64ce5ba,2550
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pyobo/resources/goc.tsv,sha256=5bb98b945fbc9e0876e2a921f328a72f8b44f5686037e341fc8432b1a1d0d616,9081
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pyobo/resources/__init__.py,sha256=43d9e293b1e0a4808238dec610aa5bc37cfd64833b345270a063697a9927da70,38
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pyobo/resources/so.tsv,sha256=50964a153100bff5eccd861bba7e167fa6f88e8bc38d229cd51591411713cc3c,82068
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pyobo/resources/so.py,sha256=4bebe643b2fc009134f057c6543209a8d40d68b3d49ae27a1c2e45e2158732b0,1466
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pyobo/resources/ro.py,sha256=df0a739171825f42441f261c09104c277016fb098baa242ff18bc965a1217c99,1508
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pyobo/resources/ro.tsv,sha256=62f9412cf00acb6c38221798ccef68c75620e9690774c5733104e29089440a88,26586
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pyobo/resources/ncbitaxon.py,sha256=92484774b0f45247cb4090b34e3851a5c175dde2da03e472d891c9953968116b,1979
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pyobo/resources/ncbitaxon.tsv.gz,sha256=e37cc78e756deb64c0e3f955e7c5fe1423dd3037cb8350753ef652aff5f2f616,22981954
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pyobo/constants.py,sha256=c1ffa4f12c1ddee556adf728ef4ac51da44f228fe6fca9b58b9ab8f263acc87b,5112
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pyobo/
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pyobo/
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pyobo/__main__.py,sha256=70e610d8e10bc45fbd4fa9ee67dc672d2bbd6cb1e4e9e8a7aec4a8cfb11c0fd3,83
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pyobo/api/__init__.py,sha256=259870a4519a6baa5df1180378837e67c688e8ecbe46e9a3d4a90e6435c79e1d,2955
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pyobo/api/alts.py,sha256=478b3162574616f2827bd73107f80f5dfdaf5971eaf6c6813109109dba89e522,3032
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pyobo/api/combine.py,sha256=ed3f108fc5b5c164352a0289b0ed641511d9c6441cadf28cd6106b86a1ec1245,1106
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pyobo/api/edges.py,sha256=4849b6809c7a2e83a48571a3d75578dae2e0e0589d15af6326a5bd1f39e57f09,1974
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pyobo/api/hierarchy.py,sha256=37f27381f08a3c859adb4a1d46132fa60889a5ccce8867620db2e4353aa5a69f,10314
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pyobo/api/metadata.py,sha256=b2d25a897fe5ef1d11d55efb4cdc07bcfb6892e67e128a9bf473112fbd0d896b,1029
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pyobo/api/names.py,sha256=2f620187285c1fccbeac23708d624bc374ec1e9d6abce65ebf5eb4f9c63070b8,10673
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pyobo/api/properties.py,sha256=6d85af1ebd5b7f4c5d232323faab9d8f8a11a419eab0a86eca36052b22b2f778,6914
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pyobo/api/relations.py,sha256=6dfda59d8ae2c3addb816d7dad2b97856916c6f2e6114f7a774bfcaff1c25747,5859
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pyobo/api/species.py,sha256=631cc978295fb8a23ea6360ba6ee7bf7b8dd0dec93917a6340381d99cf4c2b0a,2376
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pyobo/api/typedefs.py,sha256=1d3ba2d2497f5442f18238b4bdf06bf8d046df3aeba4253cb66b9039258ae9fc,1262
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pyobo/api/utils.py,sha256=ae8d2274e48d129a0d3520e48ba462af066afff928c9fcd231f569c4b322bcf5,5429
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pyobo/api/xrefs.py,sha256=9d62cbb761b36957e780d0546ce3154a33a90ae6be23bbbedadba8c735c6aab0,5242
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pyobo/cli/__init__.py,sha256=a5388bbb38e3a62d0febdc958d0da413a9c152666e6059ea74934364b0e482f9,71
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pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc7d5f7a8a05da2b7adae,5540
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pyobo/cli/cli.py,sha256=ca057c8505fa7f40730ac0aa0a77e033e30ede9074a145f0b70d7b5f622aa2bd,2939
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pyobo/cli/database.py,sha256=e880ac2c78bd437d73c99cea5c44938129852571bca35e2ab0cc7de195851ce6,11963
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