pyobo 0.10.7__py3-none-any.whl → 0.10.9__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/api/hierarchy.py +21 -11
- pyobo/api/properties.py +24 -9
- pyobo/api/xrefs.py +3 -1
- pyobo/getters.py +2 -2
- pyobo/gilda_utils.py +49 -19
- pyobo/sources/__init__.py +4 -0
- pyobo/sources/cgnc.py +1 -1
- pyobo/sources/chebi.py +4 -2
- pyobo/sources/civic_gene.py +55 -0
- pyobo/sources/cvx.py +18 -2
- pyobo/sources/famplex.py +5 -3
- pyobo/sources/mesh.py +29 -1
- pyobo/sources/ncbigene.py +5 -3
- pyobo/sources/omim_ps.py +39 -0
- pyobo/sources/rhea.py +141 -36
- pyobo/sources/umls/umls.py +17 -2
- pyobo/sources/uniprot/uniprot.py +123 -16
- pyobo/struct/__init__.py +1 -0
- pyobo/struct/struct.py +12 -6
- pyobo/struct/typedef.py +35 -5
- pyobo/utils/misc.py +22 -16
- pyobo/version.py +1 -1
- pyobo/xrefdb/sources/wikidata.py +5 -3
- {pyobo-0.10.7.dist-info → pyobo-0.10.9.dist-info}/METADATA +2 -2
- {pyobo-0.10.7.dist-info → pyobo-0.10.9.dist-info}/RECORD +29 -27
- {pyobo-0.10.7.dist-info → pyobo-0.10.9.dist-info}/WHEEL +1 -1
- {pyobo-0.10.7.dist-info → pyobo-0.10.9.dist-info}/LICENSE +0 -0
- {pyobo-0.10.7.dist-info → pyobo-0.10.9.dist-info}/entry_points.txt +0 -0
- {pyobo-0.10.7.dist-info → pyobo-0.10.9.dist-info}/top_level.txt +0 -0
pyobo/utils/misc.py
CHANGED
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@@ -52,22 +52,28 @@ def cleanup_version(data_version: str, prefix: str) -> Optional[str]:
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if prefix == "orth":
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# TODO add bioversions for this
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return "2"
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version_prefixes = [
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"http://www.orpha.net/version",
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"https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_",
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"http://humanbehaviourchange.org/ontology/bcio.owl/",
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"http://purl.org/pav/",
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"http://identifiers.org/combine.specifications/teddy.rel-",
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]
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for version_prefix in version_prefixes:
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if data_version.startswith(version_prefix):
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return data_version[len(version_prefix) :]
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version_prefixes_split = [
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"http://www.ebi.ac.uk/efo/releases/v",
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"http://www.ebi.ac.uk/swo/swo.owl/",
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"http://semanticscience.org/ontology/sio/v",
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"http://ontology.neuinfo.org/NIF/ttl/nif/version/",
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]
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for version_prefix_split in version_prefixes_split:
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if data_version.startswith(version_prefix_split):
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return data_version[len(version_prefix_split) :].split("/")[0]
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if data_version.replace(".", "").isnumeric():
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return data_version # consecutive, major.minor, or semantic versioning
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for v in reversed(data_version.split("/")):
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pyobo/version.py
CHANGED
pyobo/xrefdb/sources/wikidata.py
CHANGED
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@@ -24,7 +24,7 @@ logger = logging.getLogger(__name__)
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#: WikiData SPARQL endpoint. See https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service#Interfacing
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URL = "https://query.wikidata.org/bigdata/namespace/wdq/sparql"
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WIKIDATA_MAPPING_DIRECTORY = RAW_MODULE.
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WIKIDATA_MAPPING_DIRECTORY = RAW_MODULE.module("wikidata", "mappings")
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def get_wikidata_xrefs_df(*, use_tqdm: bool = True) -> pd.DataFrame:
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@@ -66,10 +66,12 @@ def get_wikidata_df(prefix: str, wikidata_property: str) -> pd.DataFrame:
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return df
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def iter_wikidata_mappings(
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def iter_wikidata_mappings(
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wikidata_property: str, *, cache: bool = True
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) -> Iterable[Tuple[str, str]]:
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"""Iterate over Wikidata xrefs."""
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path = WIKIDATA_MAPPING_DIRECTORY.join(name=f"{wikidata_property}.json")
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if path.exists():
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if path.exists() and cache:
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with path.open() as file:
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rows = json.load(file)
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else:
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@@ -1,6 +1,6 @@
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1
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Metadata-Version: 2.1
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Name: pyobo
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Version: 0.10.
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Version: 0.10.9
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Summary: Handling and writing OBO
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Home-page: https://github.com/pyobo/pyobo
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Download-URL: https://github.com/pyobo/pyobo/releases
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@@ -49,7 +49,7 @@ Requires-Dist: class-resolver
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Requires-Dist: psycopg2-binary
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Requires-Dist: drugbank-downloader
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Requires-Dist: chembl-downloader
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Requires-Dist: umls-downloader >=0.1.
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Requires-Dist: umls-downloader >=0.1.3
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Requires-Dist: typing-extensions
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Provides-Extra: agrovoc
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Requires-Dist: rdflib ; extra == 'agrovoc'
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@@ -2,8 +2,8 @@ pyobo/__init__.py,sha256=mZ96iZ-5ucxe2eLBi0xuSKaa2ZfeInaSR5Ajc_NkvUo,1862
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pyobo/__main__.py,sha256=cQjBabQ2wlFKcv54PFdt0SgPXNeb3oWneuOHaBgHx1Q,108
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pyobo/aws.py,sha256=EUXsN_sQEOWOV2oZXrVrkO8R6Zo_JJHGeGzzWWgpvzo,5948
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pyobo/constants.py,sha256=gj8xSUmCO0rU-eGXHOW7Vix3SAHl50cLAM3HXuoAFt4,2200
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-
pyobo/getters.py,sha256=
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pyobo/gilda_utils.py,sha256=
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pyobo/getters.py,sha256=37e7pcTqU-uVjx_XctT9pJMn7zaazsNfcyWoe7KMHi0,15565
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pyobo/gilda_utils.py,sha256=9rzlOkmq2MFac2sJ7b-XHS6UTSTiOM_rRk_xzt-uJiI,7582
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pyobo/identifier_utils.py,sha256=y4eFbJJQGoGe0HKRqQoUc_3tani22W_K4z7OZFL6Z0E,3659
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pyobo/mocks.py,sha256=R-4W3Rm5NarIHfNjxurbvBYsLHXt6jmDb6THMUt6K1w,2432
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pyobo/normalizer.py,sha256=OHME2CDQSZYSbqmP-L_-4nxete9W9mtAjUzXVs1hnjU,8293
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@@ -11,18 +11,18 @@ pyobo/obographs.py,sha256=JKE0a7e-gmxqdJoeX2zb_xQ6Tv5PAe60YhnIpAvrrYg,3758
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pyobo/plugins.py,sha256=dXWGoFuQktNeQUWSJlPz2a7FeLysggc9ry6auEZdw98,1227
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pyobo/reader.py,sha256=3VTWQMmA-AHi3RdA2jb48d2deXO-lYKqXbcMa9Qhi_4,21271
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pyobo/resource_utils.py,sha256=JBcJRihZhNwp78-qWZPrzSCGoYfyOjzBwMkfmOkO_no,4289
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pyobo/version.py,sha256=
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pyobo/version.py,sha256=ONSzSms19NKy9Bl2q8M4P_Mlo0MkqMGJ7X1SKZuec4M,977
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pyobo/api/__init__.py,sha256=Hq8p5uPW8fFYG2KfLqUsHhtLkTPqE4TqItGkedZzvXM,1326
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pyobo/api/alts.py,sha256=xmAb-gGQCJ9MbaFvoNK6E-V0B3TV9hxulkfbkHIvOso,2617
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pyobo/api/hierarchy.py,sha256=
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pyobo/api/hierarchy.py,sha256=2KtyTkqOKJzejNqVvlhPQD_w0fKzrOQp1BSx-Ina3t0,9413
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pyobo/api/metadata.py,sha256=62E7j0ZW3vYK2Rh-R7NCMKnChbYjZwPjVDoaE1AsCOc,1070
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pyobo/api/names.py,sha256=A5HprOfdt7twF2LfjdQQaIj3FNj4_GD7MZ7CrKllY5M,7559
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pyobo/api/properties.py,sha256=
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pyobo/api/properties.py,sha256=BKqUgN8nTpYrc0fROdaGGkptELgjbGT6TC_N2X8FIQM,7813
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pyobo/api/relations.py,sha256=VEQCQjPamehyGaL-wFzUYH9OeVq9pVzj70sl9K3ttKw,5996
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pyobo/api/species.py,sha256=xRPRoD6n1wcDaqlC_tHLw3rKMWa4razWsSPNa228g_4,2181
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pyobo/api/typedefs.py,sha256=TqNZ8_5ntw6PXwvqIlHtMHqD7l2jWwHn48vccUPbJiI,1061
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pyobo/api/utils.py,sha256=jxisiISIUtoW_SfNa3eOVTkEYP5ygYHaFTDibmMO7UE,1059
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pyobo/api/xrefs.py,sha256=
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pyobo/api/xrefs.py,sha256=p2ZdAcCOVnaRUQezGH3i0cTj2wVH-0mhSae98YVrMOQ,5942
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pyobo/apps/__init__.py,sha256=iACi86TkTiGxwneGmfaudZOIEqZ45YjPXng7XjPE38Y,72
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pyobo/apps/cli.py,sha256=gnXBAaESw1T1BvgMpTv-0P26hM2vKCAXPy0SOskgUwU,335
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pyobo/apps/gilda/__init__.py,sha256=jpLIHJOmR_66tdXXUWFP9NiZnpQKvjv5YpCJWoAKnUI,54
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@@ -52,25 +52,26 @@ pyobo/resources/ncbitaxon.py,sha256=kyJDMGm8qIpIpckN6NSGovCBDacG1qGYTIpvJ--HXhM,
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pyobo/resources/ncbitaxon.tsv.gz,sha256=43zHjnVt62TA4_lV58X-FCPdMDfLg1B1PvZSr_Xy9hY,22981954
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pyobo/resources/ro.py,sha256=_CYD90vftMZvu8Rj6H9kOiw6wRBbs1LWmCl-HToxMIg,1484
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pyobo/resources/ro.tsv,sha256=YvlBLPAKy2w4IheYzO9ox1Yg6WkHdMVzMQTikIlECog,26586
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pyobo/sources/__init__.py,sha256=
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pyobo/sources/__init__.py,sha256=uG7If-_xo4GfuvQ43yVQFBDUjYMGwmm5o3vyAm0Qqow,3783
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pyobo/sources/agrovoc.py,sha256=J425AyyOVAeqeyN5MhmAR9OtJom41GDvKArfyz1iIU8,795
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pyobo/sources/antibodyregistry.py,sha256=5i2qRhGgyi11Ke9xrHU1NRFxD3xMCnHQWWKh9fQCXDs,3178
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pyobo/sources/biogrid.py,sha256=Rr5gSLmOK95YPm2cYcFbGLDm3LWNckLvlarmbSIP-5M,3290
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pyobo/sources/ccle.py,sha256=KqqVokOq0HYE980plNa3987O1ixLkpcC0j9rYoQIM70,2963
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pyobo/sources/cgnc.py,sha256=
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pyobo/sources/chebi.py,sha256=
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pyobo/sources/cgnc.py,sha256=hCjFv05_aS2_Mn5Qb9VGLKGcOY87rEXZ6jH7r6WgUeg,2336
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pyobo/sources/chebi.py,sha256=7t5CaykOWXMQ9JRW8x1g_gsZhygCdjR2MGRYTFLEiTs,1230
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pyobo/sources/chembl.py,sha256=MG_bTilUwhhkeuTA3owLn1gro1QicMyGGfcd-48NGgE,2296
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pyobo/sources/civic_gene.py,sha256=SUwlb1PXwVVB-XQanyI7tRbPMGaDNiB-CXNry_idAZY,1691
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pyobo/sources/complexportal.py,sha256=nhEaUzw4riuN31OLiwpGffj66YMCeLigekblTWGk3nk,6022
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pyobo/sources/conso.py,sha256=ZLQ_T5EgrcuX9q6kCBKCwfGzAEVxgN6xADl-LKzJtbk,2460
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pyobo/sources/cpt.py,sha256=x8P15D9UX5Fwf6bmeVsU1DAFJvZ22rxVPy5ur-GUk_Q,1482
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pyobo/sources/cvx.py,sha256=
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pyobo/sources/cvx.py,sha256=FZAghQxkefWsxT1nTTUb56NgteRbAmawpOo3IdAfPAQ,2836
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pyobo/sources/depmap.py,sha256=VuZduDgCduiAHPLwPDXgWpxhMSOZCC4UsxFdj7hNkYQ,3656
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pyobo/sources/dictybase_gene.py,sha256=EgWBwUZ83ev7x5Lp_nUkgSq2zumkDjJ7_13m3f6kJz0,2564
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pyobo/sources/drugbank.py,sha256=pb2IdVQF4FqDvefwRdqlDV5j6pR9R1b3rGxHC-GSWb4,11028
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pyobo/sources/drugbank_salt.py,sha256=hx16G41mP2KXT4fsAQRCRkJMGn-z5cafs-bwm4wMtwo,1783
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pyobo/sources/drugcentral.py,sha256=05mGolBIyKCxAYzpH9LY_ZQrTVnizup2JUiWi2wW9OI,3587
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pyobo/sources/expasy.py,sha256=h8RcFtRd4wHBDVHC7tK8C1dT2M0dCknhfoWao7DLOx4,9507
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pyobo/sources/famplex.py,sha256=
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pyobo/sources/famplex.py,sha256=bn3WaJdrDf9BxsG9vnnnnGOwCrnrJ-vTMxOnxgrtUb4,5816
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pyobo/sources/flybase.py,sha256=0-BCNsp-L-CgGPN9VdJec6-8e4-fJuzaZAZiNra3ZUQ,5768
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pyobo/sources/geonames.py,sha256=XpSc-_6653MrjunVJhqbHHLtkT8kmbJZzfRuF6DoWU8,7929
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pyobo/sources/gmt_utils.py,sha256=NAWyUZ1p1HcO8RPL9mEEcL9KoaBDPuU-tbyG2QLb98k,1401
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pyobo/sources/icd_utils.py,sha256=c1Xkk9YAyKQ-vvnPud5GKq5ygZVbd1j0NFSml3RjQZ0,3155
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pyobo/sources/interpro.py,sha256=sWla5FDOkzA8elzeNHXOMD0nEVIbNK7jg4UZ0Zp7BfI,4934
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pyobo/sources/itis.py,sha256=LXS4MTL7OMmdfo-ypoF75UJkePw7VnHDrgq10RF_VUk,2967
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pyobo/sources/mesh.py,sha256=
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pyobo/sources/mesh.py,sha256=w06h1p0qeLUyNKEGLIqSdQXDtA4yqdfwnaAxF-4Xbr8,12048
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pyobo/sources/mgi.py,sha256=c0CiiH_LolAFdHPNu1lpLeAzHq20wVLyOrLRTkLYxhY,5766
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pyobo/sources/mirbase.py,sha256=NMqZfT7CbbetqCV-KdGjHJmz2uM5QvdF_M1BxKi1ZCw,6349
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pyobo/sources/mirbase_constants.py,sha256=X7KhJDp1saGrdBwUR9fQSWwebzns5f-mEF4qWSETs2k,2023
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pyobo/sources/mirbase_family.py,sha256=Yj3oXaeBWDxcmBKnvOl0q_7nzlye5EXhSJPWlV3YpT8,2167
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pyobo/sources/mirbase_mature.py,sha256=nvWcQVDMBucPu6v5DLFb_W_9fz_J_Id7HZrilkUhaFI,1504
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pyobo/sources/msigdb.py,sha256=YKgFyPgYKdYQtu22P69IVyLeBsLfgNyaNOl7q0Sy8IU,5019
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pyobo/sources/ncbigene.py,sha256=
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pyobo/sources/ncbigene.py,sha256=qipZEaaXop289vRro_NS8BB0_t-c738lJItWSjzD7PI,5055
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pyobo/sources/npass.py,sha256=t8TDdxpfvvXYo8VczT4ngoSspPAdPJuLKigvHZ9OHrE,2805
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pyobo/sources/omim_ps.py,sha256=uULW_1gmYIE66O85GdLCGbdmsi9qxcS7tZziOny0wc0,1020
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pyobo/sources/pathbank.py,sha256=yhdS4BCbGxQf0o3HCGzL2cYRY7zyvHvDzzSBkkezoog,4989
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pyobo/sources/pfam.py,sha256=aHXdXmoG6xyNkScHft_xYe4J2DzRr22EinyfjpmwEj4,1846
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pyobo/sources/pfam_clan.py,sha256=hjJ0UUEcrNoaQVWbXZ_EaTWFo4iB9VG9Sp6pcO90gxY,1340
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@@ -101,7 +103,7 @@ pyobo/sources/pombase.py,sha256=nRMxk2FuQZv6KnL8LBxqZbVtvynvneLe39i5V3dYAtw,3601
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pyobo/sources/umls/synonym_types.tsv,sha256=z--ngeAqA_Kk8ft2YD8qOU_XUxhnTxF0OhL8jRd5xqo,8551
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pyobo/sources/uniprot/__init__.py,sha256=dsL0BvfMn3O_swtNhzQpjJUlP56NUBCcjSYdFvRlwmI,225
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pyobo/sources/uniprot/uniprot_ptm.py,sha256=ze1cf0_kkqslhS-lXa7EdfasV4reUDp6niJat6yymT8,3551
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pyobo/ssg/__init__.py,sha256=Q5vYmk1LZwriShmA3TcYZ1Z1yiyjTWItcGxep5Fi2pw,5390
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pyobo/struct/typedef.py,sha256=spRRFWV-lV7yOU6HHnxAAFA-4ap6bm3l27KV-bmdLlc,13498
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pyobo/utils/__init__.py,sha256=wXtcjcasWRBtJdTSMCC3jT8yFG8ZkQC-Xdh9lLiQDAo,42
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pyobo/utils/path.py,sha256=-IVv_0H4Q790-ymmLdOlFgFSDuDubh9jZpPtDQzf-hI,3931
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pyobo/xrefdb/__init__.py,sha256=0W6AuvghFHQ1zY-Dq26z8V_MRC9xL39aWqLb-JbU8T8,74
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pyobo-0.10.9.dist-info/LICENSE,sha256=GRbxxtZEWtZiFGDENk1gntCQK4HEJYYbylEJEwpSLao,1076
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pyobo-0.10.9.dist-info/METADATA,sha256=BDEySfczBniUX3mHWKWI4XC9uxrbB_XPCRhp3Q5I8uE,20045
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pyobo-0.10.9.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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pyobo-0.10.9.dist-info/entry_points.txt,sha256=Du5V6qw_T917Z5ZoMhLTTJoolK7kkVuUWkdE7aJWea0,669
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pyobo-0.10.9.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
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pyobo-0.10.9.dist-info/RECORD,,
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