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 CHANGED
@@ -20,7 +20,6 @@ from typing import Any, TypeVar
20
20
  import bioregistry
21
21
  import click
22
22
  import pystow.utils
23
- from bioontologies import robot
24
23
  from tabulate import tabulate
25
24
  from tqdm.auto import tqdm
26
25
  from typing_extensions import Unpack
@@ -160,6 +159,8 @@ def get_ontology(
160
159
  elif ontology_format == "obo":
161
160
  pass # all gucci
162
161
  elif ontology_format == "owl":
162
+ from bioontologies import robot
163
+
163
164
  _converted_obo_path = path.with_suffix(".obo")
164
165
  if prefix in REQUIRES_NO_ROBOT_CHECK:
165
166
  robot_check = False
@@ -1,5 +1,7 @@
1
1
  """Extract registry information."""
2
2
 
3
+ from curies_processing import get_rules
4
+
3
5
  from .api import (
4
6
  DefaultCoercionError,
5
7
  EmptyStringError,
@@ -13,7 +15,6 @@ from .api import (
13
15
  standardize_ec,
14
16
  wrap_norm_prefix,
15
17
  )
16
- from .preprocessing import get_rules
17
18
  from .relations import ground_relation
18
19
 
19
20
  __all__ = [
@@ -12,10 +12,10 @@ from bioregistry import NormalizedNamableReference as Reference
12
12
  from bioregistry.constants import FailureReturnType
13
13
  from curies import ReferenceTuple
14
14
  from curies.preprocessing import BlocklistError, PreprocessingConverter
15
+ from curies_processing import get_rules
15
16
  from pydantic import ValidationError
16
17
  from typing_extensions import Doc
17
18
 
18
- from .preprocessing import get_rules
19
19
  from .relations import ground_relation
20
20
 
21
21
  __all__ = [
pyobo/obographs.py CHANGED
@@ -4,6 +4,7 @@ from __future__ import annotations
4
4
 
5
5
  import logging
6
6
  from collections.abc import Iterable
7
+ from typing import TYPE_CHECKING
7
8
 
8
9
  import bioregistry
9
10
  from bioontologies.obograph import (
@@ -16,12 +17,14 @@ from bioontologies.obograph import (
16
17
  Synonym,
17
18
  Xref,
18
19
  )
19
- from bioontologies.robot import ParseResults
20
20
  from tqdm import tqdm
21
21
 
22
22
  from pyobo.struct import Obo, OBOLiteral, Reference, Term
23
23
  from pyobo.struct.typedef import definition_source, is_a
24
24
 
25
+ if TYPE_CHECKING:
26
+ from bioontologies.robot import ParseResults
27
+
25
28
  __all__ = [
26
29
  "graph_from_obo",
27
30
  "parse_results_from_obo",
@@ -33,6 +36,8 @@ logger = logging.getLogger(__name__)
33
36
  def parse_results_from_obo(obo: Obo) -> ParseResults:
34
37
  """Get parse results from an OBO graph."""
35
38
  graph = graph_from_obo(obo)
39
+ from bioontologies.robot import ParseResults
40
+
36
41
  return ParseResults(graph_document=GraphDocument(graphs=[graph]))
37
42
 
38
43
 
pyobo/sources/credit.py CHANGED
@@ -7,7 +7,7 @@ from collections.abc import Iterable
7
7
 
8
8
  from more_itertools import chunked
9
9
 
10
- from pyobo.struct import Obo, Term
10
+ from pyobo.struct import CHARLIE_TERM, HUMAN_TERM, Obo, Reference, Term, default_reference
11
11
  from pyobo.utils.path import ensure_path
12
12
 
13
13
  __all__ = [
@@ -16,6 +16,12 @@ __all__ = [
16
16
 
17
17
  url = "https://api.github.com/repos/CASRAI-CRedIT/Dictionary/contents/Picklists/Contributor%20Roles"
18
18
  PREFIX = "credit"
19
+ ROOT = default_reference(prefix=PREFIX, identifier="contributor-role", name="contributor role")
20
+ ROOT_TERM = (
21
+ Term(reference=ROOT)
22
+ .append_contributor(CHARLIE_TERM)
23
+ .append_xref(Reference(prefix="cro", identifier="0000000"))
24
+ )
19
25
 
20
26
 
21
27
  class CreditGetter(Obo):
@@ -23,6 +29,7 @@ class CreditGetter(Obo):
23
29
 
24
30
  ontology = PREFIX
25
31
  static_version = "2022"
32
+ root_terms = [ROOT]
26
33
 
27
34
  def iter_terms(self, force: bool = False) -> Iterable[Term]:
28
35
  """Iterate over terms in the ontology."""
@@ -34,14 +41,16 @@ def get_terms(force: bool = False) -> list[Term]:
34
41
  path = ensure_path(PREFIX, url=url, name="picklist-api.json", force=force)
35
42
  with open(path) as f:
36
43
  data = json.load(f)
37
- terms = []
44
+ terms = [
45
+ CHARLIE_TERM,
46
+ HUMAN_TERM,
47
+ ROOT_TERM,
48
+ ]
38
49
  for x in data:
39
- name = x["name"].removesuffix(".md").lower()
40
-
41
50
  pp = ensure_path(PREFIX, "picklist", url=x["download_url"], backend="requests")
42
51
  with open(pp) as f:
43
52
  header, *rest = f.read().splitlines()
44
- name = header = header.removeprefix("# Contributor Roles/")
53
+ name = header.removeprefix("# Contributor Roles/")
45
54
  dd = {k.removeprefix("## "): v for k, v in chunked(rest, 2)}
46
55
  identifier = (
47
56
  dd["Canonical URL"]
@@ -50,7 +59,9 @@ def get_terms(force: bool = False) -> list[Term]:
50
59
  )
51
60
  desc = dd["Short definition"]
52
61
  terms.append(
53
- Term.from_triple(prefix=PREFIX, identifier=identifier, name=name, definition=desc)
62
+ Term.from_triple(
63
+ prefix=PREFIX, identifier=identifier, name=name, definition=desc
64
+ ).append_parent(ROOT)
54
65
  )
55
66
 
56
67
  return terms
pyobo/version.py CHANGED
@@ -12,7 +12,7 @@ __all__ = [
12
12
  "get_version",
13
13
  ]
14
14
 
15
- VERSION = "0.12.1"
15
+ VERSION = "0.12.2"
16
16
 
17
17
 
18
18
  def get_git_hash() -> str:
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: pyobo
3
- Version: 0.12.1
3
+ Version: 0.12.2
4
4
  Summary: A python package for handling and generating OBO
5
5
  Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
6
6
  Author: Charles Tapley Hoyt
@@ -39,13 +39,14 @@ Requires-Dist: cachier
39
39
  Requires-Dist: pystow>=0.7.0
40
40
  Requires-Dist: bioversions>=0.8.0
41
41
  Requires-Dist: bioregistry>=0.12.7
42
- Requires-Dist: bioontologies>=0.7.1
42
+ Requires-Dist: bioontologies>=0.7.2
43
43
  Requires-Dist: ssslm>=0.0.13
44
44
  Requires-Dist: zenodo-client>=0.3.6
45
45
  Requires-Dist: class-resolver>=0.6.0
46
46
  Requires-Dist: psycopg2-binary
47
47
  Requires-Dist: pydantic>=2.0
48
48
  Requires-Dist: curies>=0.10.13
49
+ Requires-Dist: curies-processing>=0.1.0
49
50
  Requires-Dist: python-dateutil
50
51
  Requires-Dist: networkx>=3.4
51
52
  Requires-Dist: drugbank-downloader
@@ -395,19 +396,6 @@ class MyTestCase(unittest.TestCase):
395
396
  pyobo.get_name("chebi", "1234")
396
397
  ```
397
398
 
398
- ## Preprocessing CURIEs, URIs, and unqualified identifiers
399
-
400
- In order to normalize references and identify resources, PyOBO uses the
401
- [Bioregistry](https://github.com/bioregistry/bioregistry). It used to be a part
402
- of PyOBO, but has since been externalized for more general reuse.
403
-
404
- At
405
- [src/pyobo/identifier_utils/preprocessing.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/src/pyobo/identifier_utils/preprocessing.json)
406
- is the curated set of pre-processing rules. These are used in combination with
407
- the `curies` package to do pre-processing steps on CURIEs, URIs, and unqualified
408
- identifiers beyond what is possible with the Bioregistry. See
409
- https://curies.readthedocs.io/en/latest/preprocessing.html.
410
-
411
399
  ## Troubleshooting
412
400
 
413
401
  The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO
@@ -1,201 +1,197 @@
1
- pyobo/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
2
- pyobo/getters.py,sha256=68c8982ac868863e73d1428bcdb82dfdfd0d9397e25d9dc2e0eca05d9b9d566a,17366
3
- pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
4
1
  pyobo/.DS_Store,sha256=00b8c741cd5b001c03c1a582f55bfbcda0ad16f0e55019d64f93241b74991980,8196
5
- pyobo/version.py,sha256=dab7f9a58f271077f9eb69671bc8ff659ad64f36f418250a964fa030d634373d,926
6
- pyobo/ner/__init__.py,sha256=0199b704f1235184d521069034823c3d9960ff6756205c299649b87a4bbd4041,153
7
- pyobo/ner/api.py,sha256=b34309833eac8f5dea881d531323bf682f35d377e09d807066ba1183282964dc,2167
8
- pyobo/ner/normalizer.py,sha256=4e90d93801877f72f2fab8069db986e79cc749533a068a8b07a9d7c9e37cb9c2,954
9
- pyobo/obographs.py,sha256=f4d9904d939afd04b29b42aa40acbaf6ec9d4a8f2eb3e1dc714b051b1025c41e,4239
10
- pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
11
- pyobo/resources/goc.py,sha256=6b7e352d9a7e00e08c92588a65d283be09ab5dac9fc4e9780e14b130b64ce5ba,2550
12
- pyobo/resources/goc.tsv,sha256=5bb98b945fbc9e0876e2a921f328a72f8b44f5686037e341fc8432b1a1d0d616,9081
13
- pyobo/resources/__init__.py,sha256=43d9e293b1e0a4808238dec610aa5bc37cfd64833b345270a063697a9927da70,38
14
- pyobo/resources/so.tsv,sha256=50964a153100bff5eccd861bba7e167fa6f88e8bc38d229cd51591411713cc3c,82068
15
- pyobo/resources/so.py,sha256=4bebe643b2fc009134f057c6543209a8d40d68b3d49ae27a1c2e45e2158732b0,1466
16
- pyobo/resources/ro.py,sha256=df0a739171825f42441f261c09104c277016fb098baa242ff18bc965a1217c99,1508
17
- pyobo/resources/ro.tsv,sha256=62f9412cf00acb6c38221798ccef68c75620e9690774c5733104e29089440a88,26586
18
- pyobo/resources/ncbitaxon.py,sha256=92484774b0f45247cb4090b34e3851a5c175dde2da03e472d891c9953968116b,1979
19
- pyobo/resources/ncbitaxon.tsv.gz,sha256=e37cc78e756deb64c0e3f955e7c5fe1423dd3037cb8350753ef652aff5f2f616,22981954
20
- pyobo/constants.py,sha256=c1ffa4f12c1ddee556adf728ef4ac51da44f228fe6fca9b58b9ab8f263acc87b,5112
21
2
  pyobo/__init__.py,sha256=0d90185e6e3aa041ccc27c68226c45e456e39369328e3db17706d65b52015819,3439
22
- pyobo/utils/iter.py,sha256=ad845b6da1491f131a134c94fab419a026a0608aed7afd3db98d26c4591fe736,1524
23
- pyobo/utils/misc.py,sha256=99d1f6e88b48d3f0cdbd7fff8a908556bf949278fcf0ef639e5cc8a421d0f4db,2684
24
- pyobo/utils/ndex_utils.py,sha256=128902592d345ab93fe32f2575e42e53269a0bac8dcc18370da81497e2767336,2326
25
- pyobo/utils/io.py,sha256=fa0cb5a8633a6c9fb95eb2f74e08fbf69acc4fc229b89c18dd233921b80378a9,5100
26
- pyobo/utils/cache.py,sha256=136ccd03b82afd534699a36bad129e5f3e73aba5c3184fb93d5a24af30d99227,3098
27
- pyobo/utils/__init__.py,sha256=08035263cbc6abfeaff2b5a159121d9e4f96a392c0d91f568e0d67a9b5aa2cec,17
28
- pyobo/utils/path.py,sha256=cc37f10de8e0ef90a6063cc2b1c5d1b0993e41649536f04bfddc892d61a3bc4f,3398
29
- pyobo/cli/database.py,sha256=e880ac2c78bd437d73c99cea5c44938129852571bca35e2ab0cc7de195851ce6,11963
30
- pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
3
+ pyobo/__main__.py,sha256=70e610d8e10bc45fbd4fa9ee67dc672d2bbd6cb1e4e9e8a7aec4a8cfb11c0fd3,83
4
+ pyobo/api/__init__.py,sha256=259870a4519a6baa5df1180378837e67c688e8ecbe46e9a3d4a90e6435c79e1d,2955
5
+ pyobo/api/alts.py,sha256=478b3162574616f2827bd73107f80f5dfdaf5971eaf6c6813109109dba89e522,3032
6
+ pyobo/api/combine.py,sha256=ed3f108fc5b5c164352a0289b0ed641511d9c6441cadf28cd6106b86a1ec1245,1106
7
+ pyobo/api/edges.py,sha256=4849b6809c7a2e83a48571a3d75578dae2e0e0589d15af6326a5bd1f39e57f09,1974
8
+ pyobo/api/hierarchy.py,sha256=37f27381f08a3c859adb4a1d46132fa60889a5ccce8867620db2e4353aa5a69f,10314
9
+ pyobo/api/metadata.py,sha256=b2d25a897fe5ef1d11d55efb4cdc07bcfb6892e67e128a9bf473112fbd0d896b,1029
10
+ pyobo/api/names.py,sha256=2f620187285c1fccbeac23708d624bc374ec1e9d6abce65ebf5eb4f9c63070b8,10673
11
+ pyobo/api/properties.py,sha256=6d85af1ebd5b7f4c5d232323faab9d8f8a11a419eab0a86eca36052b22b2f778,6914
12
+ pyobo/api/relations.py,sha256=6dfda59d8ae2c3addb816d7dad2b97856916c6f2e6114f7a774bfcaff1c25747,5859
13
+ pyobo/api/species.py,sha256=631cc978295fb8a23ea6360ba6ee7bf7b8dd0dec93917a6340381d99cf4c2b0a,2376
14
+ pyobo/api/typedefs.py,sha256=1d3ba2d2497f5442f18238b4bdf06bf8d046df3aeba4253cb66b9039258ae9fc,1262
15
+ pyobo/api/utils.py,sha256=ae8d2274e48d129a0d3520e48ba462af066afff928c9fcd231f569c4b322bcf5,5429
16
+ pyobo/api/xrefs.py,sha256=9d62cbb761b36957e780d0546ce3154a33a90ae6be23bbbedadba8c735c6aab0,5242
31
17
  pyobo/cli/__init__.py,sha256=a5388bbb38e3a62d0febdc958d0da413a9c152666e6059ea74934364b0e482f9,71
32
- pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc7d5f7a8a05da2b7adae,5540
33
18
  pyobo/cli/cli.py,sha256=ca057c8505fa7f40730ac0aa0a77e033e30ede9074a145f0b70d7b5f622aa2bd,2939
19
+ pyobo/cli/database.py,sha256=e880ac2c78bd437d73c99cea5c44938129852571bca35e2ab0cc7de195851ce6,11963
20
+ pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc7d5f7a8a05da2b7adae,5540
21
+ pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
34
22
  pyobo/cli/utils.py,sha256=9e6b57b311b44d61088e321efa387f6aacebd3d6d337bf8d1c589fb871b3304d,1738
35
- pyobo/struct/__init__.py,sha256=fb813dfa7de27f195c07cd5311de78403b03dfbf0a183995c8fb448033ace311,1444
36
- pyobo/struct/typedef.py,sha256=fd94429e28efcdf7bbeba4b1729fa66af5f64c34e49437d82e4b3e5a457d064d,12099
37
- pyobo/struct/struct_utils.py,sha256=7b8bfd7a322f34cf1436b83c8eab983944651ba467923045bf61ecc245800d2c,39164
38
- pyobo/struct/utils.py,sha256=ce4a4e138d894087e4374adce6a34434ad375482a691fff9eed1e88cc24aef56,906
39
- pyobo/struct/reference.py,sha256=4fc7d3b665cd18c8dfbbb2b8b49de4bc30a8e101d14ff26bf5f88e9c562bc2d3,11735
40
- pyobo/struct/vocabulary.py,sha256=56e0f6770cf7da2d6f1221e3fc8261f1c07dc8358a1f3dfb487894a25b1ed133,4335
41
- pyobo/struct/functional/dsl.py,sha256=780b4e5616b8dc823cee610945a95ffa109aa43287992dd4dd51511c461f96fb,101183
42
- pyobo/struct/functional/__init__.py,sha256=d536edb7fe86a1aad19607df3dea62b49dd0b4bb2b30f31b8431a842700a499e,32
43
- pyobo/struct/functional/obo_to_functional.py,sha256=785c46fdb00dc45f3903f67ad24ae4fcb6d187ce48208373fc9d42833a85f6b8,13273
44
- pyobo/struct/functional/utils.py,sha256=73e5c6d9227b0a162dcfb294dcad05f93ea870c8d87af7a2d16c6591f9249ad1,3487
45
- pyobo/struct/functional/macros.py,sha256=cc654f131fa685d4afc87d8c7b5e8565da1b789dd5d73045a77b3e033a8ced52,13785
46
- pyobo/struct/functional/ontology.py,sha256=bc610a206c5f502cc658cbf7dcaa9caeb112a596ab1cb07fcbd571c8a6da2894,9331
47
- pyobo/struct/struct.py,sha256=29b77204d903a948aff74f93aa043e5421cc932c22a893e70dbfd3f27b911fb7,89480
48
- pyobo/ssg/index.html,sha256=da62c16a198f7ad2468599c5d7e4da4d7b81e02a18a25a59da741a579746e676,4346
49
- pyobo/ssg/typedef.html,sha256=2ab76acc1eb18edebcf5b1b7dc3dba00bfb5d49aef36e124a3134d23e106f938,2038
50
- pyobo/ssg/base.html,sha256=fef95d5026be80bd984cd63a1a002ec4d4f74e06840f9f39bc5feaed3aeb8d8b,2844
51
- pyobo/ssg/__init__.py,sha256=8500042e3156fe3acd5fd5546b0ed52038d842150389c512b3e99267302f152a,5224
52
- pyobo/ssg/term.html,sha256=b522c82774980d37ad2bd8361280cacaee1a1dc855a351145e4fda62119e38aa,3869
53
- pyobo/reader.py,sha256=6fc2522a89772b718eaa6278e2abc7d5ca536378b537992b34bfe12bcfd10d72,52246
54
- pyobo/identifier_utils/relations/data_rdfs.json,sha256=6e3a7166d7b78385afac626c987b8024dfdc83f7dac6a21af6d08bedab8776a4,86
23
+ pyobo/constants.py,sha256=c1ffa4f12c1ddee556adf728ef4ac51da44f228fe6fca9b58b9ab8f263acc87b,5112
24
+ pyobo/getters.py,sha256=0d9a129a46213f3657cb80d7a70a73aa24567644a1d9090c57f09c67cb86921a,17375
25
+ pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
26
+ pyobo/identifier_utils/__init__.py,sha256=ef7bbb0ffb088daa04ee79446bafc8a5ee1d404e347e637361b835879755dea2,753
27
+ pyobo/identifier_utils/api.py,sha256=c308dc9f48753d14084d19362f08003f822c2e495fe0badd9b9d3bc176fbaba1,9215
55
28
  pyobo/identifier_utils/relations/__init__.py,sha256=2961f492b8530a678a9e010887b5530c3de1cc2df8f294e210a18dbb748d01db,159
56
- pyobo/identifier_utils/relations/data.json,sha256=88b6ce5fb632faa389b512b68f1b73acdd54b552a1aaa8043430eb5e0020a0bc,113169
57
29
  pyobo/identifier_utils/relations/api.py,sha256=c625bca0f09379ba7ef544d05aaf4b998ee9798945a90f3b98b6d763ef9d36df,5764
58
- pyobo/identifier_utils/relations/data_rdf.json,sha256=4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945,2
30
+ pyobo/identifier_utils/relations/data.json,sha256=88b6ce5fb632faa389b512b68f1b73acdd54b552a1aaa8043430eb5e0020a0bc,113169
59
31
  pyobo/identifier_utils/relations/data_owl.json,sha256=a70fe8850a0b32f0ca5f9358085a340297a3464d7ba61e83333fe69d6ae4c826,1066
60
- pyobo/identifier_utils/__init__.py,sha256=865d3a02c3a6d38ff13d4e30685a60368c4a7823397f93e609c2ad356c5d46a3,749
61
- pyobo/identifier_utils/api.py,sha256=310bf6e0ac55882b9bbf179b1628bfc70797ae419a962ea6e1e3cdf48e8e5c26,9212
62
- pyobo/identifier_utils/preprocessing.py,sha256=67c9109c1a4ba1f5f45368516563a044e38d4095799b520519a57044230d5fd7,618
63
- pyobo/identifier_utils/preprocessing.json,sha256=e84f2ed9bb4f2a92c83845daf739f4052d7a615bfc6c13dcc54845a306916627,34821
32
+ pyobo/identifier_utils/relations/data_rdf.json,sha256=4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945,2
33
+ pyobo/identifier_utils/relations/data_rdfs.json,sha256=6e3a7166d7b78385afac626c987b8024dfdc83f7dac6a21af6d08bedab8776a4,86
34
+ pyobo/mocks.py,sha256=8f9e392bd3ff0cfb0306e6070eb8724cb8e694fa0d951744b5c4652e15e56d72,2440
35
+ pyobo/ner/__init__.py,sha256=0199b704f1235184d521069034823c3d9960ff6756205c299649b87a4bbd4041,153
36
+ pyobo/ner/api.py,sha256=b34309833eac8f5dea881d531323bf682f35d377e09d807066ba1183282964dc,2167
37
+ pyobo/ner/normalizer.py,sha256=4e90d93801877f72f2fab8069db986e79cc749533a068a8b07a9d7c9e37cb9c2,954
38
+ pyobo/obographs.py,sha256=8b4258792727430b6c4f15833116313905abb83511f1fee565091c400323f49d,4345
39
+ pyobo/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
64
40
  pyobo/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
65
- pyobo/sources/signor/download.py,sha256=ae40c954403a95dd33e221b5e2d30e70072e4658d043d48024068b75ac5a833f,1053
66
- pyobo/sources/signor/__init__.py,sha256=6de6ff151aaca2a2d5317b437916405dff5783d50120704ed39b8f53df0d6a32,139
67
- pyobo/sources/signor/signor_complexes.py,sha256=04634cfe41b48eda51fa2eab0d2305e5729e0a59563b7e336762aae0532d064d,3802
68
- pyobo/sources/expasy.py,sha256=25f116d229b5c25858db82add7a037e8c5b405e40dbfd76d3ff67a1f581c8755,11053
69
- pyobo/sources/biogrid.py,sha256=75897a3eddd8a4d0f672f4e5e4b2007a45b22697257fb47526f149513f571fd0,3297
70
- pyobo/sources/geonames/geonames.py,sha256=148ed89cea0b8e84fcc3dd12e865e28143ec9ab986ae6627e210090f8a733a1a,10112
71
- pyobo/sources/geonames/__init__.py,sha256=2508697bc04a0524353fcdefb503126c029aeb1276b6f5fae0e303883e5633bb,177
72
- pyobo/sources/geonames/features.py,sha256=255edf0b5bcd90327dfcfa464955def40f6f5cddb6193593bdf823dd55a1cf28,688
73
- pyobo/sources/geonames/utils.py,sha256=89488531ea3f53c1680258a33285fb361c84686f4c7e9a7312d55b8b252ecdae,4012
74
- pyobo/sources/conso.py,sha256=4786079e79746e192a0c6059cb7e7144e0995f9ec4f621cf943249b336a0b06b,2320
75
- pyobo/sources/slm.py,sha256=986242c3f131a541116d6b452e8f053763607d5844befdf79bae893db85c8f62,4246
76
- pyobo/sources/unimod.py,sha256=4efb3868cca9e83287ea6bfd3a35caf2d6a41b301ce1cfa92215380c87587753,1292
77
- pyobo/sources/civic_gene.py,sha256=01639d80ea1b1656d4f794f5840fc2a3624da0d29de4c252b85e239d84a4830f,3096
78
- pyobo/sources/pombase.py,sha256=f67807c320178c897d00ab05a943d121b15682f902c1cb3c576af53bfbdb3b29,3696
79
- pyobo/sources/pid.py,sha256=3dc2cdc50abe9f61139d7a6608d6b8c8264a6663bd3aef963c1a2d2bda893f18,4460
80
- pyobo/sources/zfin.py,sha256=57d73862574abbd82e017368163ffd7e6f7875eef180a598256503d87344e16e,5339
81
- pyobo/sources/npass.py,sha256=a09682a38dc2206cb6b40b8cc483d3f0f7d24516b3250c39d4f2408ea30fb07f,2742
82
- pyobo/sources/ncbi/__init__.py,sha256=4ae3c1445e191b45fa3ec3dab96be5616c7de5850648e0dd8f20abe58c90ce69,156
83
- pyobo/sources/ncbi/ncbi_gc.py,sha256=b8682bb7b7c5cbb9b912fadef8d2efb896b88dfb5464d0b8bad34354c9e4e6bb,5470
84
- pyobo/sources/ncbi/ncbigene.py,sha256=ce9b8c7b9f434597dccf2c497dd4a521a2330dcf4c0df325018dd2fc664af7b0,5096
41
+ pyobo/reader.py,sha256=6fc2522a89772b718eaa6278e2abc7d5ca536378b537992b34bfe12bcfd10d72,52246
42
+ pyobo/reader_utils.py,sha256=5324154d08576e167d7c28b3660dbaa394e67878acf7ea9930abd0170201460a,4423
43
+ pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
44
+ pyobo/resources/__init__.py,sha256=43d9e293b1e0a4808238dec610aa5bc37cfd64833b345270a063697a9927da70,38
45
+ pyobo/resources/ncbitaxon.py,sha256=92484774b0f45247cb4090b34e3851a5c175dde2da03e472d891c9953968116b,1979
46
+ pyobo/resources/ncbitaxon.tsv.gz,sha256=e37cc78e756deb64c0e3f955e7c5fe1423dd3037cb8350753ef652aff5f2f616,22981954
47
+ pyobo/resources/ro.py,sha256=df0a739171825f42441f261c09104c277016fb098baa242ff18bc965a1217c99,1508
48
+ pyobo/resources/ro.tsv,sha256=62f9412cf00acb6c38221798ccef68c75620e9690774c5733104e29089440a88,26586
49
+ pyobo/resources/so.py,sha256=4bebe643b2fc009134f057c6543209a8d40d68b3d49ae27a1c2e45e2158732b0,1466
50
+ pyobo/resources/so.tsv,sha256=50964a153100bff5eccd861bba7e167fa6f88e8bc38d229cd51591411713cc3c,82068
51
+ pyobo/sources/README.md,sha256=0296f0a48da16d8422c3837a284fd5000a5f3a64d01e47936eb34413121b5f82,901
52
+ pyobo/sources/__init__.py,sha256=94db6754ef36ea969a347c2ae38ff9eddb44dbe177ce06d9f93e5432592bc404,4630
53
+ pyobo/sources/agrovoc.py,sha256=489b1b27b2adc5d2541bd4629a66f609f2dfce92bd78eccfd30c79f608feeace,787
54
+ pyobo/sources/antibodyregistry.py,sha256=3726d4ccf1286e7e73aebd6252f0bc67d72ea83103335bb4eec8d5d540037664,3353
85
55
  pyobo/sources/bigg/__init__.py,sha256=e292beef5071d08bfddcfaa665e714297f4b71aa5b5bdc26ef304df6f85ba582,349
86
- pyobo/sources/bigg/bigg_model.py,sha256=9f8dd98076c2512e8a0669acb5f154bb7f619643ec0e10697f6381fa4005ed80,1287
56
+ pyobo/sources/bigg/bigg_compartment.py,sha256=a454a13221fe58d1fe9ac98e5c319482ede0ae2f0946be6eae2ccdc2abd45eac,3430
87
57
  pyobo/sources/bigg/bigg_metabolite.py,sha256=cece770b13d7ed74d9a553adcba3169714f7bf4c0b8161da3c8e3ed2f9db3e9a,7728
58
+ pyobo/sources/bigg/bigg_model.py,sha256=9f8dd98076c2512e8a0669acb5f154bb7f619643ec0e10697f6381fa4005ed80,1287
88
59
  pyobo/sources/bigg/bigg_reaction.py,sha256=e3948821a7b7d86b43c732ff82917ba754ca55f87ab775201e91787e55413bd2,2459
89
- pyobo/sources/bigg/bigg_compartment.py,sha256=a454a13221fe58d1fe9ac98e5c319482ede0ae2f0946be6eae2ccdc2abd45eac,3430
90
- pyobo/sources/gmt_utils.py,sha256=ccb91b1c62f10543c7c56ee308e1da6535b5d58ccf8fc38df84e107cf4131f11,1327
91
- pyobo/sources/pubchem.py,sha256=953b1cd1d82b489e64c6571a51c517272762fb1b0c7f67c8d84716b1b5bcc535,5153
92
- pyobo/sources/msigdb.py,sha256=e3975d59a15dcc66749436af855db3958914786c50d2341609522dfb50d065dc,6810
93
- pyobo/sources/drugcentral.py,sha256=9fb9bbcbaf0b3c494163dde2e627a6695366ca1c74cb7293efd2419871a610a1,4047
94
- pyobo/sources/agrovoc.py,sha256=489b1b27b2adc5d2541bd4629a66f609f2dfce92bd78eccfd30c79f608feeace,787
95
- pyobo/sources/sgd.py,sha256=9eab044ec6e71742edc1935d7fe0f617673348119942760149a98bca7426b8d7,2073
60
+ pyobo/sources/biogrid.py,sha256=75897a3eddd8a4d0f672f4e5e4b2007a45b22697257fb47526f149513f571fd0,3297
61
+ pyobo/sources/ccle.py,sha256=167d6d6356071f2663ea696a83c2123065181b8a3a5b931e78eee5fca94b9a8b,2924
62
+ pyobo/sources/cgnc.py,sha256=5e5c2aaa325cec1f7bdf9dbe020691a3c95acd79ca7fffc9555e2575f1899754,2299
63
+ pyobo/sources/chebi.py,sha256=f9ffd7c812ce1e80b6b86aaef14cd0dc780095ba80866efe014bded072b44ce0,1202
64
+ pyobo/sources/chembl/__init__.py,sha256=95d2f4af2a6253b9c3254c19c38696d0dc9ae36e35072fd7ed106fcbb3016b3c,195
65
+ pyobo/sources/chembl/chembl_compound.py,sha256=0ecf5ac6e4f5b8efbd2f79509c4a6bffc25d5a8fa60cd589bfd853586f565ec9,1888
66
+ pyobo/sources/chembl/chembl_target.py,sha256=681d2952fc620fc5d6fca81959e9a9346e363931f87c9f101abcacc2ccbf4c9d,5408
67
+ pyobo/sources/civic_gene.py,sha256=01639d80ea1b1656d4f794f5840fc2a3624da0d29de4c252b85e239d84a4830f,3096
68
+ pyobo/sources/clinicaltrials.py,sha256=c24add689328aa31edd9b3fedaf3b514be62f9bca45dce12824ec83d77a66db2,5573
69
+ pyobo/sources/complexportal.py,sha256=78ec7567393ccc33cfd43acadb2392bf5f22f6933a8821cf3741a1f9bc6bb443,7466
70
+ pyobo/sources/conso.py,sha256=4786079e79746e192a0c6059cb7e7144e0995f9ec4f621cf943249b336a0b06b,2320
71
+ pyobo/sources/cpt.py,sha256=6fb85c50b96fbbfc5ae94470a03dfb19cffc540b3c9b16b00255df94bd5ed4b5,1466
72
+ pyobo/sources/credit.py,sha256=20a987b8b15b033772d0de0723d39a500cd35c2336ed04398643dd7d8060dab8,2175
73
+ pyobo/sources/cvx.py,sha256=97d0acbae76bf54ca8d0f35c8c94db346eb610e51cac05688a3d2f2613738551,3595
96
74
  pyobo/sources/depmap.py,sha256=7f05bfd54901e49b6c797c137dbd017e32ef626fb17feb17c1feb368f2a4960f,3585
97
- pyobo/sources/drugbank/drugbank_salt.py,sha256=69b565fe280b7a698cc3850b8b7fc8b5381f09aab7bb26e3aa7b13f5187b0b59,1646
75
+ pyobo/sources/dictybase_gene.py,sha256=78bbde62732e26cd92c2d287ca3e34b678e9f058f2d72157a0f0e8b9bd5d6164,2672
98
76
  pyobo/sources/drugbank/__init__.py,sha256=880b2dbd9419d3525c25e0089b606727ddb7501be2f1a490e2d1158440e8540a,178
99
77
  pyobo/sources/drugbank/drugbank.py,sha256=eb2fc65b2d43ac54c0c81fefb0701b1326411027cf3cfb5eac7534df925cb33c,10899
100
- pyobo/sources/rgd.py,sha256=46020f5933a846a7575ffdd8330ddde8df560d16872c9475f204da59cfdbce4e,5316
101
- pyobo/sources/__init__.py,sha256=94db6754ef36ea969a347c2ae38ff9eddb44dbe177ce06d9f93e5432592bc404,4630
102
- pyobo/sources/pharmgkb/pharmgkb_pathway.py,sha256=3eb66d425b46ff38f3be9f8aeb7291c3e22ac49b4eef25f74e703ff68fb270e7,2042
103
- pyobo/sources/pharmgkb/pharmgkb_gene.py,sha256=04c3c39bc0d900491e8d7d827cd0c17c898f2ea17d4a645544822373647413e1,4049
104
- pyobo/sources/pharmgkb/__init__.py,sha256=25df339dedc6617df9ba4a80ef2b5b620b2425ab900893cc3f4de8e5c3557a20,443
105
- pyobo/sources/pharmgkb/pharmgkb_chemical.py,sha256=698096d364d5cc0c59e659dee428eb4fb5224818fa0b567a30173a9dc9ff229c,3142
106
- pyobo/sources/pharmgkb/pharmgkb_variant.py,sha256=1a1f5f34895446614589cf9f4307bfe9218a316dee21018a4610b4b6fb163ad0,2873
107
- pyobo/sources/pharmgkb/utils.py,sha256=485b51020fd4c68bb96297ea3d3b05f707b4c0132c6a5c326dd5009b9652f9c2,2593
108
- pyobo/sources/pharmgkb/pharmgkb_disease.py,sha256=b68a85adb653b67add77ce54e9be9a41d47d683ef565fdbe13598b3fbf033f34,2554
109
- pyobo/sources/cpt.py,sha256=6fb85c50b96fbbfc5ae94470a03dfb19cffc540b3c9b16b00255df94bd5ed4b5,1466
110
- pyobo/sources/pathbank.py,sha256=496e2611d5825f6319606d55269f322c4cf206efce99a653b521ab7a57680ed4,5387
111
- pyobo/sources/gwascentral/gwascentral_phenotype.py,sha256=4af302177b18a9cdc5e6735709fefa033221353ebdf191c79d3a4ed0819fb7ca,1788
78
+ pyobo/sources/drugbank/drugbank_salt.py,sha256=69b565fe280b7a698cc3850b8b7fc8b5381f09aab7bb26e3aa7b13f5187b0b59,1646
79
+ pyobo/sources/drugcentral.py,sha256=9fb9bbcbaf0b3c494163dde2e627a6695366ca1c74cb7293efd2419871a610a1,4047
80
+ pyobo/sources/expasy.py,sha256=25f116d229b5c25858db82add7a037e8c5b405e40dbfd76d3ff67a1f581c8755,11053
81
+ pyobo/sources/famplex.py,sha256=a82be3e9607feaeab64471d53c8686872aa47f5b9b23a5eb3bc0daf98b5af7a4,5628
82
+ pyobo/sources/flybase.py,sha256=8144b7f4d17fa9cef6dd1d9201b85062a3e0e943a2c0ac0f5e15d0d49c02ebc4,5666
83
+ pyobo/sources/gard.py,sha256=f6846fa4d76df78714a92605e76f4f173f500af178b0ff8905f856909ae81197,1768
84
+ pyobo/sources/geonames/__init__.py,sha256=2508697bc04a0524353fcdefb503126c029aeb1276b6f5fae0e303883e5633bb,177
85
+ pyobo/sources/geonames/features.py,sha256=255edf0b5bcd90327dfcfa464955def40f6f5cddb6193593bdf823dd55a1cf28,688
86
+ pyobo/sources/geonames/geonames.py,sha256=148ed89cea0b8e84fcc3dd12e865e28143ec9ab986ae6627e210090f8a733a1a,10112
87
+ pyobo/sources/geonames/utils.py,sha256=89488531ea3f53c1680258a33285fb361c84686f4c7e9a7312d55b8b252ecdae,4012
88
+ pyobo/sources/gmt_utils.py,sha256=ccb91b1c62f10543c7c56ee308e1da6535b5d58ccf8fc38df84e107cf4131f11,1327
89
+ pyobo/sources/go.py,sha256=cd72c37dca9b894eb43371540adab37cfcd8a07952be4533000f19b4f110c376,1530
90
+ pyobo/sources/gtdb.py,sha256=ab420486568c8ad1d6a39200cb6979f2e5cc2d67a40addeb2303a60ecb031138,5221
112
91
  pyobo/sources/gwascentral/__init__.py,sha256=55d1c8801551fb7e81ee02ee851e175795179ff120359d3e8b583d36384e8d8d,231
92
+ pyobo/sources/gwascentral/gwascentral_phenotype.py,sha256=4af302177b18a9cdc5e6735709fefa033221353ebdf191c79d3a4ed0819fb7ca,1788
113
93
  pyobo/sources/gwascentral/gwascentral_study.py,sha256=bddb3b20e2374cc3ff14601aba36c17466897d46f1d086bf75ecf62992263bd9,2657
114
- pyobo/sources/omim_ps.py,sha256=692cb56e44090b2c600d87c0ef0a71a13b77750faa3e40886385f9dbf7a51c76,1432
115
- pyobo/sources/selventa/schem.py,sha256=bea37f6bf34b7ac863fb6751b997a57ce2c943977253766085f49122af441550,1162
116
- pyobo/sources/selventa/sdis.py,sha256=b3169dde3868d74ab6a12ce3c820e419605884ac2ccbf8da4bec0f24ac1c2e75,1287
117
- pyobo/sources/selventa/__init__.py,sha256=7082039562fdce72f6af4699209dabd4537734cf62a3be30f877b67a0cc9c17f,254
118
- pyobo/sources/selventa/scomp.py,sha256=9ec86c90b41e5eecdfe6defd49326c54a260dd1f34097dc3b89054ac487049b7,1531
119
- pyobo/sources/selventa/sfam.py,sha256=127f2d0327e4bfd8a60356682d426f41080672d7ef4c6b84a1bef0968671197b,1448
120
- pyobo/sources/mesh.py,sha256=39a11c96a65d2be65081caea7664d7e1c03980a71484c83ff03913ed2b53de2d,13245
121
- pyobo/sources/mirbase/mirbase_constants.py,sha256=e438dcc17fc5452cc561b4dfe74caf90f6a64881fbd11c3723cabe0ecd331d5b,1998
122
- pyobo/sources/mirbase/__init__.py,sha256=f3f6043634b2e79fc22a419d19303b523baff1db7e61f87dd15fa1b778f0a659,252
123
- pyobo/sources/mirbase/mirbase_family.py,sha256=4c858a861174a67e9d8504d380b838958ac92adbbe20b96dac71590f4a9e65be,1974
124
- pyobo/sources/mirbase/mirbase_mature.py,sha256=263eb9c55aad8eabb3a991938bc7273262ddc9f51f9ad84cfe46b5499dbeaf31,1302
125
- pyobo/sources/mirbase/mirbase.py,sha256=f61b8bd0f58055c10393ee2e9d9c3e1889f2104d42fc55f047137ae471b7c717,6387
126
- pyobo/sources/icd/icd11.py,sha256=5b6e59f8028cfbd41f860151d1164514be2653a50078c0fc8748c20b815ee11b,4867
94
+ pyobo/sources/hgnc/__init__.py,sha256=d5084cec674febf03108ccda073da4dd244b9034ce912da15213cc2c44d21963,157
95
+ pyobo/sources/hgnc/hgnc.py,sha256=f05121570f4e4b06f4d70bbf6950363349a726de22c6f2ed5e3e43411591bf95,16377
96
+ pyobo/sources/hgnc/hgncgenefamily.py,sha256=e3e8d0b750d59a7da3d0ac2b100e248e8dad51af54c045405a12704e36db20cd,3710
127
97
  pyobo/sources/icd/__init__.py,sha256=0eb65597be8ff1eb2c278b6564f71ab8556b5d590821907ab09d1ce8a9ba4962,142
128
98
  pyobo/sources/icd/icd10.py,sha256=61ab55ce0af6dbd27f59e25c6b8150007a96af1edcecde1f1db85bd5c4354de5,2587
99
+ pyobo/sources/icd/icd11.py,sha256=5b6e59f8028cfbd41f860151d1164514be2653a50078c0fc8748c20b815ee11b,4867
129
100
  pyobo/sources/icd/icd_utils.py,sha256=8fbc63228bd61b4f86c47eee5d6ad76433b52d7132a3fe0275680f4874c85c96,4525
130
- pyobo/sources/gtdb.py,sha256=ab420486568c8ad1d6a39200cb6979f2e5cc2d67a40addeb2303a60ecb031138,5221
131
- pyobo/sources/kegg/pathway.py,sha256=82333defe9d69a0a493b69368112d61d922195d333d081ed3679b355bfb235af,5892
101
+ pyobo/sources/interpro.py,sha256=d6d99771293946b8228fbd35183aa845b77f7c46af1e5f3f03a6887f92ba10b1,4809
102
+ pyobo/sources/itis.py,sha256=6b1d54c40ece2a97176c497aaa3113fbf78ea32845e918fc76de4a1bf254dbbf,2876
132
103
  pyobo/sources/kegg/__init__.py,sha256=8553f4b6ec15a6234c8a416ffdb34faf3b98bfe1c0d7f6cf742bcdc7e7e6e458,219
133
104
  pyobo/sources/kegg/api.py,sha256=b33bb6e604b7103e6f51c287aa1e9723a839119cf9d950d2fd4148688bd4e49c,4191
134
105
  pyobo/sources/kegg/genes.py,sha256=c74a156d1612e7150f507858ba80288ec20fc9f8c08bcb7b45faf715aa6d770d,3558
135
106
  pyobo/sources/kegg/genome.py,sha256=32aedb662b637c96c81e4da0da09d2244a99963001465aa1a572035e5386cc7a,4161
136
- pyobo/sources/hgnc/__init__.py,sha256=d5084cec674febf03108ccda073da4dd244b9034ce912da15213cc2c44d21963,157
137
- pyobo/sources/hgnc/hgnc.py,sha256=f05121570f4e4b06f4d70bbf6950363349a726de22c6f2ed5e3e43411591bf95,16377
138
- pyobo/sources/hgnc/hgncgenefamily.py,sha256=e3e8d0b750d59a7da3d0ac2b100e248e8dad51af54c045405a12704e36db20cd,3710
139
- pyobo/sources/README.md,sha256=0296f0a48da16d8422c3837a284fd5000a5f3a64d01e47936eb34413121b5f82,901
140
- pyobo/sources/antibodyregistry.py,sha256=3726d4ccf1286e7e73aebd6252f0bc67d72ea83103335bb4eec8d5d540037664,3353
107
+ pyobo/sources/kegg/pathway.py,sha256=82333defe9d69a0a493b69368112d61d922195d333d081ed3679b355bfb235af,5892
108
+ pyobo/sources/mesh.py,sha256=39a11c96a65d2be65081caea7664d7e1c03980a71484c83ff03913ed2b53de2d,13245
141
109
  pyobo/sources/mgi.py,sha256=7d40f86d4bb07bc93e1f8b45e7856f0f25314fec5e04c6548ff7e5611b1fa5cf,5541
142
- pyobo/sources/utils.py,sha256=98120062c2dba0007ac3ac0f4d3bf52c3401cd742ee7c4d496734624b589c31a,1118
110
+ pyobo/sources/mirbase/__init__.py,sha256=f3f6043634b2e79fc22a419d19303b523baff1db7e61f87dd15fa1b778f0a659,252
111
+ pyobo/sources/mirbase/mirbase.py,sha256=f61b8bd0f58055c10393ee2e9d9c3e1889f2104d42fc55f047137ae471b7c717,6387
112
+ pyobo/sources/mirbase/mirbase_constants.py,sha256=e438dcc17fc5452cc561b4dfe74caf90f6a64881fbd11c3723cabe0ecd331d5b,1998
113
+ pyobo/sources/mirbase/mirbase_family.py,sha256=4c858a861174a67e9d8504d380b838958ac92adbbe20b96dac71590f4a9e65be,1974
114
+ pyobo/sources/mirbase/mirbase_mature.py,sha256=263eb9c55aad8eabb3a991938bc7273262ddc9f51f9ad84cfe46b5499dbeaf31,1302
115
+ pyobo/sources/msigdb.py,sha256=e3975d59a15dcc66749436af855db3958914786c50d2341609522dfb50d065dc,6810
116
+ pyobo/sources/ncbi/__init__.py,sha256=4ae3c1445e191b45fa3ec3dab96be5616c7de5850648e0dd8f20abe58c90ce69,156
117
+ pyobo/sources/ncbi/ncbi_gc.py,sha256=b8682bb7b7c5cbb9b912fadef8d2efb896b88dfb5464d0b8bad34354c9e4e6bb,5470
118
+ pyobo/sources/ncbi/ncbigene.py,sha256=ce9b8c7b9f434597dccf2c497dd4a521a2330dcf4c0df325018dd2fc664af7b0,5096
119
+ pyobo/sources/nih_reporter.py,sha256=cac85ef3050695cb97c94e81caa409bc252bebd49354485ac03e409a69bd9094,1612
143
120
  pyobo/sources/nlm/__init__.py,sha256=74b7831ddabf96fb72d6984972a33e7b0f152843d4f3c8b210cc202e4227c6c7,178
144
- pyobo/sources/nlm/nlm_publisher.py,sha256=96be828e8d8c76569ddc94e49f772b69f58a2f595c1d7dad16e29d9c8a0a6b9c,984
145
121
  pyobo/sources/nlm/nlm_catalog.py,sha256=a205c3878cf2471ebdfd86c682e1f4c96114e7edd2bc79cb06f132c6d800e990,1339
122
+ pyobo/sources/nlm/nlm_publisher.py,sha256=96be828e8d8c76569ddc94e49f772b69f58a2f595c1d7dad16e29d9c8a0a6b9c,984
146
123
  pyobo/sources/nlm/utils.py,sha256=6c4057cf3d9f8e39c515c8ebabfabc99faf57f4fd188a66843b1f5f20a55e070,4861
147
- pyobo/sources/nih_reporter.py,sha256=cac85ef3050695cb97c94e81caa409bc252bebd49354485ac03e409a69bd9094,1612
148
- pyobo/sources/famplex.py,sha256=a82be3e9607feaeab64471d53c8686872aa47f5b9b23a5eb3bc0daf98b5af7a4,5628
149
- pyobo/sources/go.py,sha256=cd72c37dca9b894eb43371540adab37cfcd8a07952be4533000f19b4f110c376,1530
150
- pyobo/sources/dictybase_gene.py,sha256=78bbde62732e26cd92c2d287ca3e34b678e9f058f2d72157a0f0e8b9bd5d6164,2672
151
- pyobo/sources/gard.py,sha256=f6846fa4d76df78714a92605e76f4f173f500af178b0ff8905f856909ae81197,1768
152
- pyobo/sources/clinicaltrials.py,sha256=c24add689328aa31edd9b3fedaf3b514be62f9bca45dce12824ec83d77a66db2,5573
153
- pyobo/sources/interpro.py,sha256=d6d99771293946b8228fbd35183aa845b77f7c46af1e5f3f03a6887f92ba10b1,4809
154
- pyobo/sources/ccle.py,sha256=167d6d6356071f2663ea696a83c2123065181b8a3a5b931e78eee5fca94b9a8b,2924
155
- pyobo/sources/chembl/chembl_target.py,sha256=681d2952fc620fc5d6fca81959e9a9346e363931f87c9f101abcacc2ccbf4c9d,5408
156
- pyobo/sources/chembl/__init__.py,sha256=95d2f4af2a6253b9c3254c19c38696d0dc9ae36e35072fd7ed106fcbb3016b3c,195
157
- pyobo/sources/chembl/chembl_compound.py,sha256=0ecf5ac6e4f5b8efbd2f79509c4a6bffc25d5a8fa60cd589bfd853586f565ec9,1888
158
- pyobo/sources/uniprot/uniprot.py,sha256=dfa7eb88c59df10cdf1879d6bac2e60638a4d73b19f3a0b4767d499209336f46,6317
159
- pyobo/sources/uniprot/__init__.py,sha256=0b475fdba434a9f49c080f7d23846497d2f6a1e1a839d3fcfa88a119c9b0a6d1,200
160
- pyobo/sources/uniprot/uniprot_ptm.py,sha256=a130397ef41e135d0a4c7a624f0d379c776d0e13f869871690f4e1f8cc4d3b9d,2192
161
- pyobo/sources/reactome.py,sha256=b98ca4f6efbdff59215a1e44b02d96247dba680e593a4829c87545fc922d4134,5612
162
- pyobo/sources/pfam/pfam_clan.py,sha256=f2d81d273deb28f0492ae54cf5350b365baa3fcfde289d6ae332219af7cc56ac,1205
124
+ pyobo/sources/npass.py,sha256=a09682a38dc2206cb6b40b8cc483d3f0f7d24516b3250c39d4f2408ea30fb07f,2742
125
+ pyobo/sources/omim_ps.py,sha256=692cb56e44090b2c600d87c0ef0a71a13b77750faa3e40886385f9dbf7a51c76,1432
126
+ pyobo/sources/pathbank.py,sha256=496e2611d5825f6319606d55269f322c4cf206efce99a653b521ab7a57680ed4,5387
163
127
  pyobo/sources/pfam/__init__.py,sha256=03acb66f67b42c28abe2c020e5308be580e2e9c56197d464de5a05e5505ac5e3,150
164
128
  pyobo/sources/pfam/pfam.py,sha256=99d6d1e8093f9b23699f05d0b2c1a1e87318feebd29343873397bc4697ce1b47,1718
129
+ pyobo/sources/pfam/pfam_clan.py,sha256=f2d81d273deb28f0492ae54cf5350b365baa3fcfde289d6ae332219af7cc56ac,1205
130
+ pyobo/sources/pharmgkb/__init__.py,sha256=25df339dedc6617df9ba4a80ef2b5b620b2425ab900893cc3f4de8e5c3557a20,443
131
+ pyobo/sources/pharmgkb/pharmgkb_chemical.py,sha256=698096d364d5cc0c59e659dee428eb4fb5224818fa0b567a30173a9dc9ff229c,3142
132
+ pyobo/sources/pharmgkb/pharmgkb_disease.py,sha256=b68a85adb653b67add77ce54e9be9a41d47d683ef565fdbe13598b3fbf033f34,2554
133
+ pyobo/sources/pharmgkb/pharmgkb_gene.py,sha256=04c3c39bc0d900491e8d7d827cd0c17c898f2ea17d4a645544822373647413e1,4049
134
+ pyobo/sources/pharmgkb/pharmgkb_pathway.py,sha256=3eb66d425b46ff38f3be9f8aeb7291c3e22ac49b4eef25f74e703ff68fb270e7,2042
135
+ pyobo/sources/pharmgkb/pharmgkb_variant.py,sha256=1a1f5f34895446614589cf9f4307bfe9218a316dee21018a4610b4b6fb163ad0,2873
136
+ pyobo/sources/pharmgkb/utils.py,sha256=485b51020fd4c68bb96297ea3d3b05f707b4c0132c6a5c326dd5009b9652f9c2,2593
137
+ pyobo/sources/pid.py,sha256=3dc2cdc50abe9f61139d7a6608d6b8c8264a6663bd3aef963c1a2d2bda893f18,4460
138
+ pyobo/sources/pombase.py,sha256=f67807c320178c897d00ab05a943d121b15682f902c1cb3c576af53bfbdb3b29,3696
139
+ pyobo/sources/pubchem.py,sha256=953b1cd1d82b489e64c6571a51c517272762fb1b0c7f67c8d84716b1b5bcc535,5153
140
+ pyobo/sources/reactome.py,sha256=b98ca4f6efbdff59215a1e44b02d96247dba680e593a4829c87545fc922d4134,5612
141
+ pyobo/sources/rgd.py,sha256=46020f5933a846a7575ffdd8330ddde8df560d16872c9475f204da59cfdbce4e,5316
165
142
  pyobo/sources/rhea.py,sha256=75b872549d72a00428c685a9e3b38a7a02c098c87aaa87beeff0da7c90de5ab9,8164
166
- pyobo/sources/wikipathways.py,sha256=ae9b7b955580db4d27ebe863cf12bfcd07b1af660678666829dab662645aa63e,2637
167
- pyobo/sources/cvx.py,sha256=97d0acbae76bf54ca8d0f35c8c94db346eb610e51cac05688a3d2f2613738551,3595
168
- pyobo/sources/itis.py,sha256=6b1d54c40ece2a97176c497aaa3113fbf78ea32845e918fc76de4a1bf254dbbf,2876
143
+ pyobo/sources/ror.py,sha256=212fca52d31e2a002776b6cb8e17282bc8a5a7e8ce7a20f0cc64f2e51f5c2309,8882
144
+ pyobo/sources/selventa/__init__.py,sha256=7082039562fdce72f6af4699209dabd4537734cf62a3be30f877b67a0cc9c17f,254
145
+ pyobo/sources/selventa/schem.py,sha256=bea37f6bf34b7ac863fb6751b997a57ce2c943977253766085f49122af441550,1162
146
+ pyobo/sources/selventa/scomp.py,sha256=9ec86c90b41e5eecdfe6defd49326c54a260dd1f34097dc3b89054ac487049b7,1531
147
+ pyobo/sources/selventa/sdis.py,sha256=b3169dde3868d74ab6a12ce3c820e419605884ac2ccbf8da4bec0f24ac1c2e75,1287
148
+ pyobo/sources/selventa/sfam.py,sha256=127f2d0327e4bfd8a60356682d426f41080672d7ef4c6b84a1bef0968671197b,1448
149
+ pyobo/sources/sgd.py,sha256=9eab044ec6e71742edc1935d7fe0f617673348119942760149a98bca7426b8d7,2073
150
+ pyobo/sources/signor/__init__.py,sha256=6de6ff151aaca2a2d5317b437916405dff5783d50120704ed39b8f53df0d6a32,139
151
+ pyobo/sources/signor/download.py,sha256=ae40c954403a95dd33e221b5e2d30e70072e4658d043d48024068b75ac5a833f,1053
152
+ pyobo/sources/signor/signor_complexes.py,sha256=04634cfe41b48eda51fa2eab0d2305e5729e0a59563b7e336762aae0532d064d,3802
153
+ pyobo/sources/slm.py,sha256=986242c3f131a541116d6b452e8f053763607d5844befdf79bae893db85c8f62,4246
154
+ pyobo/sources/umls/__init__.py,sha256=10d80d5d02a1cdef73cb1b178e49fbdfe05daa6767b4be19cb5a91e36183b4ff,141
155
+ pyobo/sources/umls/__main__.py,sha256=358e97a9eb60a5177f2cf9bde554d7d8bdeb241ffb877250b6d8270c9f5c1613,108
156
+ pyobo/sources/umls/get_synonym_types.py,sha256=fd5266a8217b628fca6bef678e579dba3251445bc0f474d0f6f6c92c80bd7bb2,1724
169
157
  pyobo/sources/umls/sty.py,sha256=80a4fba019e163606f4fcebbf2373b6036ce2c839e62f371745356e5d31f7e54,1479
170
158
  pyobo/sources/umls/synonym_types.tsv,sha256=f133bab18eff4073470462d29ea3a9a6dca42223d4cd77171d7696988f48745a,8550
171
- pyobo/sources/umls/__init__.py,sha256=10d80d5d02a1cdef73cb1b178e49fbdfe05daa6767b4be19cb5a91e36183b4ff,141
172
159
  pyobo/sources/umls/umls.py,sha256=5bc2f3eb8f5a8abb605a21cfbc44b4e137b2c3c24c0a70825ec4a6d48dde6025,4287
173
- pyobo/sources/umls/get_synonym_types.py,sha256=fd5266a8217b628fca6bef678e579dba3251445bc0f474d0f6f6c92c80bd7bb2,1724
174
- pyobo/sources/umls/__main__.py,sha256=358e97a9eb60a5177f2cf9bde554d7d8bdeb241ffb877250b6d8270c9f5c1613,108
175
- pyobo/sources/complexportal.py,sha256=78ec7567393ccc33cfd43acadb2392bf5f22f6933a8821cf3741a1f9bc6bb443,7466
176
- pyobo/sources/credit.py,sha256=7643164ed0aa81333dd2415af23ec170fc94efc89b1656ea2d7f66551b6aff9a,1795
177
- pyobo/sources/chebi.py,sha256=f9ffd7c812ce1e80b6b86aaef14cd0dc780095ba80866efe014bded072b44ce0,1202
178
- pyobo/sources/ror.py,sha256=212fca52d31e2a002776b6cb8e17282bc8a5a7e8ce7a20f0cc64f2e51f5c2309,8882
179
- pyobo/sources/flybase.py,sha256=8144b7f4d17fa9cef6dd1d9201b85062a3e0e943a2c0ac0f5e15d0d49c02ebc4,5666
180
- pyobo/sources/cgnc.py,sha256=5e5c2aaa325cec1f7bdf9dbe020691a3c95acd79ca7fffc9555e2575f1899754,2299
181
- pyobo/api/species.py,sha256=631cc978295fb8a23ea6360ba6ee7bf7b8dd0dec93917a6340381d99cf4c2b0a,2376
182
- pyobo/api/metadata.py,sha256=b2d25a897fe5ef1d11d55efb4cdc07bcfb6892e67e128a9bf473112fbd0d896b,1029
183
- pyobo/api/combine.py,sha256=ed3f108fc5b5c164352a0289b0ed641511d9c6441cadf28cd6106b86a1ec1245,1106
184
- pyobo/api/properties.py,sha256=6d85af1ebd5b7f4c5d232323faab9d8f8a11a419eab0a86eca36052b22b2f778,6914
185
- pyobo/api/relations.py,sha256=6dfda59d8ae2c3addb816d7dad2b97856916c6f2e6114f7a774bfcaff1c25747,5859
186
- pyobo/api/__init__.py,sha256=259870a4519a6baa5df1180378837e67c688e8ecbe46e9a3d4a90e6435c79e1d,2955
187
- pyobo/api/edges.py,sha256=4849b6809c7a2e83a48571a3d75578dae2e0e0589d15af6326a5bd1f39e57f09,1974
188
- pyobo/api/hierarchy.py,sha256=37f27381f08a3c859adb4a1d46132fa60889a5ccce8867620db2e4353aa5a69f,10314
189
- pyobo/api/names.py,sha256=2f620187285c1fccbeac23708d624bc374ec1e9d6abce65ebf5eb4f9c63070b8,10673
190
- pyobo/api/utils.py,sha256=ae8d2274e48d129a0d3520e48ba462af066afff928c9fcd231f569c4b322bcf5,5429
191
- pyobo/api/typedefs.py,sha256=1d3ba2d2497f5442f18238b4bdf06bf8d046df3aeba4253cb66b9039258ae9fc,1262
192
- pyobo/api/xrefs.py,sha256=9d62cbb761b36957e780d0546ce3154a33a90ae6be23bbbedadba8c735c6aab0,5242
193
- pyobo/api/alts.py,sha256=478b3162574616f2827bd73107f80f5dfdaf5971eaf6c6813109109dba89e522,3032
194
- pyobo/__main__.py,sha256=70e610d8e10bc45fbd4fa9ee67dc672d2bbd6cb1e4e9e8a7aec4a8cfb11c0fd3,83
195
- pyobo/reader_utils.py,sha256=5324154d08576e167d7c28b3660dbaa394e67878acf7ea9930abd0170201460a,4423
196
- pyobo/mocks.py,sha256=8f9e392bd3ff0cfb0306e6070eb8724cb8e694fa0d951744b5c4652e15e56d72,2440
197
- pyobo-0.12.1.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
198
- pyobo-0.12.1.dist-info/WHEEL,sha256=1c77bbda0b527f376a68ced20cbc1aac3efc7bc4d7c10cc4323a905ef79ae8db,78
199
- pyobo-0.12.1.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
200
- pyobo-0.12.1.dist-info/METADATA,sha256=891eda0af949aecf1dc5064aaba32edf807fc6ec4d43d7eebd8b0af65dc3b388,22299
201
- pyobo-0.12.1.dist-info/RECORD,,
160
+ pyobo/sources/unimod.py,sha256=4efb3868cca9e83287ea6bfd3a35caf2d6a41b301ce1cfa92215380c87587753,1292
161
+ pyobo/sources/uniprot/__init__.py,sha256=0b475fdba434a9f49c080f7d23846497d2f6a1e1a839d3fcfa88a119c9b0a6d1,200
162
+ pyobo/sources/uniprot/uniprot.py,sha256=dfa7eb88c59df10cdf1879d6bac2e60638a4d73b19f3a0b4767d499209336f46,6317
163
+ pyobo/sources/uniprot/uniprot_ptm.py,sha256=a130397ef41e135d0a4c7a624f0d379c776d0e13f869871690f4e1f8cc4d3b9d,2192
164
+ pyobo/sources/utils.py,sha256=98120062c2dba0007ac3ac0f4d3bf52c3401cd742ee7c4d496734624b589c31a,1118
165
+ pyobo/sources/wikipathways.py,sha256=ae9b7b955580db4d27ebe863cf12bfcd07b1af660678666829dab662645aa63e,2637
166
+ pyobo/sources/zfin.py,sha256=57d73862574abbd82e017368163ffd7e6f7875eef180a598256503d87344e16e,5339
167
+ pyobo/ssg/__init__.py,sha256=8500042e3156fe3acd5fd5546b0ed52038d842150389c512b3e99267302f152a,5224
168
+ pyobo/ssg/base.html,sha256=fef95d5026be80bd984cd63a1a002ec4d4f74e06840f9f39bc5feaed3aeb8d8b,2844
169
+ pyobo/ssg/index.html,sha256=da62c16a198f7ad2468599c5d7e4da4d7b81e02a18a25a59da741a579746e676,4346
170
+ pyobo/ssg/term.html,sha256=b522c82774980d37ad2bd8361280cacaee1a1dc855a351145e4fda62119e38aa,3869
171
+ pyobo/ssg/typedef.html,sha256=2ab76acc1eb18edebcf5b1b7dc3dba00bfb5d49aef36e124a3134d23e106f938,2038
172
+ pyobo/struct/__init__.py,sha256=fb813dfa7de27f195c07cd5311de78403b03dfbf0a183995c8fb448033ace311,1444
173
+ pyobo/struct/functional/__init__.py,sha256=d536edb7fe86a1aad19607df3dea62b49dd0b4bb2b30f31b8431a842700a499e,32
174
+ pyobo/struct/functional/dsl.py,sha256=780b4e5616b8dc823cee610945a95ffa109aa43287992dd4dd51511c461f96fb,101183
175
+ pyobo/struct/functional/macros.py,sha256=cc654f131fa685d4afc87d8c7b5e8565da1b789dd5d73045a77b3e033a8ced52,13785
176
+ pyobo/struct/functional/obo_to_functional.py,sha256=785c46fdb00dc45f3903f67ad24ae4fcb6d187ce48208373fc9d42833a85f6b8,13273
177
+ pyobo/struct/functional/ontology.py,sha256=bc610a206c5f502cc658cbf7dcaa9caeb112a596ab1cb07fcbd571c8a6da2894,9331
178
+ pyobo/struct/functional/utils.py,sha256=73e5c6d9227b0a162dcfb294dcad05f93ea870c8d87af7a2d16c6591f9249ad1,3487
179
+ pyobo/struct/reference.py,sha256=4fc7d3b665cd18c8dfbbb2b8b49de4bc30a8e101d14ff26bf5f88e9c562bc2d3,11735
180
+ pyobo/struct/struct.py,sha256=29b77204d903a948aff74f93aa043e5421cc932c22a893e70dbfd3f27b911fb7,89480
181
+ pyobo/struct/struct_utils.py,sha256=7b8bfd7a322f34cf1436b83c8eab983944651ba467923045bf61ecc245800d2c,39164
182
+ pyobo/struct/typedef.py,sha256=fd94429e28efcdf7bbeba4b1729fa66af5f64c34e49437d82e4b3e5a457d064d,12099
183
+ pyobo/struct/utils.py,sha256=ce4a4e138d894087e4374adce6a34434ad375482a691fff9eed1e88cc24aef56,906
184
+ pyobo/struct/vocabulary.py,sha256=56e0f6770cf7da2d6f1221e3fc8261f1c07dc8358a1f3dfb487894a25b1ed133,4335
185
+ pyobo/utils/__init__.py,sha256=08035263cbc6abfeaff2b5a159121d9e4f96a392c0d91f568e0d67a9b5aa2cec,17
186
+ pyobo/utils/cache.py,sha256=136ccd03b82afd534699a36bad129e5f3e73aba5c3184fb93d5a24af30d99227,3098
187
+ pyobo/utils/io.py,sha256=fa0cb5a8633a6c9fb95eb2f74e08fbf69acc4fc229b89c18dd233921b80378a9,5100
188
+ pyobo/utils/iter.py,sha256=ad845b6da1491f131a134c94fab419a026a0608aed7afd3db98d26c4591fe736,1524
189
+ pyobo/utils/misc.py,sha256=99d1f6e88b48d3f0cdbd7fff8a908556bf949278fcf0ef639e5cc8a421d0f4db,2684
190
+ pyobo/utils/ndex_utils.py,sha256=128902592d345ab93fe32f2575e42e53269a0bac8dcc18370da81497e2767336,2326
191
+ pyobo/utils/path.py,sha256=cc37f10de8e0ef90a6063cc2b1c5d1b0993e41649536f04bfddc892d61a3bc4f,3398
192
+ pyobo/version.py,sha256=d76710b61a3b9c38c2f582b5788dc0c462786829754363c869633e386dccebd6,926
193
+ pyobo-0.12.2.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
194
+ pyobo-0.12.2.dist-info/WHEEL,sha256=ec89e25a684ec3ad8fb2a9be806e47666a27f7dcdcf9b55bff3f1d3ed5e60e0a,78
195
+ pyobo-0.12.2.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
196
+ pyobo-0.12.2.dist-info/METADATA,sha256=37f00c716dd218308afda6c1d5543267fae9c0dab78c5e17879388a6491b9a36,21626
197
+ pyobo-0.12.2.dist-info/RECORD,,
@@ -1,4 +1,4 @@
1
1
  Wheel-Version: 1.0
2
- Generator: uv 0.7.2
2
+ Generator: uv 0.7.8
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any