pyobo 0.12.9__py3-none-any.whl → 0.12.11__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.
Files changed (41) hide show
  1. pyobo/__init__.py +6 -0
  2. pyobo/api/__init__.py +11 -1
  3. pyobo/api/alts.py +18 -4
  4. pyobo/api/embedding.py +108 -9
  5. pyobo/api/names.py +28 -6
  6. pyobo/api/xrefs.py +26 -1
  7. pyobo/constants.py +38 -2
  8. pyobo/getters.py +8 -3
  9. pyobo/ner/api.py +14 -10
  10. pyobo/ner/scispacy_utils.py +15 -21
  11. pyobo/sources/__init__.py +2 -0
  12. pyobo/sources/antibodyregistry.py +3 -3
  13. pyobo/sources/bigg/bigg_compartment.py +1 -1
  14. pyobo/sources/complexportal.py +3 -3
  15. pyobo/sources/conso.py +3 -3
  16. pyobo/sources/famplex.py +3 -3
  17. pyobo/sources/goldbook.py +86 -0
  18. pyobo/sources/hgnc/hgnc.py +157 -96
  19. pyobo/sources/hgnc/hgncgenefamily.py +14 -13
  20. pyobo/sources/msigdb.py +3 -3
  21. pyobo/sources/omim_ps.py +8 -2
  22. pyobo/sources/reactome.py +3 -3
  23. pyobo/sources/rgd.py +7 -11
  24. pyobo/sources/slm.py +3 -3
  25. pyobo/sources/uniprot/uniprot.py +3 -3
  26. pyobo/sources/wikipathways.py +7 -2
  27. pyobo/struct/__init__.py +2 -2
  28. pyobo/struct/functional/macros.py +1 -1
  29. pyobo/struct/functional/obo_to_functional.py +7 -3
  30. pyobo/struct/obo/reader.py +1 -1
  31. pyobo/struct/struct.py +88 -18
  32. pyobo/struct/struct_utils.py +19 -5
  33. pyobo/struct/typedef.py +16 -3
  34. pyobo/struct/vocabulary.py +4 -3
  35. pyobo/utils/path.py +5 -4
  36. pyobo/version.py +1 -1
  37. {pyobo-0.12.9.dist-info → pyobo-0.12.11.dist-info}/METADATA +8 -1
  38. {pyobo-0.12.9.dist-info → pyobo-0.12.11.dist-info}/RECORD +41 -40
  39. {pyobo-0.12.9.dist-info → pyobo-0.12.11.dist-info}/WHEEL +0 -0
  40. {pyobo-0.12.9.dist-info → pyobo-0.12.11.dist-info}/entry_points.txt +0 -0
  41. {pyobo-0.12.9.dist-info → pyobo-0.12.11.dist-info}/licenses/LICENSE +0 -0
pyobo/utils/path.py CHANGED
@@ -84,7 +84,7 @@ def ensure_df(
84
84
  dtype=str,
85
85
  verify: bool = True,
86
86
  backend: Literal["requests", "urllib"] | None = None,
87
- **kwargs,
87
+ **kwargs: Any,
88
88
  ) -> pd.DataFrame:
89
89
  """Download a file and open as a dataframe."""
90
90
  _path = ensure_path(
@@ -107,12 +107,11 @@ def ensure_json(
107
107
  version: VersionHint = None,
108
108
  name: str | None = None,
109
109
  force: bool = False,
110
- sep: str = "\t",
111
110
  dtype=str,
112
111
  verify: bool = True,
113
112
  backend: Literal["requests", "urllib"] | None = None,
114
- **kwargs,
115
- ) -> pd.DataFrame:
113
+ **kwargs: Any,
114
+ ) -> Any:
116
115
  """Download a file and open as JSON."""
117
116
  _path = ensure_path(
118
117
  prefix,
@@ -151,6 +150,8 @@ class CacheArtifact(enum.Enum):
151
150
  prefixes = "prefixes.json"
152
151
  metadata = "metadata.json"
153
152
 
153
+ embeddings = "embeddings.tsv.gz"
154
+
154
155
 
155
156
  def get_cache_path(
156
157
  ontology: str,
pyobo/version.py CHANGED
@@ -12,7 +12,7 @@ __all__ = [
12
12
  "get_version",
13
13
  ]
14
14
 
15
- VERSION = "0.12.9"
15
+ VERSION = "0.12.11"
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: 0.12.9
3
+ Version: 0.12.11
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
@@ -55,10 +55,15 @@ Requires-Dist: nih-reporter-downloader>=0.0.1
55
55
  Requires-Dist: typing-extensions
56
56
  Requires-Dist: rdflib
57
57
  Requires-Dist: obographs>=0.0.8
58
+ Requires-Dist: sssom-pydantic
58
59
  Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
59
60
  Requires-Dist: ssslm[gilda] ; extra == 'gilda'
60
61
  Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
62
+ Requires-Dist: grape ; extra == 'grape'
63
+ Requires-Dist: embiggen ; extra == 'grape'
64
+ Requires-Dist: ensmallen ; extra == 'grape'
61
65
  Requires-Dist: protmapper ; extra == 'pid'
66
+ Requires-Dist: pykeen ; extra == 'pykeen'
62
67
  Requires-Dist: scispacy ; python_full_version < '3.13' and extra == 'scispacy'
63
68
  Requires-Dist: spacy ; python_full_version < '3.13' and extra == 'scispacy'
64
69
  Requires-Dist: scipy<1.11 ; python_full_version < '3.13' and extra == 'scispacy'
@@ -74,7 +79,9 @@ Project-URL: Repository, https://github.com/biopragmatics/pyobo.git
74
79
  Provides-Extra: drugcentral
75
80
  Provides-Extra: gilda
76
81
  Provides-Extra: gilda-slim
82
+ Provides-Extra: grape
77
83
  Provides-Extra: pid
84
+ Provides-Extra: pykeen
78
85
  Provides-Extra: scispacy
79
86
  Provides-Extra: sources
80
87
  Description-Content-Type: text/markdown
@@ -1,28 +1,28 @@
1
1
  pyobo/.DS_Store,sha256=icmyUcy152KPoCV2jHO6ZiHzdoYZ79aYVdPXzcGzMEQ,8196
2
- pyobo/__init__.py,sha256=9pWTUfKGgpfZuQ4BS1zrHChealMlCrqrlR5htZJ80xg,3891
2
+ pyobo/__init__.py,sha256=WQCfhng88j77GTYJKw5YmTv6p0U7sRA5RVMMts1DWSc,4063
3
3
  pyobo/__main__.py,sha256=cOYQ2OELxF-9T6nuZ9xnLSu9bLHk6einrsSoz7EcD9M,83
4
- pyobo/api/__init__.py,sha256=sFrxkD5A6bof7MuL-34Lz3nU4ZBL9vSw5L5EwzGR5Rk,3145
5
- pyobo/api/alts.py,sha256=R4sxYldGFvKCe9cxB_gPXf2vWXHq9saBMQkQnbqJ5SI,3032
4
+ pyobo/api/__init__.py,sha256=noKWkj7WTMRUnkFAPRxv7LoaTOwjJOpS4y6BLxILOdE,3334
5
+ pyobo/api/alts.py,sha256=v177QYdo5LVmlau0CF6FiN3vGYisuWBHFJnzZVpWv68,3477
6
6
  pyobo/api/combine.py,sha256=7T8Qj8W1wWQ1KgKJsO1kFRHZxkQcrfKM1hBrhqHsEkU,1106
7
7
  pyobo/api/edges.py,sha256=SEm2gJx6LoOkhXGj11V42uLg4FidFa9jJqW9Hznlfwk,1974
8
- pyobo/api/embedding.py,sha256=Biw5DLCEP0R2IPXcP-cnCbUlWXerQPHiSXJww_x4kn8,4438
8
+ pyobo/api/embedding.py,sha256=lLJDj_QsL7eqjHq_qaoJ4Dzhi3ucWtMoMfduDsUp1PU,8291
9
9
  pyobo/api/hierarchy.py,sha256=Ek1Rkr7qwTinz5DfCIlSXNLe4geMH_6Zta9dgoQIVXs,10318
10
10
  pyobo/api/metadata.py,sha256=stJaiX_l7x0R1V77TNwHvPtokuZ-Eoqb9HMRL70NiWs,1029
11
- pyobo/api/names.py,sha256=Z00vuReU7CGKL39EZvMAMQu3VGLKYlJFzMBHT4kV4xA,10935
11
+ pyobo/api/names.py,sha256=Jr5ECN0KQmq3PwZ7pmcYuTDztSKuH4lFAgbRo7UM7-I,11591
12
12
  pyobo/api/properties.py,sha256=2LFERWJtvopI8OtfTrmPLj_SdeVvVHP4DcpQf8TO9tk,6944
13
13
  pyobo/api/relations.py,sha256=Kebguj5khScU2c0Pm8dJrewu8je9DnKlNenRtmYWGKI,5875
14
14
  pyobo/api/species.py,sha256=YxzJeClfuKI-pjYLpu5797jdDeyTkXpjQDgdmc9MKwo,2376
15
15
  pyobo/api/typedefs.py,sha256=HTui0kl_VELxgji0vfBr-NBG3zrrpCU8tmuQOSWK6fw,1262
16
16
  pyobo/api/utils.py,sha256=SCMsy4QyYVhn-QK0h90Ef1XUMbyHKR1fvteRESzs-bk,5192
17
- pyobo/api/xrefs.py,sha256=nWLLt2GzaVfngNBUbOMVSjOpCua-I7u-2tuoxzXGqrA,5242
17
+ pyobo/api/xrefs.py,sha256=oQ7D2p9mrzb-LtLkXlJ_LYRArs5eqq9Zwwx9_0Yov_o,6053
18
18
  pyobo/cli/__init__.py,sha256=pTiLuzjjpi0P69yVjQ2kE6nBUmZuYFnqdJNDZLDkgvk,71
19
19
  pyobo/cli/cli.py,sha256=5bY_7ZVZOoHwhZtCxx-AYL5ybyBzjS65NU5v5X9DsLA,2842
20
20
  pyobo/cli/database.py,sha256=grPVG1d78yhog5lvEAu3wwHkBASKhtmabwmvx49WRIc,12121
21
21
  pyobo/cli/database_utils.py,sha256=jQ7qSg-oZk-Q-RC121NkUbqXeNg0K8fV96igXaK3ra4,5540
22
22
  pyobo/cli/lookup.py,sha256=GxG753GXnDRf-N9JRWKRmQC5XiN8fEN5l1le5C3jHHY,9163
23
23
  pyobo/cli/utils.py,sha256=nmtXsxG0TWEIjjIe-jh_aqzr09bTN7-NHFifuHGzME0,1738
24
- pyobo/constants.py,sha256=G5EyZhuccwrMn11DRaTXMzTHa5RGdtGRzYqrcYAn6R0,5791
25
- pyobo/getters.py,sha256=X2gQCZhlj2sHDhL7vVLMjSgPFC1TYSh6x07jvMQG3rg,18197
24
+ pyobo/constants.py,sha256=vqaf3xj0Sv39PETE3PJuuZ5SZTpoprsngKOzwpca1CU,7129
25
+ pyobo/getters.py,sha256=exZNjlseRoWhshQYArWwN2KLvkk4NmCQnHM88YUYf-w,18340
26
26
  pyobo/gilda_utils.py,sha256=uThAArALSNzJi-hrR9lUvtQci5VIw4Cqq2L6mtkp0Ko,1990
27
27
  pyobo/identifier_utils/__init__.py,sha256=iSHAZhOwqWZmYpOfpXNLuKouSYj7ZSViaX7BF5uT8so,793
28
28
  pyobo/identifier_utils/api.py,sha256=fik5crIOOhsHIuH-ia_oOQeKZeX5bBMj5S6occWaMeY,9365
@@ -34,9 +34,9 @@ pyobo/identifier_utils/relations/data_rdf.json,sha256=T1PNoYwrqgwDVLtfmj7L5e0Sq0
34
34
  pyobo/identifier_utils/relations/data_rdfs.json,sha256=bjpxZte3g4WvrGJsmHuAJN_cg_faxqIa9tCL7auHdqQ,86
35
35
  pyobo/mocks.py,sha256=j545K9P_DPsDBuYHDrhyTLjmlPoNlRdEtcRlLhXlbXI,2440
36
36
  pyobo/ner/__init__.py,sha256=7Os84d8_gZktUxyUW9Tn2dW33rYFWSO8cviJJef-ZeE,373
37
- pyobo/ner/api.py,sha256=s0MJgz6sj13qiB1TEyO_aC8103fgnYBwZroRgygpZNw,2167
37
+ pyobo/ner/api.py,sha256=dy51kXQbfx7C8ZIwxlsu78HjsdYtdgdkbF0KuaDJoG4,2396
38
38
  pyobo/ner/normalizer.py,sha256=pdvwFG9elriK83FKqjQfT2s-ZuC-QZZuMPudjfay21w,954
39
- pyobo/ner/scispacy_utils.py,sha256=trEwCeLzMJdD_b7SmSrbZrw1DgGlMDI39iH6RyNOLjs,8201
39
+ pyobo/ner/scispacy_utils.py,sha256=4NRGJ1JJB-OmlVthHhyms1iPMwJYrkVMQP1jgZfJ18U,8170
40
40
  pyobo/plugins.py,sha256=wEr-NpyZ7Z6uEr0uGDNOeXLOGZokGbFmo3e-z2PNKJM,1232
41
41
  pyobo/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
42
42
  pyobo/resource_utils.py,sha256=bloSKbHfMLz0hB8AkhMkfLOGqw6FyO8CEU6LNg0PVMk,4406
@@ -48,11 +48,11 @@ pyobo/resources/ro.tsv,sha256=YvlBLPAKy2w4IheYzO9ox1Yg6WkHdMVzMQTikIlECog,26586
48
48
  pyobo/resources/so.py,sha256=S-vmQ7L8AJE08FfGVDIJqNQNaLPUmuJ6HC5F4hWHMrA,1466
49
49
  pyobo/resources/so.tsv,sha256=UJZKFTEAv_XszYYbun4Wf6b4jovDjSKc1RWRQRcTzDw,82068
50
50
  pyobo/sources/README.md,sha256=ApbwpI2hbYQiw4N6KE_VAApfOmTQHkeTbrNEExIbX4I,901
51
- pyobo/sources/__init__.py,sha256=5MGuBu0B3fx8F6gPGfmjLFfpDr2KxatPWpXfeMVtfwc,5029
51
+ pyobo/sources/__init__.py,sha256=ZQnId3SEss43nc4gsAnKl3-k5BUSNptm2cHOGGFt2aw,5088
52
52
  pyobo/sources/agrovoc.py,sha256=SJsbJ7KtxdJUG9Rimmb2CfLfzpK9eOzP0wx59gj-6s4,787
53
- pyobo/sources/antibodyregistry.py,sha256=NybUzPEobn5zrr1iUvC8Z9cuqDEDM1u07sjV1UADdmQ,3353
53
+ pyobo/sources/antibodyregistry.py,sha256=GbmW9vJ1TXul5mSJ4TkdI3uwMhjz7My-ROi2doV9v4g,3361
54
54
  pyobo/sources/bigg/__init__.py,sha256=4pK-71Bx0Iv93PqmZecUKX9LcapbW9wm7zBN9vhbpYI,349
55
- pyobo/sources/bigg/bigg_compartment.py,sha256=pFShMiH-WNH-msmOXDGUgu3gri8JRr5urizNwqvUXqw,3430
55
+ pyobo/sources/bigg/bigg_compartment.py,sha256=lvhAZGyMiCLIcr2JJvht4cINofOvrp9oMfHu5Io5fGk,3399
56
56
  pyobo/sources/bigg/bigg_metabolite.py,sha256=zs53CxPX7XTZpVOty6MWlxT3v0wLgWHaPI4-0vnbPpo,7728
57
57
  pyobo/sources/bigg/bigg_model.py,sha256=n43ZgHbCUS6KBmmstfFUu39hlkPsDhBpf2OB-kAF7YA,1287
58
58
  pyobo/sources/bigg/bigg_reaction.py,sha256=45SIIae32GtDxzL_gpF7p1TKVfh6t3UgHpF4flVBO9I,2459
@@ -68,8 +68,8 @@ pyobo/sources/chembl/chembl_target.py,sha256=BRo7ZeXvcBXSxKoqcu0VmkufaEULTVYhkj-
68
68
  pyobo/sources/chembl/chembl_tissue.py,sha256=gxYceIooVJ10i2_nUIi48SXzw-1lG17vIs9NRwRqwds,1938
69
69
  pyobo/sources/civic_gene.py,sha256=AWOdgOobFlbU95T1hA_Co2JNoNKd5MJSuF4jnYSkgw8,3096
70
70
  pyobo/sources/clinicaltrials.py,sha256=_MWExCo9GkOq0SD547yFD0THwRxr2L8TMKjZyXcQjgc,5459
71
- pyobo/sources/complexportal.py,sha256=a3DEDov1xwdf6u_qACdBi5a8fhvdT9kneB6KM2nLk7k,7645
72
- pyobo/sources/conso.py,sha256=R4YHnnl0bhkqDGBZy35xROCZX57E9iHPlDJJszagsGs,2320
71
+ pyobo/sources/complexportal.py,sha256=SqeC7GRXNYIumrmE93c9jM0MP2qeo6tNap2Diivh99I,7653
72
+ pyobo/sources/conso.py,sha256=1Wo63PQJUOvsESMptsZ6HmACu98TJfSZ4VB_13ZoEys,2328
73
73
  pyobo/sources/cpt.py,sha256=b7hcULlvu_xa6URwoD37Gc_8VAs8mxawAlXflL1e1LU,1466
74
74
  pyobo/sources/credit.py,sha256=IKmHuLFbAzdy0N4HI9OaUAzTXCM27QQ5hkPdfYBg2rg,2175
75
75
  pyobo/sources/cvx.py,sha256=l9Csuudr9Uyo0PNcjJTbNG62EOUcrAVoij0vJhNzhVE,3595
@@ -80,7 +80,7 @@ pyobo/sources/drugbank/drugbank.py,sha256=WiFsy_6INZkgetmbUYkE1vPpg5dLwjBfz3cVJj
80
80
  pyobo/sources/drugbank/drugbank_salt.py,sha256=abVl_igLemmMw4ULi3_ItTgfCaq3uybjqnsT9Rh7C1k,1646
81
81
  pyobo/sources/drugcentral.py,sha256=xIG_sPebbV-_S1vUQLzOuLqHa_RM-zAOfZ8oqr1aqbc,4052
82
82
  pyobo/sources/expasy.py,sha256=o0KcbRxF5GNupSjUBe9BznnfrW60sZr7Df2Eo4noOB4,11057
83
- pyobo/sources/famplex.py,sha256=qCvj6WB_6uq2RHHVPIaGhyqkf1ubI6XrO8Da-Yta96Q,5628
83
+ pyobo/sources/famplex.py,sha256=FPkIH_NNvG6muNyujdwdScJ64GNDXIsw6a7qF7o1sM4,5636
84
84
  pyobo/sources/flybase.py,sha256=gUS39NF_qc723R2SAbhQYqPg6UOiwKwPXhXQ1JwC68Q,5666
85
85
  pyobo/sources/gard.py,sha256=9oRvpNdt94cUqSYF529PFz9QCvF4sP-JBfhWkJroEZc,1768
86
86
  pyobo/sources/geonames/__init__.py,sha256=JQhpe8BKBSQ1P83vtQMSbAKa6xJ2tvX64OMDiD5WM7s,177
@@ -89,13 +89,14 @@ pyobo/sources/geonames/geonames.py,sha256=FI7YnOoLjoT8w90S6GXigUPsmrmGrmYn4hAJD4
89
89
  pyobo/sources/geonames/utils.py,sha256=iUiFMeo_U8FoAlijMoX7NhyEaG9MfppzEtVbiyUuza4,4012
90
90
  pyobo/sources/gmt_utils.py,sha256=zLkbHGLxBUPHxW7jCOHaZTW11YzPj8ON-E4QfPQTHxE,1327
91
91
  pyobo/sources/go.py,sha256=b3zbPGKd6wDclw68fA4Iq9awEZTIVRx37iXeruKQqmk,1536
92
+ pyobo/sources/goldbook.py,sha256=d4ednC3aWkIJD8VBRQpssMOiKZepUiduG9FMjV0769o,2502
92
93
  pyobo/sources/gtdb.py,sha256=LrJfruJCkEUs1NCCPQUpHyL6r2dzMttToNPgmqudIr0,5222
93
94
  pyobo/sources/gwascentral/__init__.py,sha256=VdHIgBVR-36B7gLuhR4XV5UXn_EgNZ0-i1g9NjhOjY0,231
94
95
  pyobo/sources/gwascentral/gwascentral_phenotype.py,sha256=SvMCF3sYqc3F5nNXCf76AzIhNT698ZHHnTpO0IGft8o,1788
95
96
  pyobo/sources/gwascentral/gwascentral_study.py,sha256=fzDiRuWU84085gclzuWNLbxDEsIdVysqXScMU0BdXnM,2672
96
97
  pyobo/sources/hgnc/__init__.py,sha256=1QhM7GdP6_AxCMzaBz2k3SRLkDTOkS2hUhPMLETSGWM,157
97
- pyobo/sources/hgnc/hgnc.py,sha256=esV7w3fiXm2sD1racQBfUKO_C4LBr_iP_nBywE84ztI,16699
98
- pyobo/sources/hgnc/hgncgenefamily.py,sha256=4-jQt1DVmn2j0KwrEA4kjo2tUa9UwEVAWhJwTjbbIM0,3710
98
+ pyobo/sources/hgnc/hgnc.py,sha256=jaCEZZR2YzjrrZNFtvEbfhrVu9HTLX7_sWkshgi022M,20332
99
+ pyobo/sources/hgnc/hgncgenefamily.py,sha256=NGkQXlyac0283WHeYXr3_o__Ak-hpbNnB0NIr2J0QGo,3912
99
100
  pyobo/sources/iana_media_type.py,sha256=X20G2a1ozF-JPaqNs3tUrNoeSb7jv_YsClKSTPH-8io,5024
100
101
  pyobo/sources/icd/__init__.py,sha256=DrZVl76P8essJ4tlZPcauFVrXVkIIZB6sJ0c6Km6SWI,142
101
102
  pyobo/sources/icd/icd10.py,sha256=YatVzgr229J_WeJca4FQAHqWrx7c7N4fHbhb1cQ1TeU,2587
@@ -117,7 +118,7 @@ pyobo/sources/mirbase/mirbase.py,sha256=9huL0PWAVcEDk-4unZw-GInyEE1C_FXwRxN65HG3
117
118
  pyobo/sources/mirbase/mirbase_constants.py,sha256=5DjcwX_FRSzFYbTf50yvkPamSIH70Rw3I8q-Ds0zHVs,1998
118
119
  pyobo/sources/mirbase/mirbase_family.py,sha256=TIWKhhF0pn6dhQTTgLg4lYrJKtu-ILltrHFZD0qeZb4,1974
119
120
  pyobo/sources/mirbase/mirbase_mature.py,sha256=Jj65xVqtjquzqZGTi8cnMmLdyfUfmthM_ka1SZ2-rzE,1302
120
- pyobo/sources/msigdb.py,sha256=45ddWaFdzGZ0lDavhV2zlYkUeGxQ0jQWCVIt-1DQZdw,6810
121
+ pyobo/sources/msigdb.py,sha256=CXXN4YZc99twaleFAvknMyx_AQlGYxgb-veKh_SLmhM,6818
121
122
  pyobo/sources/ncbi/__init__.py,sha256=SuPBRF4ZG0X6PsPauWvlYWx95YUGSODdjyCr5YyQzmk,156
122
123
  pyobo/sources/ncbi/ncbi_gc.py,sha256=uGgrt7fFy7m5Evre-NLvuJa4jftUZNC4utNDVMnk5rs,5470
123
124
  pyobo/sources/ncbi/ncbigene.py,sha256=zpuMe59DRZfczyxJfdSlIaIzDc9MDfMlAY3S_GZK97A,5096
@@ -127,7 +128,7 @@ pyobo/sources/nlm/nlm_catalog.py,sha256=ogXDh4zyRx69_YbGguH0yWEU5-3SvHnLBvEyxtgA
127
128
  pyobo/sources/nlm/nlm_publisher.py,sha256=lr6Cjo2Mdlad3JTkn3crafWKL1lcHX2tFuKdnIoKa5w,984
128
129
  pyobo/sources/nlm/utils.py,sha256=bEBXzz2fjjnFFcjrq_q8mfr1f0_RiKZoQ7H18gpV4HA,4861
129
130
  pyobo/sources/npass.py,sha256=oJaCo43CIGy2tAuMxIPT8PfSRRazJQw51PJAjqMPsH8,2742
130
- pyobo/sources/omim_ps.py,sha256=aSy1bkQJCyxgDYfA7wpxoTt3dQ-qPkCIY4X52_elHHY,1432
131
+ pyobo/sources/omim_ps.py,sha256=cqtM98a0ZW-hY8flbRKte0ODzQUR5Ob4IY1qrhK60SI,1618
131
132
  pyobo/sources/pathbank.py,sha256=SW4mEdWCX2MZYG1VJp8yLEzyBu_OmaZTtSGreldoDtQ,5387
132
133
  pyobo/sources/pfam/__init__.py,sha256=A6y2b2e0LCir4sAg5TCL5YDi6cVhl9Rk3loF5VBaxeM,150
133
134
  pyobo/sources/pfam/pfam.py,sha256=mdbR6Ak_myNpnwXQssGh6HMY_uvSk0OHM5e8RpfOG0c,1718
@@ -142,8 +143,8 @@ pyobo/sources/pharmgkb/utils.py,sha256=SFtRAg_Uxou5YpfqPTsF9we0wBMsalwybdUAm5ZS-
142
143
  pyobo/sources/pid.py,sha256=PcLNxQq-n2ETnXpmCNa4yCZKZmO9Ou-WPBotK9qJPxg,4460
143
144
  pyobo/sources/pombase.py,sha256=9ngHwyAXjIl9AKsFqUPRIbFWgvkCwcs8V2r1O_vbOyk,3696
144
145
  pyobo/sources/pubchem.py,sha256=lTsc0dgrSJ5kxlcaUcUXJydi-xsMf2fI2EcWsbW8xTU,5153
145
- pyobo/sources/reactome.py,sha256=35Qt2Ru6zF59QIxeiv4Ui6lVCf58rKeu06rcLiuANWk,5834
146
- pyobo/sources/rgd.py,sha256=RgIPWTOoRqdXX_3YMw3d6N9WDRaHLJR18gTaWc_bzk4,5316
146
+ pyobo/sources/reactome.py,sha256=yzeCCy19Hxr7KFUrg1tePjN40eZLN9G4dm4q0A7izbI,5842
147
+ pyobo/sources/rgd.py,sha256=I6HC7_GZqFPXlRIuuroOgZM7wG85jcE3Po-sry8a1XU,5194
147
148
  pyobo/sources/rhea.py,sha256=dbhyVJ1yoAQoxoWp47OKegLAmMh6qoe-7_DafJDeWrk,8164
148
149
  pyobo/sources/ror.py,sha256=IS_KUtMeKgAndrbLjhcoK8ilp-jOeiDwzGTy5R9cIwk,8882
149
150
  pyobo/sources/selventa/__init__.py,sha256=cIIDlWL9znL2r0aZIJ2r1FN3NM9io74w-He2egzJwX8,254
@@ -155,7 +156,7 @@ pyobo/sources/sgd.py,sha256=nqsETsbnF0LtwZNdf-D2F2czSBGZQnYBSamLynQmuNc,2073
155
156
  pyobo/sources/signor/__init__.py,sha256=beb_FRqsoqLVMXtDeRZAXf9Xg9UBIHBO05uPU98NajI,139
156
157
  pyobo/sources/signor/download.py,sha256=rkDJVEA6ld0z4iG14tMOcAcuRljQQ9SAJAaLdaxagz8,1053
157
158
  pyobo/sources/signor/signor_complexes.py,sha256=BGNM_kG0jtpR-i6rDSMF5XKeCllWO34zZ2Kq4FMtBk0,3802
158
- pyobo/sources/slm.py,sha256=mGJCw_ExpUERbWtFLo8FN2NgfVhEvv33m66JPbhcj2I,4246
159
+ pyobo/sources/slm.py,sha256=inQ8KpWyisRx3XpF6bOtc7OD_7Y0hjYrdDFXClrCcMs,4254
159
160
  pyobo/sources/spdx.py,sha256=JjVDNUmN6Nc8bT_2_OoqJpeKnZzuwPmdUEynTl_YAVM,2530
160
161
  pyobo/sources/umls/__init__.py,sha256=ENgNXQKhze9zyxsXjkn73-BdqmdntL4Zy1qR42GDtP8,141
161
162
  pyobo/sources/umls/__main__.py,sha256=NY6XqetgpRd_LPm95VTX2L3rJB_7h3JQttgnDJ9cFhM,108
@@ -165,46 +166,46 @@ pyobo/sources/umls/synonym_types.tsv,sha256=8TO6sY7_QHNHBGLSnqOpptykIiPUzXcXHXaW
165
166
  pyobo/sources/umls/umls.py,sha256=W8Lz649airtgWiHPvES04Teyw8JMCnCCXsSm1I3eYCU,4287
166
167
  pyobo/sources/unimod.py,sha256=Tvs4aMyp6DKH6mv9OjXK8takGzAc4c-pIhU4DIdYd1M,1292
167
168
  pyobo/sources/uniprot/__init__.py,sha256=C0df26Q0qfScCA99I4Rkl9L2oeGoOdP8-oihGcmwptE,200
168
- pyobo/sources/uniprot/uniprot.py,sha256=b2lQ1aTwyUZxbH-kWotf4GgMk9GjQXgOOXlqTci5cIw,6325
169
+ pyobo/sources/uniprot/uniprot.py,sha256=rrXlYHXYzHU2pr944AWxH3Ksa4tIUdOTVG-8g-VFEm0,6333
169
170
  pyobo/sources/uniprot/uniprot_ptm.py,sha256=oTA5fvQeE10KTHpiTw03nHdtDhP4aYcWkPTh-MxNO50,2192
170
171
  pyobo/sources/utils.py,sha256=mBIAYsLboAB6w6wPTTv1LDQBzXQu58TUlnNGJLWJwxo,1118
171
- pyobo/sources/wikipathways.py,sha256=tL6-0xKvpWYmdFhIBvZbFPCK7Ufnkre9bPtMAMuprh8,6380
172
+ pyobo/sources/wikipathways.py,sha256=SPKQaLF1PvuRMR5bySAvXXg1zhGmKgY1OfI3H1ZtQXA,6575
172
173
  pyobo/sources/zfin.py,sha256=V9c4YldKu9guAXNoFj_9fm94de7xgKWYJWUD2HNE4W4,5339
173
174
  pyobo/ssg/__init__.py,sha256=hQAELjFW_jrNX9VUaw7VIDjYQhUDicUSs-mSZzAvFSo,5224
174
175
  pyobo/ssg/base.html,sha256=_vldUCa-gL2YTNY6GgAuxNT3TgaED585vF_q7TrrjYs,2844
175
176
  pyobo/ssg/index.html,sha256=2mLBahmPetJGhZnF1-TaTXuB4CoYolpZ2nQaV5dG5nY,4346
176
177
  pyobo/ssg/term.html,sha256=tSLIJ3SYDTetK9g2EoDKyu4aHchVo1EUXk_aYhGeOKo,3869
177
178
  pyobo/ssg/typedef.html,sha256=KrdqzB6xjt689bG33D26AL-11JrvNuEkoxNNI-EG-Tg,2038
178
- pyobo/struct/__init__.py,sha256=fv1gJHCgn4n5ggInuu4QuWebeoQislVOF8QOlwAHGfg,1516
179
+ pyobo/struct/__init__.py,sha256=cx6cTB_ZCw84uz-XNV5YkM2xudpo0w2j4y_hFFFFeaU,1522
179
180
  pyobo/struct/functional/__init__.py,sha256=1Tbtt_6GoarRlgffPepitJ3QtLsrMPMbhDGoQnAKSZ4,32
180
181
  pyobo/struct/functional/dsl.py,sha256=odDX33lzSkKcRjcrsteraFSc00wIOPBHJtxXe9c9RHE,101591
181
- pyobo/struct/functional/macros.py,sha256=uzklvI_CGkDNphb0jY_N-_J_89S5ZIRnWriSkZDwBvA,13786
182
- pyobo/struct/functional/obo_to_functional.py,sha256=cei8fSwD3HlCy6Vvrba3j1hXkkIMY8kXLeuQLDCN1cs,13493
182
+ pyobo/struct/functional/macros.py,sha256=yYHGmAEMpin47U7U3S7aCC3o02khWyoON4Xgpv-gHN4,13811
183
+ pyobo/struct/functional/obo_to_functional.py,sha256=65OmttFto-tm6-7T0RQlgIKo34swVqTpz2B9ykPLNuw,13727
183
184
  pyobo/struct/functional/ontology.py,sha256=-a8jx-61NsI3dgCBEYNP-VeswAy8wWxLBlAEFMJucyI,9342
184
185
  pyobo/struct/functional/utils.py,sha256=c-XG2SJ7ChYtz7KU3K0F-T6ocMjYevei0WxlkfkkmtE,3487
185
186
  pyobo/struct/obo/__init__.py,sha256=xJAFJ4yueWBQv3BrtTuHHJ7AzOqCgOuHgKY4RQocsW0,157
186
- pyobo/struct/obo/reader.py,sha256=7e83tlkt3NTd7QbzvZ6p_8W7zRzBGyR4OZI74Hj_SX4,50797
187
+ pyobo/struct/obo/reader.py,sha256=fzh1YiNblhmA4rfehOO37WmCfi2r5I4R72ubWwmK4eE,50799
187
188
  pyobo/struct/obo/reader_utils.py,sha256=UyQVTQhXbhZ9fCizZg26o5TmeHis9-qZMKvQFwIBRgo,4423
188
189
  pyobo/struct/obograph/__init__.py,sha256=B4rNP9OCTnMXm8YpQ0rar1swn4GIw9b4gQD-IVuqHyw,452
189
190
  pyobo/struct/obograph/export.py,sha256=yk3MHulDM_SMohfwiFdeB62-XGJ2ZNgRUZGjGjiyonY,9945
190
191
  pyobo/struct/obograph/reader.py,sha256=264yVeD8a3jGx9EaGUZVxFbSQ_pwQ_6ckVw9S8wiJfM,8525
191
192
  pyobo/struct/obograph/utils.py,sha256=je0kSkC24MU9pWRHq1_K-J5jWhjWESY6NI3TpZqvZ_Q,1516
192
193
  pyobo/struct/reference.py,sha256=qgwTa-0VIoDklQ7LjlYH-mf2WG0_uO7KlHt0PSBail4,11744
193
- pyobo/struct/struct.py,sha256=_1rJa5vmVNyjtE2wdnGUkWtyHd2l5AQJnr4TZ3206YM,93789
194
- pyobo/struct/struct_utils.py,sha256=_D689bNlGg1_r-4vQQ-imVEOxzq95XBqBFxqFMV077U,40346
195
- pyobo/struct/typedef.py,sha256=iLm8-DVY0v_dK_RwoNKCeOF7nI6XlaieS2CaCHePSlI,13088
194
+ pyobo/struct/struct.py,sha256=-JaApTZ7e50bRJ2dXPdAVuJ0ElIVJIJ-HHRsVdaiMxM,96291
195
+ pyobo/struct/struct_utils.py,sha256=tqaUOYKfM3NAa9NfIrWUbaEFJuSOi05_fXPh1cNMY2w,40911
196
+ pyobo/struct/typedef.py,sha256=X5eDKtFsuXXbmFxAS3GxNHQaES5s6UyowAI7_c8Qcao,13364
196
197
  pyobo/struct/utils.py,sha256=zkpOE42JQIfkN0rc5qNENK03VIKmkf_57tHojMJK71Y,906
197
- pyobo/struct/vocabulary.py,sha256=Kt30TrZKtV8-4G-HAixxEgePhzyENvxF2aL_ff7JtT4,5243
198
+ pyobo/struct/vocabulary.py,sha256=87VqrkU1BrarSW4C2sVbe3qnkn-4jwztCOrnBXy5Ujs,5262
198
199
  pyobo/utils/__init__.py,sha256=CANSY8vGq_6v8rWhWRIdnk-Wo5LA2R9Wjg1nqbWqLOw,17
199
200
  pyobo/utils/cache.py,sha256=x7Dnw8vHYsoslXWiV9L9ZdTu5ZueIR1ki5Ncdpb7H10,3136
200
201
  pyobo/utils/io.py,sha256=QTvGjNDkaIf78Tca23B5RW_aVweKiSsxmgwSKXcMSNo,3921
201
202
  pyobo/utils/iter.py,sha256=rYRbbaFJHxMaE0yU-rQZoCagYIrtev09uY0mxFkf5zY,1524
202
203
  pyobo/utils/misc.py,sha256=499pencyDqW9_xm0H0Cq0FhOw0MoNoq-9IVQTKh-eaE,7992
203
204
  pyobo/utils/ndex_utils.py,sha256=EokCWS00Wrk_4y8ldeQuUyaaC6yNzBg3DagUl-J2czY,2326
204
- pyobo/utils/path.py,sha256=Ep8lTRWgFU9_XF5vqJV5B3G4PcUBglIitMkaUNxjzvo,4091
205
- pyobo/version.py,sha256=J-kjTBsp13Gn9z_AZZpwjfHq3kBfqfmvaT-s9SxrWLQ,926
206
- pyobo-0.12.9.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
207
- pyobo-0.12.9.dist-info/WHEEL,sha256=Pi5uDq5Fdo_Rr-HD5h9BiPn9Et29Y9Sh8NhcJNnFU1c,79
208
- pyobo-0.12.9.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
209
- pyobo-0.12.9.dist-info/METADATA,sha256=WoRJx_9HRg8cs2EDXmteoZObNFc-ZLK7QdjxusVpiXI,22095
210
- pyobo-0.12.9.dist-info/RECORD,,
205
+ pyobo/utils/path.py,sha256=snV58UHxHO6GI2QPPE46ssR4RWozaw83V59sS_I9BY8,4109
206
+ pyobo/version.py,sha256=v0j2YjxitLkr27imJK-XFpLZk5UCOkggapvETMVWd4I,927
207
+ pyobo-0.12.11.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
208
+ pyobo-0.12.11.dist-info/WHEEL,sha256=Pi5uDq5Fdo_Rr-HD5h9BiPn9Et29Y9Sh8NhcJNnFU1c,79
209
+ pyobo-0.12.11.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
210
+ pyobo-0.12.11.dist-info/METADATA,sha256=pUsxtOFil50llmHEkOeZi_NcSwly-ezHUMZyZ1EJ2YM,22340
211
+ pyobo-0.12.11.dist-info/RECORD,,