pyobo 0.12.1__py3-none-any.whl → 0.12.3__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 (33) hide show
  1. pyobo/__init__.py +12 -4
  2. pyobo/getters.py +11 -3
  3. pyobo/identifier_utils/__init__.py +4 -1
  4. pyobo/identifier_utils/api.py +4 -3
  5. pyobo/sources/__init__.py +2 -0
  6. pyobo/sources/credit.py +17 -6
  7. pyobo/sources/drugbank/drugbank.py +1 -1
  8. pyobo/sources/gwascentral/gwascentral_study.py +1 -1
  9. pyobo/sources/intact.py +79 -0
  10. pyobo/struct/__init__.py +2 -1
  11. pyobo/struct/functional/ontology.py +2 -2
  12. pyobo/struct/obo/__init__.py +9 -0
  13. pyobo/{reader.py → struct/obo/reader.py} +21 -18
  14. pyobo/struct/obograph/__init__.py +16 -0
  15. pyobo/struct/obograph/export.py +315 -0
  16. pyobo/struct/obograph/reader.py +242 -0
  17. pyobo/struct/obograph/utils.py +47 -0
  18. pyobo/struct/struct.py +13 -23
  19. pyobo/struct/struct_utils.py +22 -14
  20. pyobo/struct/typedef.py +4 -0
  21. pyobo/struct/vocabulary.py +7 -0
  22. pyobo/version.py +1 -1
  23. {pyobo-0.12.1.dist-info → pyobo-0.12.3.dist-info}/METADATA +5 -16
  24. {pyobo-0.12.1.dist-info → pyobo-0.12.3.dist-info}/RECORD +171 -170
  25. {pyobo-0.12.1.dist-info → pyobo-0.12.3.dist-info}/WHEEL +1 -1
  26. pyobo/identifier_utils/preprocessing.json +0 -873
  27. pyobo/identifier_utils/preprocessing.py +0 -27
  28. pyobo/obographs.py +0 -147
  29. pyobo/resources/goc.py +0 -75
  30. pyobo/resources/goc.tsv +0 -188
  31. /pyobo/{reader_utils.py → struct/obo/reader_utils.py} +0 -0
  32. {pyobo-0.12.1.dist-info → pyobo-0.12.3.dist-info}/entry_points.txt +0 -0
  33. {pyobo-0.12.1.dist-info → pyobo-0.12.3.dist-info}/licenses/LICENSE +0 -0
{pyobo-0.12.1.dist-info → pyobo-0.12.3.dist-info}/RECORD RENAMED
@@ -1,201 +1,202 @@
1
- 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/__init__.py,sha256=0d90185e6e3aa041ccc27c68226c45e456e39369328e3db17706d65b52015819,3439
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- pyobo/utils/iter.py,sha256=ad845b6da1491f131a134c94fab419a026a0608aed7afd3db98d26c4591fe736,1524
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- pyobo/utils/misc.py,sha256=99d1f6e88b48d3f0cdbd7fff8a908556bf949278fcf0ef639e5cc8a421d0f4db,2684
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- pyobo/utils/ndex_utils.py,sha256=128902592d345ab93fe32f2575e42e53269a0bac8dcc18370da81497e2767336,2326
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- pyobo/utils/io.py,sha256=fa0cb5a8633a6c9fb95eb2f74e08fbf69acc4fc229b89c18dd233921b80378a9,5100
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- pyobo/utils/cache.py,sha256=136ccd03b82afd534699a36bad129e5f3e73aba5c3184fb93d5a24af30d99227,3098
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- pyobo/utils/__init__.py,sha256=08035263cbc6abfeaff2b5a159121d9e4f96a392c0d91f568e0d67a9b5aa2cec,17
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- pyobo/utils/path.py,sha256=cc37f10de8e0ef90a6063cc2b1c5d1b0993e41649536f04bfddc892d61a3bc4f,3398
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- pyobo/cli/database.py,sha256=e880ac2c78bd437d73c99cea5c44938129852571bca35e2ab0cc7de195851ce6,11963
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- pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
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+ pyobo/__init__.py,sha256=ae0b55a37ac88a8423fd32252683d3447102bcce078fe4c2a418f78196e9d648,3434
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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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18
  pyobo/cli/cli.py,sha256=ca057c8505fa7f40730ac0aa0a77e033e30ede9074a145f0b70d7b5f622aa2bd,2939
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+ pyobo/cli/database.py,sha256=e880ac2c78bd437d73c99cea5c44938129852571bca35e2ab0cc7de195851ce6,11963
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+ pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
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22
  pyobo/cli/utils.py,sha256=9e6b57b311b44d61088e321efa387f6aacebd3d6d337bf8d1c589fb871b3304d,1738
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- pyobo/struct/__init__.py,sha256=fb813dfa7de27f195c07cd5311de78403b03dfbf0a183995c8fb448033ace311,1444
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- pyobo/struct/typedef.py,sha256=fd94429e28efcdf7bbeba4b1729fa66af5f64c34e49437d82e4b3e5a457d064d,12099
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- pyobo/struct/struct_utils.py,sha256=7b8bfd7a322f34cf1436b83c8eab983944651ba467923045bf61ecc245800d2c,39164
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- pyobo/struct/utils.py,sha256=ce4a4e138d894087e4374adce6a34434ad375482a691fff9eed1e88cc24aef56,906
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- pyobo/struct/reference.py,sha256=4fc7d3b665cd18c8dfbbb2b8b49de4bc30a8e101d14ff26bf5f88e9c562bc2d3,11735
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- pyobo/struct/vocabulary.py,sha256=56e0f6770cf7da2d6f1221e3fc8261f1c07dc8358a1f3dfb487894a25b1ed133,4335
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- pyobo/struct/functional/dsl.py,sha256=780b4e5616b8dc823cee610945a95ffa109aa43287992dd4dd51511c461f96fb,101183
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- pyobo/struct/functional/__init__.py,sha256=d536edb7fe86a1aad19607df3dea62b49dd0b4bb2b30f31b8431a842700a499e,32
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- pyobo/struct/functional/obo_to_functional.py,sha256=785c46fdb00dc45f3903f67ad24ae4fcb6d187ce48208373fc9d42833a85f6b8,13273
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- pyobo/struct/functional/utils.py,sha256=73e5c6d9227b0a162dcfb294dcad05f93ea870c8d87af7a2d16c6591f9249ad1,3487
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- pyobo/struct/functional/macros.py,sha256=cc654f131fa685d4afc87d8c7b5e8565da1b789dd5d73045a77b3e033a8ced52,13785
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- pyobo/struct/functional/ontology.py,sha256=bc610a206c5f502cc658cbf7dcaa9caeb112a596ab1cb07fcbd571c8a6da2894,9331
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- pyobo/struct/struct.py,sha256=29b77204d903a948aff74f93aa043e5421cc932c22a893e70dbfd3f27b911fb7,89480
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- pyobo/ssg/index.html,sha256=da62c16a198f7ad2468599c5d7e4da4d7b81e02a18a25a59da741a579746e676,4346
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- pyobo/ssg/typedef.html,sha256=2ab76acc1eb18edebcf5b1b7dc3dba00bfb5d49aef36e124a3134d23e106f938,2038
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- pyobo/ssg/base.html,sha256=fef95d5026be80bd984cd63a1a002ec4d4f74e06840f9f39bc5feaed3aeb8d8b,2844
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- pyobo/ssg/__init__.py,sha256=8500042e3156fe3acd5fd5546b0ed52038d842150389c512b3e99267302f152a,5224
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- pyobo/ssg/term.html,sha256=b522c82774980d37ad2bd8361280cacaee1a1dc855a351145e4fda62119e38aa,3869
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- pyobo/reader.py,sha256=6fc2522a89772b718eaa6278e2abc7d5ca536378b537992b34bfe12bcfd10d72,52246
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- pyobo/identifier_utils/relations/data_rdfs.json,sha256=6e3a7166d7b78385afac626c987b8024dfdc83f7dac6a21af6d08bedab8776a4,86
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+ pyobo/constants.py,sha256=c1ffa4f12c1ddee556adf728ef4ac51da44f228fe6fca9b58b9ab8f263acc87b,5112
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+ pyobo/getters.py,sha256=0bbd39aeba8b4511230ebadd209b2c9c64b117f81d80e1a1327230a068a13eeb,17618
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+ pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
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+ pyobo/identifier_utils/__init__.py,sha256=8921c06613b0a9666662939fa5734bb8aa2e4988fb652562697ec1179b93f2ca,793
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+ pyobo/identifier_utils/api.py,sha256=b65d99d4b8d223341d7d3bd4b7bc2e41ce7b52e218b0779b90bacde6a9beaa61,9247
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  pyobo/identifier_utils/relations/__init__.py,sha256=2961f492b8530a678a9e010887b5530c3de1cc2df8f294e210a18dbb748d01db,159
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- pyobo/identifier_utils/relations/data.json,sha256=88b6ce5fb632faa389b512b68f1b73acdd54b552a1aaa8043430eb5e0020a0bc,113169
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  pyobo/identifier_utils/relations/api.py,sha256=c625bca0f09379ba7ef544d05aaf4b998ee9798945a90f3b98b6d763ef9d36df,5764
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- pyobo/identifier_utils/relations/data_rdf.json,sha256=4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945,2
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+ pyobo/identifier_utils/relations/data.json,sha256=88b6ce5fb632faa389b512b68f1b73acdd54b552a1aaa8043430eb5e0020a0bc,113169
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  pyobo/identifier_utils/relations/data_owl.json,sha256=a70fe8850a0b32f0ca5f9358085a340297a3464d7ba61e83333fe69d6ae4c826,1066
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- pyobo/identifier_utils/__init__.py,sha256=865d3a02c3a6d38ff13d4e30685a60368c4a7823397f93e609c2ad356c5d46a3,749
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- pyobo/identifier_utils/api.py,sha256=310bf6e0ac55882b9bbf179b1628bfc70797ae419a962ea6e1e3cdf48e8e5c26,9212
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- pyobo/identifier_utils/preprocessing.py,sha256=67c9109c1a4ba1f5f45368516563a044e38d4095799b520519a57044230d5fd7,618
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- pyobo/identifier_utils/preprocessing.json,sha256=e84f2ed9bb4f2a92c83845daf739f4052d7a615bfc6c13dcc54845a306916627,34821
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+ pyobo/identifier_utils/relations/data_rdf.json,sha256=4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945,2
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+ pyobo/identifier_utils/relations/data_rdfs.json,sha256=6e3a7166d7b78385afac626c987b8024dfdc83f7dac6a21af6d08bedab8776a4,86
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+ pyobo/mocks.py,sha256=8f9e392bd3ff0cfb0306e6070eb8724cb8e694fa0d951744b5c4652e15e56d72,2440
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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/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
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  pyobo/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
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- pyobo/sources/signor/download.py,sha256=ae40c954403a95dd33e221b5e2d30e70072e4658d043d48024068b75ac5a833f,1053
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- pyobo/sources/signor/__init__.py,sha256=6de6ff151aaca2a2d5317b437916405dff5783d50120704ed39b8f53df0d6a32,139
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- pyobo/sources/signor/signor_complexes.py,sha256=04634cfe41b48eda51fa2eab0d2305e5729e0a59563b7e336762aae0532d064d,3802
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- pyobo/sources/expasy.py,sha256=25f116d229b5c25858db82add7a037e8c5b405e40dbfd76d3ff67a1f581c8755,11053
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- pyobo/sources/biogrid.py,sha256=75897a3eddd8a4d0f672f4e5e4b2007a45b22697257fb47526f149513f571fd0,3297
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- pyobo/sources/geonames/geonames.py,sha256=148ed89cea0b8e84fcc3dd12e865e28143ec9ab986ae6627e210090f8a733a1a,10112
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- pyobo/sources/geonames/__init__.py,sha256=2508697bc04a0524353fcdefb503126c029aeb1276b6f5fae0e303883e5633bb,177
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- pyobo/sources/geonames/features.py,sha256=255edf0b5bcd90327dfcfa464955def40f6f5cddb6193593bdf823dd55a1cf28,688
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- pyobo/sources/geonames/utils.py,sha256=89488531ea3f53c1680258a33285fb361c84686f4c7e9a7312d55b8b252ecdae,4012
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- pyobo/sources/conso.py,sha256=4786079e79746e192a0c6059cb7e7144e0995f9ec4f621cf943249b336a0b06b,2320
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- pyobo/sources/slm.py,sha256=986242c3f131a541116d6b452e8f053763607d5844befdf79bae893db85c8f62,4246
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- pyobo/sources/unimod.py,sha256=4efb3868cca9e83287ea6bfd3a35caf2d6a41b301ce1cfa92215380c87587753,1292
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- pyobo/sources/civic_gene.py,sha256=01639d80ea1b1656d4f794f5840fc2a3624da0d29de4c252b85e239d84a4830f,3096
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- pyobo/sources/pombase.py,sha256=f67807c320178c897d00ab05a943d121b15682f902c1cb3c576af53bfbdb3b29,3696
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- pyobo/sources/pid.py,sha256=3dc2cdc50abe9f61139d7a6608d6b8c8264a6663bd3aef963c1a2d2bda893f18,4460
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- pyobo/sources/zfin.py,sha256=57d73862574abbd82e017368163ffd7e6f7875eef180a598256503d87344e16e,5339
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- pyobo/sources/npass.py,sha256=a09682a38dc2206cb6b40b8cc483d3f0f7d24516b3250c39d4f2408ea30fb07f,2742
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- pyobo/sources/ncbi/__init__.py,sha256=4ae3c1445e191b45fa3ec3dab96be5616c7de5850648e0dd8f20abe58c90ce69,156
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- pyobo/sources/ncbi/ncbi_gc.py,sha256=b8682bb7b7c5cbb9b912fadef8d2efb896b88dfb5464d0b8bad34354c9e4e6bb,5470
84
- pyobo/sources/ncbi/ncbigene.py,sha256=ce9b8c7b9f434597dccf2c497dd4a521a2330dcf4c0df325018dd2fc664af7b0,5096
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+ pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
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+ pyobo/resources/__init__.py,sha256=43d9e293b1e0a4808238dec610aa5bc37cfd64833b345270a063697a9927da70,38
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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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103
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104
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{pyobo-0.12.1.dist-info → pyobo-0.12.3.dist-info}/WHEEL RENAMED
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  Tag: py3-none-any