pyobo 0.12.6__py3-none-any.whl → 0.12.8__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 (210) hide show
  1. pyobo/.DS_Store +0 -0
  2. pyobo/__init__.py +4 -0
  3. pyobo/__main__.py +0 -0
  4. pyobo/api/__init__.py +2 -1
  5. pyobo/api/alts.py +0 -0
  6. pyobo/api/combine.py +0 -0
  7. pyobo/api/edges.py +0 -0
  8. pyobo/api/embedding.py +26 -1
  9. pyobo/api/hierarchy.py +0 -0
  10. pyobo/api/metadata.py +0 -0
  11. pyobo/api/names.py +0 -0
  12. pyobo/api/properties.py +0 -0
  13. pyobo/api/relations.py +0 -0
  14. pyobo/api/species.py +0 -0
  15. pyobo/api/typedefs.py +0 -0
  16. pyobo/api/utils.py +0 -0
  17. pyobo/api/xrefs.py +0 -0
  18. pyobo/cli/__init__.py +0 -0
  19. pyobo/cli/cli.py +0 -0
  20. pyobo/cli/database.py +0 -0
  21. pyobo/cli/database_utils.py +0 -0
  22. pyobo/cli/lookup.py +0 -0
  23. pyobo/cli/utils.py +0 -0
  24. pyobo/constants.py +0 -0
  25. pyobo/getters.py +0 -0
  26. pyobo/gilda_utils.py +0 -0
  27. pyobo/identifier_utils/__init__.py +0 -0
  28. pyobo/identifier_utils/api.py +0 -0
  29. pyobo/identifier_utils/relations/__init__.py +0 -0
  30. pyobo/identifier_utils/relations/api.py +0 -0
  31. pyobo/identifier_utils/relations/data.json +0 -0
  32. pyobo/identifier_utils/relations/data_owl.json +0 -0
  33. pyobo/identifier_utils/relations/data_rdf.json +0 -0
  34. pyobo/identifier_utils/relations/data_rdfs.json +0 -0
  35. pyobo/mocks.py +0 -0
  36. pyobo/ner/__init__.py +0 -0
  37. pyobo/ner/api.py +0 -0
  38. pyobo/ner/normalizer.py +0 -0
  39. pyobo/plugins.py +0 -0
  40. pyobo/py.typed +0 -0
  41. pyobo/resource_utils.py +0 -0
  42. pyobo/resources/__init__.py +0 -0
  43. pyobo/resources/ncbitaxon.py +0 -0
  44. pyobo/resources/ncbitaxon.tsv.gz +0 -0
  45. pyobo/resources/ro.py +0 -0
  46. pyobo/resources/ro.tsv +0 -0
  47. pyobo/resources/so.py +0 -0
  48. pyobo/resources/so.tsv +0 -0
  49. pyobo/sources/README.md +0 -0
  50. pyobo/sources/__init__.py +2 -0
  51. pyobo/sources/agrovoc.py +0 -0
  52. pyobo/sources/antibodyregistry.py +0 -0
  53. pyobo/sources/bigg/__init__.py +0 -0
  54. pyobo/sources/bigg/bigg_compartment.py +0 -0
  55. pyobo/sources/bigg/bigg_metabolite.py +0 -0
  56. pyobo/sources/bigg/bigg_model.py +0 -0
  57. pyobo/sources/bigg/bigg_reaction.py +0 -0
  58. pyobo/sources/biogrid.py +0 -0
  59. pyobo/sources/ccle.py +0 -0
  60. pyobo/sources/cgnc.py +0 -0
  61. pyobo/sources/chebi.py +0 -0
  62. pyobo/sources/chembl/__init__.py +0 -0
  63. pyobo/sources/chembl/chembl_cell.py +0 -0
  64. pyobo/sources/chembl/chembl_compound.py +0 -0
  65. pyobo/sources/chembl/chembl_mechanism.py +0 -0
  66. pyobo/sources/chembl/chembl_target.py +1 -1
  67. pyobo/sources/chembl/chembl_tissue.py +0 -0
  68. pyobo/sources/civic_gene.py +0 -0
  69. pyobo/sources/clinicaltrials.py +0 -0
  70. pyobo/sources/complexportal.py +0 -0
  71. pyobo/sources/conso.py +0 -0
  72. pyobo/sources/cpt.py +0 -0
  73. pyobo/sources/credit.py +0 -0
  74. pyobo/sources/cvx.py +0 -0
  75. pyobo/sources/depmap.py +0 -0
  76. pyobo/sources/dictybase_gene.py +0 -0
  77. pyobo/sources/drugbank/__init__.py +0 -0
  78. pyobo/sources/drugbank/drugbank.py +0 -0
  79. pyobo/sources/drugbank/drugbank_salt.py +0 -0
  80. pyobo/sources/drugcentral.py +0 -0
  81. pyobo/sources/expasy.py +0 -0
  82. pyobo/sources/famplex.py +0 -0
  83. pyobo/sources/flybase.py +0 -0
  84. pyobo/sources/gard.py +0 -0
  85. pyobo/sources/geonames/__init__.py +0 -0
  86. pyobo/sources/geonames/features.py +0 -0
  87. pyobo/sources/geonames/geonames.py +0 -0
  88. pyobo/sources/geonames/utils.py +0 -0
  89. pyobo/sources/gmt_utils.py +0 -0
  90. pyobo/sources/go.py +0 -0
  91. pyobo/sources/gtdb.py +0 -0
  92. pyobo/sources/gwascentral/__init__.py +0 -0
  93. pyobo/sources/gwascentral/gwascentral_phenotype.py +0 -0
  94. pyobo/sources/gwascentral/gwascentral_study.py +0 -0
  95. pyobo/sources/hgnc/__init__.py +0 -0
  96. pyobo/sources/hgnc/hgnc.py +0 -0
  97. pyobo/sources/hgnc/hgncgenefamily.py +0 -0
  98. pyobo/sources/iana_media_type.py +65 -9
  99. pyobo/sources/icd/__init__.py +0 -0
  100. pyobo/sources/icd/icd10.py +0 -0
  101. pyobo/sources/icd/icd11.py +0 -0
  102. pyobo/sources/icd/icd_utils.py +0 -0
  103. pyobo/sources/iconclass.py +55 -0
  104. pyobo/sources/intact.py +0 -0
  105. pyobo/sources/interpro.py +0 -0
  106. pyobo/sources/itis.py +0 -0
  107. pyobo/sources/kegg/__init__.py +0 -0
  108. pyobo/sources/kegg/api.py +0 -0
  109. pyobo/sources/kegg/genes.py +0 -0
  110. pyobo/sources/kegg/genome.py +0 -0
  111. pyobo/sources/kegg/pathway.py +0 -0
  112. pyobo/sources/mesh.py +0 -0
  113. pyobo/sources/mgi.py +0 -0
  114. pyobo/sources/mirbase/__init__.py +0 -0
  115. pyobo/sources/mirbase/mirbase.py +0 -0
  116. pyobo/sources/mirbase/mirbase_constants.py +0 -0
  117. pyobo/sources/mirbase/mirbase_family.py +0 -0
  118. pyobo/sources/mirbase/mirbase_mature.py +0 -0
  119. pyobo/sources/msigdb.py +0 -0
  120. pyobo/sources/ncbi/__init__.py +0 -0
  121. pyobo/sources/ncbi/ncbi_gc.py +0 -0
  122. pyobo/sources/ncbi/ncbigene.py +0 -0
  123. pyobo/sources/nih_reporter.py +0 -0
  124. pyobo/sources/nlm/__init__.py +0 -0
  125. pyobo/sources/nlm/nlm_catalog.py +0 -0
  126. pyobo/sources/nlm/nlm_publisher.py +0 -0
  127. pyobo/sources/nlm/utils.py +0 -0
  128. pyobo/sources/npass.py +0 -0
  129. pyobo/sources/omim_ps.py +0 -0
  130. pyobo/sources/pathbank.py +0 -0
  131. pyobo/sources/pfam/__init__.py +0 -0
  132. pyobo/sources/pfam/pfam.py +0 -0
  133. pyobo/sources/pfam/pfam_clan.py +0 -0
  134. pyobo/sources/pharmgkb/__init__.py +0 -0
  135. pyobo/sources/pharmgkb/pharmgkb_chemical.py +0 -0
  136. pyobo/sources/pharmgkb/pharmgkb_disease.py +0 -0
  137. pyobo/sources/pharmgkb/pharmgkb_gene.py +0 -0
  138. pyobo/sources/pharmgkb/pharmgkb_pathway.py +0 -0
  139. pyobo/sources/pharmgkb/pharmgkb_variant.py +0 -0
  140. pyobo/sources/pharmgkb/utils.py +0 -0
  141. pyobo/sources/pid.py +0 -0
  142. pyobo/sources/pombase.py +0 -0
  143. pyobo/sources/pubchem.py +0 -0
  144. pyobo/sources/reactome.py +0 -0
  145. pyobo/sources/rgd.py +0 -0
  146. pyobo/sources/rhea.py +0 -0
  147. pyobo/sources/ror.py +0 -0
  148. pyobo/sources/selventa/__init__.py +0 -0
  149. pyobo/sources/selventa/schem.py +0 -0
  150. pyobo/sources/selventa/scomp.py +0 -0
  151. pyobo/sources/selventa/sdis.py +0 -0
  152. pyobo/sources/selventa/sfam.py +0 -0
  153. pyobo/sources/sgd.py +0 -0
  154. pyobo/sources/signor/__init__.py +0 -0
  155. pyobo/sources/signor/download.py +0 -0
  156. pyobo/sources/signor/signor_complexes.py +0 -0
  157. pyobo/sources/slm.py +0 -0
  158. pyobo/sources/spdx.py +0 -0
  159. pyobo/sources/umls/__init__.py +0 -0
  160. pyobo/sources/umls/__main__.py +0 -0
  161. pyobo/sources/umls/get_synonym_types.py +0 -0
  162. pyobo/sources/umls/sty.py +0 -0
  163. pyobo/sources/umls/synonym_types.tsv +0 -0
  164. pyobo/sources/umls/umls.py +0 -0
  165. pyobo/sources/unimod.py +0 -0
  166. pyobo/sources/uniprot/__init__.py +0 -0
  167. pyobo/sources/uniprot/uniprot.py +0 -0
  168. pyobo/sources/uniprot/uniprot_ptm.py +0 -0
  169. pyobo/sources/utils.py +0 -0
  170. pyobo/sources/wikipathways.py +0 -0
  171. pyobo/sources/zfin.py +0 -0
  172. pyobo/ssg/__init__.py +0 -0
  173. pyobo/ssg/base.html +0 -0
  174. pyobo/ssg/index.html +0 -0
  175. pyobo/ssg/term.html +0 -0
  176. pyobo/ssg/typedef.html +0 -0
  177. pyobo/struct/__init__.py +0 -0
  178. pyobo/struct/functional/__init__.py +0 -0
  179. pyobo/struct/functional/dsl.py +0 -0
  180. pyobo/struct/functional/macros.py +0 -0
  181. pyobo/struct/functional/obo_to_functional.py +9 -3
  182. pyobo/struct/functional/ontology.py +0 -0
  183. pyobo/struct/functional/utils.py +0 -0
  184. pyobo/struct/obo/__init__.py +0 -0
  185. pyobo/struct/obo/reader.py +0 -0
  186. pyobo/struct/obo/reader_utils.py +0 -0
  187. pyobo/struct/obograph/__init__.py +0 -0
  188. pyobo/struct/obograph/export.py +8 -2
  189. pyobo/struct/obograph/reader.py +0 -0
  190. pyobo/struct/obograph/utils.py +0 -0
  191. pyobo/struct/reference.py +0 -0
  192. pyobo/struct/struct.py +12 -0
  193. pyobo/struct/struct_utils.py +17 -3
  194. pyobo/struct/typedef.py +1 -0
  195. pyobo/struct/utils.py +0 -0
  196. pyobo/struct/vocabulary.py +0 -0
  197. pyobo/utils/__init__.py +0 -0
  198. pyobo/utils/cache.py +0 -0
  199. pyobo/utils/io.py +0 -0
  200. pyobo/utils/iter.py +0 -0
  201. pyobo/utils/misc.py +0 -0
  202. pyobo/utils/ndex_utils.py +0 -0
  203. pyobo/utils/path.py +0 -0
  204. pyobo/version.py +1 -1
  205. {pyobo-0.12.6.dist-info → pyobo-0.12.8.dist-info}/METADATA +1 -1
  206. pyobo-0.12.8.dist-info/RECORD +209 -0
  207. {pyobo-0.12.6.dist-info → pyobo-0.12.8.dist-info}/WHEEL +1 -1
  208. {pyobo-0.12.6.dist-info → pyobo-0.12.8.dist-info}/licenses/LICENSE +0 -0
  209. pyobo-0.12.6.dist-info/RECORD +0 -208
  210. {pyobo-0.12.6.dist-info → pyobo-0.12.8.dist-info}/entry_points.txt +0 -0
@@ -1,208 +0,0 @@
1
- pyobo/.DS_Store,sha256=89c9b251ccb5e7628fa025768c73ba6621f3768619efd69855d3d7cdc1b33044,8196
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- pyobo/__init__.py,sha256=570b3a632caf50b46fff8e64712a22f08892df6997c07cddd59372e2bbadb79c,3598
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- pyobo/__main__.py,sha256=70e610d8e10bc45fbd4fa9ee67dc672d2bbd6cb1e4e9e8a7aec4a8cfb11c0fd3,83
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- pyobo/api/metadata.py,sha256=b2d25a897fe5ef1d11d55efb4cdc07bcfb6892e67e128a9bf473112fbd0d896b,1029
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- pyobo/api/names.py,sha256=674d2fb91794ec218a2f7f4466f300310bb75462ca625245ccc0474f8915e310,10935
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- pyobo/api/properties.py,sha256=6d85af1ebd5b7f4c5d232323faab9d8f8a11a419eab0a86eca36052b22b2f778,6914
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- pyobo/api/utils.py,sha256=48232ccb8432615867f902b487dd047f55d431bc87291d5fbed791112cecf9b9,5192
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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.py,sha256=82b3d51b577bf3286883996f100bb7c301e404048a86d99a6f09afc78f564487,12121
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- pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc7d5f7a8a05da2b7adae,5540
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- pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
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- pyobo/getters.py,sha256=5f68100998658f6b070e12fbbd52cc8d280f142d5361287ac74ee3bcc406deb8,18197
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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=7e293972b20e3a1b0722e1fe89afe839078a65e5f96c1323e52ea871c59a31e6,9365
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- pyobo/identifier_utils/relations/__init__.py,sha256=2961f492b8530a678a9e010887b5530c3de1cc2df8f294e210a18dbb748d01db,159
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- pyobo/identifier_utils/relations/data_owl.json,sha256=a70fe8850a0b32f0ca5f9358085a340297a3464d7ba61e83333fe69d6ae4c826,1066
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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/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
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- pyobo/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
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- pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
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- pyobo/sources/README.md,sha256=0296f0a48da16d8422c3837a284fd5000a5f3a64d01e47936eb34413121b5f82,901
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- pyobo/sources/__init__.py,sha256=cb178c90d47f5279e0704cc5ec87e96932b4f6d1f3c4bf18b29cc4d94ff50fb4,4967
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- pyobo/sources/agrovoc.py,sha256=489b1b27b2adc5d2541bd4629a66f609f2dfce92bd78eccfd30c79f608feeace,787
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- pyobo/sources/antibodyregistry.py,sha256=3726d4ccf1286e7e73aebd6252f0bc67d72ea83103335bb4eec8d5d540037664,3353
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- pyobo/sources/bigg/__init__.py,sha256=e292beef5071d08bfddcfaa665e714297f4b71aa5b5bdc26ef304df6f85ba582,349
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- pyobo/sources/bigg/bigg_compartment.py,sha256=a454a13221fe58d1fe9ac98e5c319482ede0ae2f0946be6eae2ccdc2abd45eac,3430
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- pyobo/sources/bigg/bigg_metabolite.py,sha256=cece770b13d7ed74d9a553adcba3169714f7bf4c0b8161da3c8e3ed2f9db3e9a,7728
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- pyobo/sources/bigg/bigg_model.py,sha256=9f8dd98076c2512e8a0669acb5f154bb7f619643ec0e10697f6381fa4005ed80,1287
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- pyobo/sources/bigg/bigg_reaction.py,sha256=e3948821a7b7d86b43c732ff82917ba754ca55f87ab775201e91787e55413bd2,2459
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- pyobo/sources/biogrid.py,sha256=75897a3eddd8a4d0f672f4e5e4b2007a45b22697257fb47526f149513f571fd0,3297
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- pyobo/sources/ccle.py,sha256=167d6d6356071f2663ea696a83c2123065181b8a3a5b931e78eee5fca94b9a8b,2924
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- pyobo/sources/cgnc.py,sha256=5e5c2aaa325cec1f7bdf9dbe020691a3c95acd79ca7fffc9555e2575f1899754,2299
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- pyobo/sources/chebi.py,sha256=f9ffd7c812ce1e80b6b86aaef14cd0dc780095ba80866efe014bded072b44ce0,1202
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- pyobo/sources/chembl/__init__.py,sha256=99fa98183223a148faea8a2ad8052fcd7d832c585e49d4acbf0c8ab7da4ba276,414
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