pyobo 0.10.12__py3-none-any.whl → 0.11.1__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 (153) hide show
  1. pyobo/__init__.py +0 -2
  2. pyobo/__main__.py +0 -2
  3. pyobo/api/__init__.py +0 -2
  4. pyobo/api/alts.py +6 -7
  5. pyobo/api/hierarchy.py +14 -15
  6. pyobo/api/metadata.py +3 -4
  7. pyobo/api/names.py +31 -32
  8. pyobo/api/properties.py +6 -7
  9. pyobo/api/relations.py +12 -11
  10. pyobo/api/species.py +5 -6
  11. pyobo/api/typedefs.py +1 -3
  12. pyobo/api/utils.py +61 -5
  13. pyobo/api/xrefs.py +4 -5
  14. pyobo/aws.py +3 -5
  15. pyobo/cli/__init__.py +0 -2
  16. pyobo/cli/aws.py +0 -2
  17. pyobo/cli/cli.py +0 -4
  18. pyobo/cli/database.py +1 -3
  19. pyobo/cli/lookup.py +0 -2
  20. pyobo/cli/utils.py +0 -2
  21. pyobo/constants.py +1 -33
  22. pyobo/getters.py +19 -26
  23. pyobo/gilda_utils.py +19 -17
  24. pyobo/identifier_utils.py +10 -10
  25. pyobo/mocks.py +5 -6
  26. pyobo/normalizer.py +24 -24
  27. pyobo/obographs.py +8 -5
  28. pyobo/plugins.py +3 -4
  29. pyobo/py.typed +0 -0
  30. pyobo/reader.py +19 -21
  31. pyobo/registries/__init__.py +0 -2
  32. pyobo/registries/metaregistry.py +6 -8
  33. pyobo/resource_utils.py +1 -3
  34. pyobo/resources/__init__.py +0 -2
  35. pyobo/resources/ncbitaxon.py +2 -3
  36. pyobo/resources/ro.py +2 -4
  37. pyobo/resources/so.py +55 -0
  38. pyobo/resources/so.tsv +2604 -0
  39. pyobo/sources/README.md +15 -0
  40. pyobo/sources/__init__.py +0 -2
  41. pyobo/sources/agrovoc.py +3 -3
  42. pyobo/sources/antibodyregistry.py +2 -3
  43. pyobo/sources/biogrid.py +4 -4
  44. pyobo/sources/ccle.py +3 -4
  45. pyobo/sources/cgnc.py +1 -3
  46. pyobo/sources/chebi.py +2 -4
  47. pyobo/sources/chembl.py +1 -3
  48. pyobo/sources/civic_gene.py +2 -3
  49. pyobo/sources/complexportal.py +57 -20
  50. pyobo/sources/conso.py +2 -4
  51. pyobo/sources/cpt.py +1 -3
  52. pyobo/sources/credit.py +1 -1
  53. pyobo/sources/cvx.py +1 -3
  54. pyobo/sources/depmap.py +3 -4
  55. pyobo/sources/dictybase_gene.py +15 -12
  56. pyobo/sources/drugbank.py +6 -7
  57. pyobo/sources/drugbank_salt.py +3 -4
  58. pyobo/sources/drugcentral.py +9 -8
  59. pyobo/sources/expasy.py +33 -16
  60. pyobo/sources/famplex.py +3 -5
  61. pyobo/sources/flybase.py +5 -6
  62. pyobo/sources/geonames.py +1 -1
  63. pyobo/sources/gmt_utils.py +5 -6
  64. pyobo/sources/go.py +4 -6
  65. pyobo/sources/gwascentral_phenotype.py +1 -3
  66. pyobo/sources/gwascentral_study.py +2 -3
  67. pyobo/sources/hgnc.py +30 -26
  68. pyobo/sources/hgncgenefamily.py +9 -11
  69. pyobo/sources/icd10.py +3 -4
  70. pyobo/sources/icd11.py +3 -4
  71. pyobo/sources/icd_utils.py +6 -7
  72. pyobo/sources/interpro.py +3 -5
  73. pyobo/sources/itis.py +1 -3
  74. pyobo/sources/kegg/__init__.py +0 -2
  75. pyobo/sources/kegg/api.py +3 -4
  76. pyobo/sources/kegg/genes.py +3 -4
  77. pyobo/sources/kegg/genome.py +19 -9
  78. pyobo/sources/kegg/pathway.py +5 -6
  79. pyobo/sources/mesh.py +19 -21
  80. pyobo/sources/mgi.py +1 -3
  81. pyobo/sources/mirbase.py +13 -9
  82. pyobo/sources/mirbase_constants.py +0 -2
  83. pyobo/sources/mirbase_family.py +1 -3
  84. pyobo/sources/mirbase_mature.py +1 -3
  85. pyobo/sources/msigdb.py +4 -5
  86. pyobo/sources/ncbigene.py +3 -5
  87. pyobo/sources/npass.py +2 -4
  88. pyobo/sources/omim_ps.py +1 -3
  89. pyobo/sources/pathbank.py +35 -28
  90. pyobo/sources/pfam.py +1 -3
  91. pyobo/sources/pfam_clan.py +1 -3
  92. pyobo/sources/pid.py +3 -5
  93. pyobo/sources/pombase.py +7 -6
  94. pyobo/sources/pubchem.py +2 -3
  95. pyobo/sources/reactome.py +30 -11
  96. pyobo/sources/rgd.py +3 -4
  97. pyobo/sources/rhea.py +7 -8
  98. pyobo/sources/ror.py +3 -2
  99. pyobo/sources/selventa/__init__.py +0 -2
  100. pyobo/sources/selventa/schem.py +1 -3
  101. pyobo/sources/selventa/scomp.py +1 -3
  102. pyobo/sources/selventa/sdis.py +1 -3
  103. pyobo/sources/selventa/sfam.py +1 -3
  104. pyobo/sources/sgd.py +1 -3
  105. pyobo/sources/slm.py +29 -17
  106. pyobo/sources/umls/__init__.py +0 -2
  107. pyobo/sources/umls/__main__.py +0 -2
  108. pyobo/sources/umls/get_synonym_types.py +1 -1
  109. pyobo/sources/umls/umls.py +2 -4
  110. pyobo/sources/uniprot/__init__.py +0 -2
  111. pyobo/sources/uniprot/uniprot.py +11 -10
  112. pyobo/sources/uniprot/uniprot_ptm.py +6 -5
  113. pyobo/sources/utils.py +3 -5
  114. pyobo/sources/wikipathways.py +1 -3
  115. pyobo/sources/zfin.py +20 -9
  116. pyobo/ssg/__init__.py +3 -2
  117. pyobo/struct/__init__.py +0 -2
  118. pyobo/struct/reference.py +22 -23
  119. pyobo/struct/struct.py +132 -116
  120. pyobo/struct/typedef.py +14 -10
  121. pyobo/struct/utils.py +0 -2
  122. pyobo/utils/__init__.py +0 -2
  123. pyobo/utils/cache.py +14 -6
  124. pyobo/utils/io.py +9 -10
  125. pyobo/utils/iter.py +5 -6
  126. pyobo/utils/misc.py +1 -3
  127. pyobo/utils/ndex_utils.py +6 -7
  128. pyobo/utils/path.py +4 -5
  129. pyobo/version.py +3 -5
  130. pyobo/xrefdb/__init__.py +0 -2
  131. pyobo/xrefdb/canonicalizer.py +27 -18
  132. pyobo/xrefdb/priority.py +0 -2
  133. pyobo/xrefdb/sources/__init__.py +3 -4
  134. pyobo/xrefdb/sources/biomappings.py +0 -2
  135. pyobo/xrefdb/sources/cbms2019.py +0 -2
  136. pyobo/xrefdb/sources/chembl.py +0 -2
  137. pyobo/xrefdb/sources/compath.py +1 -3
  138. pyobo/xrefdb/sources/famplex.py +3 -5
  139. pyobo/xrefdb/sources/gilda.py +0 -2
  140. pyobo/xrefdb/sources/intact.py +5 -5
  141. pyobo/xrefdb/sources/ncit.py +1 -3
  142. pyobo/xrefdb/sources/pubchem.py +2 -5
  143. pyobo/xrefdb/sources/wikidata.py +2 -4
  144. pyobo/xrefdb/xrefs_pipeline.py +15 -16
  145. {pyobo-0.10.12.dist-info → pyobo-0.11.1.dist-info}/LICENSE +1 -1
  146. pyobo-0.11.1.dist-info/METADATA +711 -0
  147. pyobo-0.11.1.dist-info/RECORD +173 -0
  148. {pyobo-0.10.12.dist-info → pyobo-0.11.1.dist-info}/WHEEL +1 -1
  149. pyobo-0.11.1.dist-info/entry_points.txt +2 -0
  150. pyobo-0.10.12.dist-info/METADATA +0 -499
  151. pyobo-0.10.12.dist-info/RECORD +0 -169
  152. pyobo-0.10.12.dist-info/entry_points.txt +0 -15
  153. {pyobo-0.10.12.dist-info → pyobo-0.11.1.dist-info}/top_level.txt +0 -0
pyobo-0.10.12.dist-info/entry_points.txt DELETED
@@ -1,15 +0,0 @@
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- [console_scripts]
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- pyobo = pyobo.cli:main
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- recurify = pyobo.cli:recurify
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-
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- [pyobo.xrefs]
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- biomappings = pyobo.xrefdb.sources.biomappings:get_biomappings_df
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- cbms2019 = pyobo.xrefdb.sources.cbms2019:get_cbms2019_xrefs_df
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- chembl = pyobo.xrefdb.sources.chembl:get_chembl_xrefs_df
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- compath = pyobo.xrefdb.sources.compath:get_compath_xrefs_df
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- famplex = pyobo.xrefdb.sources.famplex:get_famplex_xrefs_df
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- gilda = pyobo.xrefdb.sources.gilda:get_gilda_xrefs_df
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- intact = pyobo.xrefdb.sources.intact:get_xrefs_df
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- ncit = pyobo.xrefdb.sources.ncit:get_ncit_xrefs_df
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- pubchem = pyobo.xrefdb.sources.pubchem:get_pubchem_mesh_df
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- wikidata = pyobo.xrefdb.sources.wikidata:get_wikidata_xrefs_df