pyobo 0.11.1__py3-none-any.whl → 0.12.0__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 (242) hide show
  1. pyobo/.DS_Store +0 -0
  2. pyobo/__init__.py +95 -20
  3. pyobo/__main__.py +0 -0
  4. pyobo/api/__init__.py +81 -10
  5. pyobo/api/alts.py +52 -42
  6. pyobo/api/combine.py +39 -0
  7. pyobo/api/edges.py +68 -0
  8. pyobo/api/hierarchy.py +231 -203
  9. pyobo/api/metadata.py +14 -19
  10. pyobo/api/names.py +207 -127
  11. pyobo/api/properties.py +117 -113
  12. pyobo/api/relations.py +68 -94
  13. pyobo/api/species.py +24 -21
  14. pyobo/api/typedefs.py +11 -11
  15. pyobo/api/utils.py +66 -13
  16. pyobo/api/xrefs.py +108 -114
  17. pyobo/cli/__init__.py +0 -0
  18. pyobo/cli/cli.py +35 -50
  19. pyobo/cli/database.py +183 -161
  20. pyobo/{xrefdb/xrefs_pipeline.py → cli/database_utils.py} +54 -73
  21. pyobo/cli/lookup.py +163 -195
  22. pyobo/cli/utils.py +19 -6
  23. pyobo/constants.py +102 -3
  24. pyobo/getters.py +196 -118
  25. pyobo/gilda_utils.py +79 -200
  26. pyobo/identifier_utils/__init__.py +41 -0
  27. pyobo/identifier_utils/api.py +296 -0
  28. pyobo/identifier_utils/model.py +130 -0
  29. pyobo/identifier_utils/preprocessing.json +812 -0
  30. pyobo/identifier_utils/preprocessing.py +61 -0
  31. pyobo/identifier_utils/relations/__init__.py +8 -0
  32. pyobo/identifier_utils/relations/api.py +162 -0
  33. pyobo/identifier_utils/relations/data.json +5824 -0
  34. pyobo/identifier_utils/relations/data_owl.json +57 -0
  35. pyobo/identifier_utils/relations/data_rdf.json +1 -0
  36. pyobo/identifier_utils/relations/data_rdfs.json +7 -0
  37. pyobo/mocks.py +9 -6
  38. pyobo/ner/__init__.py +9 -0
  39. pyobo/ner/api.py +72 -0
  40. pyobo/ner/normalizer.py +33 -0
  41. pyobo/obographs.py +43 -39
  42. pyobo/plugins.py +5 -4
  43. pyobo/py.typed +0 -0
  44. pyobo/reader.py +1358 -395
  45. pyobo/reader_utils.py +155 -0
  46. pyobo/resource_utils.py +42 -22
  47. pyobo/resources/__init__.py +0 -0
  48. pyobo/resources/goc.py +75 -0
  49. pyobo/resources/goc.tsv +188 -0
  50. pyobo/resources/ncbitaxon.py +4 -5
  51. pyobo/resources/ncbitaxon.tsv.gz +0 -0
  52. pyobo/resources/ro.py +3 -2
  53. pyobo/resources/ro.tsv +0 -0
  54. pyobo/resources/so.py +0 -0
  55. pyobo/resources/so.tsv +0 -0
  56. pyobo/sources/README.md +12 -8
  57. pyobo/sources/__init__.py +52 -29
  58. pyobo/sources/agrovoc.py +0 -0
  59. pyobo/sources/antibodyregistry.py +11 -12
  60. pyobo/sources/bigg/__init__.py +13 -0
  61. pyobo/sources/bigg/bigg_compartment.py +81 -0
  62. pyobo/sources/bigg/bigg_metabolite.py +229 -0
  63. pyobo/sources/bigg/bigg_model.py +46 -0
  64. pyobo/sources/bigg/bigg_reaction.py +77 -0
  65. pyobo/sources/biogrid.py +1 -2
  66. pyobo/sources/ccle.py +7 -12
  67. pyobo/sources/cgnc.py +0 -5
  68. pyobo/sources/chebi.py +1 -1
  69. pyobo/sources/chembl/__init__.py +9 -0
  70. pyobo/sources/{chembl.py → chembl/chembl_compound.py} +13 -25
  71. pyobo/sources/chembl/chembl_target.py +160 -0
  72. pyobo/sources/civic_gene.py +55 -15
  73. pyobo/sources/clinicaltrials.py +160 -0
  74. pyobo/sources/complexportal.py +24 -24
  75. pyobo/sources/conso.py +14 -22
  76. pyobo/sources/cpt.py +0 -0
  77. pyobo/sources/credit.py +1 -9
  78. pyobo/sources/cvx.py +27 -5
  79. pyobo/sources/depmap.py +9 -12
  80. pyobo/sources/dictybase_gene.py +2 -7
  81. pyobo/sources/drugbank/__init__.py +9 -0
  82. pyobo/sources/{drugbank.py → drugbank/drugbank.py} +11 -16
  83. pyobo/sources/{drugbank_salt.py → drugbank/drugbank_salt.py} +3 -8
  84. pyobo/sources/drugcentral.py +17 -13
  85. pyobo/sources/expasy.py +31 -34
  86. pyobo/sources/famplex.py +13 -18
  87. pyobo/sources/flybase.py +3 -8
  88. pyobo/sources/gard.py +62 -0
  89. pyobo/sources/geonames/__init__.py +9 -0
  90. pyobo/sources/geonames/features.py +28 -0
  91. pyobo/sources/{geonames.py → geonames/geonames.py} +87 -26
  92. pyobo/sources/geonames/utils.py +115 -0
  93. pyobo/sources/gmt_utils.py +6 -7
  94. pyobo/sources/go.py +20 -13
  95. pyobo/sources/gtdb.py +154 -0
  96. pyobo/sources/gwascentral/__init__.py +9 -0
  97. pyobo/sources/{gwascentral_phenotype.py → gwascentral/gwascentral_phenotype.py} +5 -7
  98. pyobo/sources/{gwascentral_study.py → gwascentral/gwascentral_study.py} +1 -7
  99. pyobo/sources/hgnc/__init__.py +9 -0
  100. pyobo/sources/{hgnc.py → hgnc/hgnc.py} +56 -70
  101. pyobo/sources/{hgncgenefamily.py → hgnc/hgncgenefamily.py} +8 -18
  102. pyobo/sources/icd/__init__.py +9 -0
  103. pyobo/sources/{icd10.py → icd/icd10.py} +35 -37
  104. pyobo/sources/icd/icd11.py +148 -0
  105. pyobo/sources/{icd_utils.py → icd/icd_utils.py} +66 -20
  106. pyobo/sources/interpro.py +4 -9
  107. pyobo/sources/itis.py +0 -5
  108. pyobo/sources/kegg/__init__.py +0 -0
  109. pyobo/sources/kegg/api.py +16 -38
  110. pyobo/sources/kegg/genes.py +9 -20
  111. pyobo/sources/kegg/genome.py +1 -7
  112. pyobo/sources/kegg/pathway.py +9 -21
  113. pyobo/sources/mesh.py +58 -24
  114. pyobo/sources/mgi.py +3 -10
  115. pyobo/sources/mirbase/__init__.py +11 -0
  116. pyobo/sources/{mirbase.py → mirbase/mirbase.py} +8 -11
  117. pyobo/sources/{mirbase_constants.py → mirbase/mirbase_constants.py} +0 -0
  118. pyobo/sources/{mirbase_family.py → mirbase/mirbase_family.py} +4 -8
  119. pyobo/sources/{mirbase_mature.py → mirbase/mirbase_mature.py} +3 -7
  120. pyobo/sources/msigdb.py +74 -39
  121. pyobo/sources/ncbi/__init__.py +9 -0
  122. pyobo/sources/ncbi/ncbi_gc.py +162 -0
  123. pyobo/sources/{ncbigene.py → ncbi/ncbigene.py} +18 -19
  124. pyobo/sources/nih_reporter.py +60 -0
  125. pyobo/sources/nlm/__init__.py +9 -0
  126. pyobo/sources/nlm/nlm_catalog.py +48 -0
  127. pyobo/sources/nlm/nlm_publisher.py +36 -0
  128. pyobo/sources/nlm/utils.py +116 -0
  129. pyobo/sources/npass.py +6 -8
  130. pyobo/sources/omim_ps.py +10 -3
  131. pyobo/sources/pathbank.py +4 -8
  132. pyobo/sources/pfam/__init__.py +9 -0
  133. pyobo/sources/{pfam.py → pfam/pfam.py} +3 -8
  134. pyobo/sources/{pfam_clan.py → pfam/pfam_clan.py} +2 -7
  135. pyobo/sources/pharmgkb/__init__.py +15 -0
  136. pyobo/sources/pharmgkb/pharmgkb_chemical.py +89 -0
  137. pyobo/sources/pharmgkb/pharmgkb_disease.py +77 -0
  138. pyobo/sources/pharmgkb/pharmgkb_gene.py +108 -0
  139. pyobo/sources/pharmgkb/pharmgkb_pathway.py +63 -0
  140. pyobo/sources/pharmgkb/pharmgkb_variant.py +84 -0
  141. pyobo/sources/pharmgkb/utils.py +86 -0
  142. pyobo/sources/pid.py +1 -6
  143. pyobo/sources/pombase.py +6 -10
  144. pyobo/sources/pubchem.py +4 -9
  145. pyobo/sources/reactome.py +5 -11
  146. pyobo/sources/rgd.py +11 -16
  147. pyobo/sources/rhea.py +37 -36
  148. pyobo/sources/ror.py +69 -42
  149. pyobo/sources/selventa/__init__.py +0 -0
  150. pyobo/sources/selventa/schem.py +4 -7
  151. pyobo/sources/selventa/scomp.py +1 -6
  152. pyobo/sources/selventa/sdis.py +4 -7
  153. pyobo/sources/selventa/sfam.py +1 -6
  154. pyobo/sources/sgd.py +6 -11
  155. pyobo/sources/signor/__init__.py +7 -0
  156. pyobo/sources/signor/download.py +41 -0
  157. pyobo/sources/signor/signor_complexes.py +105 -0
  158. pyobo/sources/slm.py +12 -15
  159. pyobo/sources/umls/__init__.py +7 -1
  160. pyobo/sources/umls/__main__.py +0 -0
  161. pyobo/sources/umls/get_synonym_types.py +20 -4
  162. pyobo/sources/umls/sty.py +57 -0
  163. pyobo/sources/umls/synonym_types.tsv +1 -1
  164. pyobo/sources/umls/umls.py +18 -22
  165. pyobo/sources/unimod.py +46 -0
  166. pyobo/sources/uniprot/__init__.py +1 -1
  167. pyobo/sources/uniprot/uniprot.py +40 -32
  168. pyobo/sources/uniprot/uniprot_ptm.py +4 -34
  169. pyobo/sources/utils.py +3 -2
  170. pyobo/sources/wikipathways.py +7 -10
  171. pyobo/sources/zfin.py +5 -10
  172. pyobo/ssg/__init__.py +12 -16
  173. pyobo/ssg/base.html +0 -0
  174. pyobo/ssg/index.html +26 -13
  175. pyobo/ssg/term.html +12 -2
  176. pyobo/ssg/typedef.html +0 -0
  177. pyobo/struct/__init__.py +54 -8
  178. pyobo/struct/functional/__init__.py +1 -0
  179. pyobo/struct/functional/dsl.py +2572 -0
  180. pyobo/struct/functional/macros.py +423 -0
  181. pyobo/struct/functional/obo_to_functional.py +385 -0
  182. pyobo/struct/functional/ontology.py +270 -0
  183. pyobo/struct/functional/utils.py +112 -0
  184. pyobo/struct/reference.py +331 -136
  185. pyobo/struct/struct.py +1413 -643
  186. pyobo/struct/struct_utils.py +1078 -0
  187. pyobo/struct/typedef.py +162 -210
  188. pyobo/struct/utils.py +12 -5
  189. pyobo/struct/vocabulary.py +138 -0
  190. pyobo/utils/__init__.py +0 -0
  191. pyobo/utils/cache.py +13 -11
  192. pyobo/utils/io.py +17 -31
  193. pyobo/utils/iter.py +5 -5
  194. pyobo/utils/misc.py +41 -53
  195. pyobo/utils/ndex_utils.py +0 -0
  196. pyobo/utils/path.py +76 -70
  197. pyobo/version.py +3 -3
  198. {pyobo-0.11.1.dist-info → pyobo-0.12.0.dist-info}/METADATA +224 -225
  199. pyobo-0.12.0.dist-info/RECORD +202 -0
  200. pyobo-0.12.0.dist-info/WHEEL +4 -0
  201. {pyobo-0.11.1.dist-info → pyobo-0.12.0.dist-info}/entry_points.txt +1 -0
  202. {pyobo-0.11.1.dist-info → pyobo-0.12.0.dist-info/licenses}/LICENSE +0 -0
  203. pyobo/apps/__init__.py +0 -3
  204. pyobo/apps/cli.py +0 -24
  205. pyobo/apps/gilda/__init__.py +0 -3
  206. pyobo/apps/gilda/__main__.py +0 -8
  207. pyobo/apps/gilda/app.py +0 -48
  208. pyobo/apps/gilda/cli.py +0 -36
  209. pyobo/apps/gilda/templates/base.html +0 -33
  210. pyobo/apps/gilda/templates/home.html +0 -11
  211. pyobo/apps/gilda/templates/matches.html +0 -32
  212. pyobo/apps/mapper/__init__.py +0 -3
  213. pyobo/apps/mapper/__main__.py +0 -11
  214. pyobo/apps/mapper/cli.py +0 -37
  215. pyobo/apps/mapper/mapper.py +0 -187
  216. pyobo/apps/mapper/templates/base.html +0 -35
  217. pyobo/apps/mapper/templates/mapper_home.html +0 -64
  218. pyobo/aws.py +0 -162
  219. pyobo/cli/aws.py +0 -47
  220. pyobo/identifier_utils.py +0 -142
  221. pyobo/normalizer.py +0 -232
  222. pyobo/registries/__init__.py +0 -16
  223. pyobo/registries/metaregistry.json +0 -507
  224. pyobo/registries/metaregistry.py +0 -135
  225. pyobo/sources/icd11.py +0 -105
  226. pyobo/xrefdb/__init__.py +0 -1
  227. pyobo/xrefdb/canonicalizer.py +0 -214
  228. pyobo/xrefdb/priority.py +0 -59
  229. pyobo/xrefdb/sources/__init__.py +0 -60
  230. pyobo/xrefdb/sources/biomappings.py +0 -36
  231. pyobo/xrefdb/sources/cbms2019.py +0 -91
  232. pyobo/xrefdb/sources/chembl.py +0 -83
  233. pyobo/xrefdb/sources/compath.py +0 -82
  234. pyobo/xrefdb/sources/famplex.py +0 -64
  235. pyobo/xrefdb/sources/gilda.py +0 -50
  236. pyobo/xrefdb/sources/intact.py +0 -113
  237. pyobo/xrefdb/sources/ncit.py +0 -133
  238. pyobo/xrefdb/sources/pubchem.py +0 -27
  239. pyobo/xrefdb/sources/wikidata.py +0 -116
  240. pyobo-0.11.1.dist-info/RECORD +0 -173
  241. pyobo-0.11.1.dist-info/WHEEL +0 -5
  242. pyobo-0.11.1.dist-info/top_level.txt +0 -1

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