pyobo 0.12.7__py3-none-any.whl → 0.12.9__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 (211) hide show
  1. pyobo/.DS_Store +0 -0
  2. pyobo/__init__.py +12 -1
  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 +36 -6
  9. pyobo/api/hierarchy.py +6 -4
  10. pyobo/api/metadata.py +0 -0
  11. pyobo/api/names.py +0 -0
  12. pyobo/api/properties.py +12 -3
  13. pyobo/api/relations.py +9 -5
  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 +8 -0
  37. pyobo/ner/api.py +0 -0
  38. pyobo/ner/normalizer.py +2 -2
  39. pyobo/ner/scispacy_utils.py +241 -0
  40. pyobo/plugins.py +0 -0
  41. pyobo/py.typed +0 -0
  42. pyobo/resource_utils.py +0 -0
  43. pyobo/resources/__init__.py +0 -0
  44. pyobo/resources/ncbitaxon.py +0 -0
  45. pyobo/resources/ncbitaxon.tsv.gz +0 -0
  46. pyobo/resources/ro.py +0 -0
  47. pyobo/resources/ro.tsv +0 -0
  48. pyobo/resources/so.py +0 -0
  49. pyobo/resources/so.tsv +0 -0
  50. pyobo/sources/README.md +0 -0
  51. pyobo/sources/__init__.py +2 -0
  52. pyobo/sources/agrovoc.py +0 -0
  53. pyobo/sources/antibodyregistry.py +0 -0
  54. pyobo/sources/bigg/__init__.py +0 -0
  55. pyobo/sources/bigg/bigg_compartment.py +0 -0
  56. pyobo/sources/bigg/bigg_metabolite.py +0 -0
  57. pyobo/sources/bigg/bigg_model.py +0 -0
  58. pyobo/sources/bigg/bigg_reaction.py +0 -0
  59. pyobo/sources/biogrid.py +0 -0
  60. pyobo/sources/ccle.py +0 -0
  61. pyobo/sources/cgnc.py +0 -0
  62. pyobo/sources/chebi.py +0 -0
  63. pyobo/sources/chembl/__init__.py +0 -0
  64. pyobo/sources/chembl/chembl_cell.py +0 -0
  65. pyobo/sources/chembl/chembl_compound.py +0 -0
  66. pyobo/sources/chembl/chembl_mechanism.py +0 -0
  67. pyobo/sources/chembl/chembl_target.py +1 -1
  68. pyobo/sources/chembl/chembl_tissue.py +0 -0
  69. pyobo/sources/civic_gene.py +0 -0
  70. pyobo/sources/clinicaltrials.py +0 -0
  71. pyobo/sources/complexportal.py +0 -0
  72. pyobo/sources/conso.py +0 -0
  73. pyobo/sources/cpt.py +0 -0
  74. pyobo/sources/credit.py +0 -0
  75. pyobo/sources/cvx.py +0 -0
  76. pyobo/sources/depmap.py +0 -0
  77. pyobo/sources/dictybase_gene.py +0 -0
  78. pyobo/sources/drugbank/__init__.py +0 -0
  79. pyobo/sources/drugbank/drugbank.py +0 -0
  80. pyobo/sources/drugbank/drugbank_salt.py +0 -0
  81. pyobo/sources/drugcentral.py +0 -0
  82. pyobo/sources/expasy.py +4 -1
  83. pyobo/sources/famplex.py +0 -0
  84. pyobo/sources/flybase.py +0 -0
  85. pyobo/sources/gard.py +0 -0
  86. pyobo/sources/geonames/__init__.py +0 -0
  87. pyobo/sources/geonames/features.py +0 -0
  88. pyobo/sources/geonames/geonames.py +0 -0
  89. pyobo/sources/geonames/utils.py +0 -0
  90. pyobo/sources/gmt_utils.py +0 -0
  91. pyobo/sources/go.py +6 -3
  92. pyobo/sources/gtdb.py +1 -0
  93. pyobo/sources/gwascentral/__init__.py +0 -0
  94. pyobo/sources/gwascentral/gwascentral_phenotype.py +0 -0
  95. pyobo/sources/gwascentral/gwascentral_study.py +0 -0
  96. pyobo/sources/hgnc/__init__.py +0 -0
  97. pyobo/sources/hgnc/hgnc.py +0 -0
  98. pyobo/sources/hgnc/hgncgenefamily.py +0 -0
  99. pyobo/sources/iana_media_type.py +3 -1
  100. pyobo/sources/icd/__init__.py +0 -0
  101. pyobo/sources/icd/icd10.py +0 -0
  102. pyobo/sources/icd/icd11.py +0 -0
  103. pyobo/sources/icd/icd_utils.py +0 -0
  104. pyobo/sources/iconclass.py +55 -0
  105. pyobo/sources/intact.py +0 -0
  106. pyobo/sources/interpro.py +0 -0
  107. pyobo/sources/itis.py +0 -0
  108. pyobo/sources/kegg/__init__.py +0 -0
  109. pyobo/sources/kegg/api.py +0 -0
  110. pyobo/sources/kegg/genes.py +0 -0
  111. pyobo/sources/kegg/genome.py +0 -0
  112. pyobo/sources/kegg/pathway.py +0 -0
  113. pyobo/sources/mesh.py +0 -0
  114. pyobo/sources/mgi.py +0 -0
  115. pyobo/sources/mirbase/__init__.py +0 -0
  116. pyobo/sources/mirbase/mirbase.py +0 -0
  117. pyobo/sources/mirbase/mirbase_constants.py +0 -0
  118. pyobo/sources/mirbase/mirbase_family.py +0 -0
  119. pyobo/sources/mirbase/mirbase_mature.py +0 -0
  120. pyobo/sources/msigdb.py +0 -0
  121. pyobo/sources/ncbi/__init__.py +0 -0
  122. pyobo/sources/ncbi/ncbi_gc.py +0 -0
  123. pyobo/sources/ncbi/ncbigene.py +0 -0
  124. pyobo/sources/nih_reporter.py +0 -0
  125. pyobo/sources/nlm/__init__.py +0 -0
  126. pyobo/sources/nlm/nlm_catalog.py +0 -0
  127. pyobo/sources/nlm/nlm_publisher.py +0 -0
  128. pyobo/sources/nlm/utils.py +0 -0
  129. pyobo/sources/npass.py +0 -0
  130. pyobo/sources/omim_ps.py +0 -0
  131. pyobo/sources/pathbank.py +0 -0
  132. pyobo/sources/pfam/__init__.py +0 -0
  133. pyobo/sources/pfam/pfam.py +0 -0
  134. pyobo/sources/pfam/pfam_clan.py +0 -0
  135. pyobo/sources/pharmgkb/__init__.py +0 -0
  136. pyobo/sources/pharmgkb/pharmgkb_chemical.py +0 -0
  137. pyobo/sources/pharmgkb/pharmgkb_disease.py +0 -0
  138. pyobo/sources/pharmgkb/pharmgkb_gene.py +0 -0
  139. pyobo/sources/pharmgkb/pharmgkb_pathway.py +0 -0
  140. pyobo/sources/pharmgkb/pharmgkb_variant.py +0 -0
  141. pyobo/sources/pharmgkb/utils.py +0 -0
  142. pyobo/sources/pid.py +0 -0
  143. pyobo/sources/pombase.py +0 -0
  144. pyobo/sources/pubchem.py +0 -0
  145. pyobo/sources/reactome.py +0 -0
  146. pyobo/sources/rgd.py +0 -0
  147. pyobo/sources/rhea.py +0 -0
  148. pyobo/sources/ror.py +0 -0
  149. pyobo/sources/selventa/__init__.py +0 -0
  150. pyobo/sources/selventa/schem.py +0 -0
  151. pyobo/sources/selventa/scomp.py +0 -0
  152. pyobo/sources/selventa/sdis.py +0 -0
  153. pyobo/sources/selventa/sfam.py +0 -0
  154. pyobo/sources/sgd.py +0 -0
  155. pyobo/sources/signor/__init__.py +0 -0
  156. pyobo/sources/signor/download.py +0 -0
  157. pyobo/sources/signor/signor_complexes.py +0 -0
  158. pyobo/sources/slm.py +0 -0
  159. pyobo/sources/spdx.py +0 -0
  160. pyobo/sources/umls/__init__.py +0 -0
  161. pyobo/sources/umls/__main__.py +0 -0
  162. pyobo/sources/umls/get_synonym_types.py +0 -0
  163. pyobo/sources/umls/sty.py +0 -0
  164. pyobo/sources/umls/synonym_types.tsv +0 -0
  165. pyobo/sources/umls/umls.py +0 -0
  166. pyobo/sources/unimod.py +0 -0
  167. pyobo/sources/uniprot/__init__.py +0 -0
  168. pyobo/sources/uniprot/uniprot.py +0 -0
  169. pyobo/sources/uniprot/uniprot_ptm.py +0 -0
  170. pyobo/sources/utils.py +0 -0
  171. pyobo/sources/wikipathways.py +0 -0
  172. pyobo/sources/zfin.py +0 -0
  173. pyobo/ssg/__init__.py +0 -0
  174. pyobo/ssg/base.html +0 -0
  175. pyobo/ssg/index.html +0 -0
  176. pyobo/ssg/term.html +0 -0
  177. pyobo/ssg/typedef.html +0 -0
  178. pyobo/struct/__init__.py +0 -0
  179. pyobo/struct/functional/__init__.py +0 -0
  180. pyobo/struct/functional/dsl.py +0 -0
  181. pyobo/struct/functional/macros.py +12 -12
  182. pyobo/struct/functional/obo_to_functional.py +0 -0
  183. pyobo/struct/functional/ontology.py +0 -0
  184. pyobo/struct/functional/utils.py +0 -0
  185. pyobo/struct/obo/__init__.py +0 -0
  186. pyobo/struct/obo/reader.py +0 -0
  187. pyobo/struct/obo/reader_utils.py +0 -0
  188. pyobo/struct/obograph/__init__.py +0 -0
  189. pyobo/struct/obograph/export.py +0 -0
  190. pyobo/struct/obograph/reader.py +0 -0
  191. pyobo/struct/obograph/utils.py +0 -0
  192. pyobo/struct/reference.py +3 -1
  193. pyobo/struct/struct.py +22 -14
  194. pyobo/struct/struct_utils.py +0 -0
  195. pyobo/struct/typedef.py +0 -0
  196. pyobo/struct/utils.py +0 -0
  197. pyobo/struct/vocabulary.py +0 -0
  198. pyobo/utils/__init__.py +0 -0
  199. pyobo/utils/cache.py +0 -0
  200. pyobo/utils/io.py +0 -0
  201. pyobo/utils/iter.py +0 -0
  202. pyobo/utils/misc.py +0 -0
  203. pyobo/utils/ndex_utils.py +0 -0
  204. pyobo/utils/path.py +0 -0
  205. pyobo/version.py +1 -1
  206. {pyobo-0.12.7.dist-info → pyobo-0.12.9.dist-info}/METADATA +5 -1
  207. pyobo-0.12.9.dist-info/RECORD +210 -0
  208. {pyobo-0.12.7.dist-info → pyobo-0.12.9.dist-info}/WHEEL +1 -1
  209. {pyobo-0.12.7.dist-info → pyobo-0.12.9.dist-info}/licenses/LICENSE +0 -0
  210. pyobo-0.12.7.dist-info/RECORD +0 -208
  211. {pyobo-0.12.7.dist-info → pyobo-0.12.9.dist-info}/entry_points.txt +0 -0
pyobo/utils/cache.py CHANGED
File without changes
pyobo/utils/io.py CHANGED
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pyobo/utils/iter.py CHANGED
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pyobo/utils/misc.py CHANGED
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pyobo/utils/ndex_utils.py CHANGED
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pyobo/utils/path.py CHANGED
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pyobo/version.py CHANGED
@@ -12,7 +12,7 @@ __all__ = [
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  "get_version",
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  ]
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- VERSION = "0.12.7"
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+ VERSION = "0.12.9"
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  def get_git_hash() -> str:
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pyobo
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- Version: 0.12.7
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+ Version: 0.12.9
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  Summary: A python package for handling and generating OBO
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  Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
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  Author: Charles Tapley Hoyt
@@ -59,6 +59,9 @@ Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
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  Requires-Dist: ssslm[gilda] ; extra == 'gilda'
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  Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
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  Requires-Dist: protmapper ; extra == 'pid'
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+ Requires-Dist: scispacy ; python_full_version < '3.13' and extra == 'scispacy'
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+ Requires-Dist: spacy ; python_full_version < '3.13' and extra == 'scispacy'
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+ Requires-Dist: scipy<1.11 ; python_full_version < '3.13' and extra == 'scispacy'
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  Requires-Dist: pyobo[drugcentral,pid] ; extra == 'sources'
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  Maintainer: Charles Tapley Hoyt
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  Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
@@ -72,6 +75,7 @@ Provides-Extra: drugcentral
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  Provides-Extra: gilda
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  Provides-Extra: gilda-slim
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  Provides-Extra: pid
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+ Provides-Extra: scispacy
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  Provides-Extra: sources
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  Description-Content-Type: text/markdown
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+ pyobo/resource_utils.py,sha256=bloSKbHfMLz0hB8AkhMkfLOGqw6FyO8CEU6LNg0PVMk,4406
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+ pyobo/sources/README.md,sha256=ApbwpI2hbYQiw4N6KE_VAApfOmTQHkeTbrNEExIbX4I,901
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+ pyobo/sources/antibodyregistry.py,sha256=NybUzPEobn5zrr1iUvC8Z9cuqDEDM1u07sjV1UADdmQ,3353
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+ pyobo/sources/bigg/__init__.py,sha256=4pK-71Bx0Iv93PqmZecUKX9LcapbW9wm7zBN9vhbpYI,349
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