pyobo 0.12.0__py3-none-any.whl → 0.12.2__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/.DS_Store +0 -0
  2. pyobo/api/properties.py +8 -12
  3. pyobo/api/xrefs.py +1 -2
  4. pyobo/cli/database.py +30 -2
  5. pyobo/cli/database_utils.py +5 -11
  6. pyobo/getters.py +20 -79
  7. pyobo/gilda_utils.py +3 -80
  8. pyobo/identifier_utils/__init__.py +3 -10
  9. pyobo/identifier_utils/api.py +21 -12
  10. pyobo/obographs.py +11 -2
  11. pyobo/reader.py +13 -17
  12. pyobo/sources/cgnc.py +9 -1
  13. pyobo/sources/credit.py +17 -6
  14. pyobo/sources/flybase.py +5 -5
  15. pyobo/sources/omim_ps.py +4 -4
  16. pyobo/sources/pharmgkb/pharmgkb_gene.py +1 -1
  17. pyobo/struct/functional/ontology.py +3 -1
  18. pyobo/struct/reference.py +4 -4
  19. pyobo/struct/struct.py +112 -55
  20. pyobo/utils/cache.py +3 -4
  21. pyobo/utils/io.py +38 -14
  22. pyobo/utils/path.py +16 -19
  23. pyobo/version.py +1 -1
  24. {pyobo-0.12.0.dist-info → pyobo-0.12.2.dist-info}/METADATA +67 -118
  25. {pyobo-0.12.0.dist-info → pyobo-0.12.2.dist-info}/RECORD +164 -169
  26. {pyobo-0.12.0.dist-info → pyobo-0.12.2.dist-info}/WHEEL +1 -1
  27. pyobo/identifier_utils/model.py +0 -130
  28. pyobo/identifier_utils/preprocessing.json +0 -812
  29. pyobo/identifier_utils/preprocessing.py +0 -61
  30. pyobo/resources/goc.py +0 -75
  31. pyobo/resources/goc.tsv +0 -188
  32. {pyobo-0.12.0.dist-info → pyobo-0.12.2.dist-info}/entry_points.txt +0 -0
  33. {pyobo-0.12.0.dist-info → pyobo-0.12.2.dist-info}/licenses/LICENSE +0 -0
pyobo/identifier_utils/preprocessing.json DELETED
@@ -1,812 +0,0 @@
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- "CGP:curators",
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- "CS:0",
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- "CTD:curators",
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- "ClinGen:AminoacidopathyGeneCurationPanel",
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- "Codex:\\:260",
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- "Compound:eye",
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- "DDB:pf",
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- "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html",
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- "ehdaa2": {
733
- "CS": "carnegie.stage:"
734
- },
735
- "doid": {
736
- "MIM:PS": "omim.ps:"
737
- },
738
- "emapa": {
739
- "TS:": "theiler:"
740
- },
741
- "enm": {
742
- "Thesaurus:C": "NCIT:C"
743
- },
744
- "idocovid19": {
745
- "UniProtKN:": "uniprot:"
746
- },
747
- "idomal": {
748
- "http://purl.org/obo/owl/PO\\:PO_": "PO:"
749
- },
750
- "ito": {
751
- "format:": "edam.format:",
752
- "operation:": "edam.operation:",
753
- "topic:": "edam.topic:"
754
- },
755
- "mcro": {
756
- "format:": "edam.format:",
757
- "operation:": "edam.operation:",
758
- "topic:": "edam.topic:"
759
- },
760
- "mdm": {
761
- "drugbank:DB:": "drugbank:DB"
762
- },
763
- "phipo": {
764
- "created:by": "dcterms:creator",
765
- "created:date": "dcterms:created",
766
- "creation:date": "dcterms:created"
767
- },
768
- "pr": {
769
- "OMA:": "uniprot:",
770
- "iPTMnet:": "uniprot:"
771
- },
772
- "senso": {
773
- "odo:SENSO_": "senso:"
774
- },
775
- "sio": {
776
- "ns2:": "skos:"
777
- },
778
- "srao": {
779
- "topic:": "edam.topic:"
780
- },
781
- "t4fs": {
782
- "TF4S:": "t4fs:"
783
- },
784
- "uniprot.disease": {
785
- "http://purl.obolibrary.org/obo/TEMP#": "uniprot.disease:"
786
- },
787
- "uniprot.location": {
788
- "http://purl.obolibrary.org/obo/TEMP#": "uniprot.location:"
789
- },
790
- "worldavatar.kin": {
791
- "OntoKin:": "worldavatar.kin:"
792
- },
793
- "xlmod": {
794
- "CID_Fragment:": "obo:xlmod#CID_Fragment",
795
- "baseSpecificities:": "obo:xlmod#baseSpecificities",
796
- "bridgeFormula:": "obo:xlmod#bridgeFormula",
797
- "deadEndFormula:": "obo:xlmod#deadEndFormula",
798
- "doubletDeltaMass:": "obo:xlmod#doubletDeltaMass",
799
- "hydrophilicPEGchain:": "obo:xlmod#hydrophilicPEGchain",
800
- "maxAbsorption:": "obo:xlmod#maxAbsorption",
801
- "monoIsotopicMass:": "obo:xlmod#monoIsotopicMass",
802
- "reactionSites:": "obo:xlmod#reactionSites",
803
- "reporterMass:": "obo:xlmod#reporterMass",
804
- "secondaryBaseSpecificities:": "obo:xlmod#secondaryBaseSpecificities",
805
- "secondarySpecificities:": "obo:xlmod#secondarySpecificities",
806
- "spacerLength:": "obo:xlmod#spacerLength",
807
- "specificities:": "obo:xlmod#specificities",
808
- "waveLengthRange:": "obo:xlmod#waveLengthRange"
809
- }
810
- }
811
- }
812
- }