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Pathogen-Host Interaction Phenotype Ontology
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in_subset property values violate ODK rules #383

Open jseager7 opened 1 year ago

jseager7 commented 1 year ago

PHIPO has started violating the iri-range validation rule from the ODK. I think this is because we're using plain text values (xsd:string) in the range of oboInOwl:inSubset annotation properties.

I've disabled the rule that checks for these for now (see commit 6287d894f95b36a245b59635b1809251f3c95dba), but we should really fix this.

Judging by what other ontologies seem to be doing, it seems like we should be using oboInOwl:SubsetProperty values as the range for the oboInOwl:inSubset annotation property: that's how FYPO has added its subsets. Although, the iri-range query doesn't make any reference to oboInOwl:SubsetProperty (only oboInOwl:inSubset), so I'm not sure this is the actual problem.

Shown below are the list of offending terms. Since there are so many, it would be better to use a script to replace the text values with oboInOwl:SubsetProperty values.


term value
PHIPO:0000001 qc_do_not_manually_annotate
PHIPO:0000001 qc_do_not_annotate
PHIPO:0000002 qc_do_not_annotate
PHIPO:0000002 qc_do_not_manually_annotate
PHIPO:0000003 qc_do_not_manually_annotate
PHIPO:0000003 qc_do_not_annotate
PHIPO:0000004 qc_extension_only
PHIPO:0000006 qc_do_not_manually_annotate
PHIPO:0000006 qc_do_not_annotate
PHIPO:0000007 qc_do_not_annotate
PHIPO:0000008 qc_do_not_annotate
PHIPO:0000009 qc_extension_only
PHIPO:0000010 qc_extension_only
PHIPO:0000011 qc_do_not_annotate
PHIPO:0000011 qc_do_not_manually_annotate
PHIPO:0000012 qc_do_not_annotate
PHIPO:0000014 qc_extension_only
PHIPO:0000015 qc_extension_only
PHIPO:0000017 qc_do_not_manually_annotate
PHIPO:0000017 qc_do_not_annotate
PHIPO:0000023 pathogen_phenotype
PHIPO:0000024 pathogen_phenotype
PHIPO:0000026 pathogen_phenotype
PHIPO:0000027 pathogen_phenotype
PHIPO:0000028 pathogen_phenotype
PHIPO:0000030 pathogen_phenotype
PHIPO:0000031 pathogen_phenotype
PHIPO:0000032 pathogen_phenotype
PHIPO:0000034 qc_do_not_manually_annotate
PHIPO:0000034 qc_do_not_annotate
PHIPO:0000035 qc_extension_only
PHIPO:0000038 qc_do_not_manually_annotate
PHIPO:0000038 qc_do_not_annotate
PHIPO:0000039 qc_do_not_manually_annotate
PHIPO:0000039 qc_do_not_annotate
PHIPO:0000040 qc_do_not_manually_annotate
PHIPO:0000040 qc_do_not_annotate
PHIPO:0000104 pathogen_phenotype
PHIPO:0000105 pathogen_phenotype
PHIPO:0000106 pathogen_phenotype
PHIPO:0000107 pathogen_phenotype
PHIPO:0000108 pathogen_phenotype
PHIPO:0000109 pathogen_phenotype
PHIPO:0000110 pathogen_phenotype
PHIPO:0000111 pathogen_phenotype
PHIPO:0000112 pathogen_phenotype
PHIPO:0000113 pathogen_phenotype
PHIPO:0000114 pathogen_phenotype
PHIPO:0000115 pathogen_phenotype
PHIPO:0000116 pathogen_phenotype
PHIPO:0000117 pathogen_phenotype
PHIPO:0000118 pathogen_phenotype
PHIPO:0000119 pathogen_phenotype
PHIPO:0000120 pathogen_phenotype
PHIPO:0000124 pathogen_phenotype
PHIPO:0000125 pathogen_phenotype
PHIPO:0000126 pathogen_phenotype
PHIPO:0000132 qc_do_not_manually_annotate
PHIPO:0000132 qc_do_not_annotate
PHIPO:0000142 qc_do_not_annotate
PHIPO:0000142 qc_do_not_manually_annotate
PHIPO:0000143 qc_do_not_annotate
PHIPO:0000143 qc_do_not_manually_annotate
PHIPO:0000157 qc_do_not_manually_annotate
PHIPO:0000157 qc_do_not_annotate
PHIPO:0000158 qc_do_not_annotate
PHIPO:0000158 qc_do_not_manually_annotate
PHIPO:0000160 qc_do_not_annotate
PHIPO:0000160 qc_do_not_manually_annotate
PHIPO:0000160 pathogen_phenotype
PHIPO:0000161 qc_do_not_annotate
PHIPO:0000161 qc_do_not_manually_annotate
PHIPO:0000162 qc_do_not_annotate
PHIPO:0000162 qc_do_not_manually_annotate
PHIPO:0000207 qc_extension_only
PHIPO:0000235 qc_do_not_manually_annotate
PHIPO:0000235 qc_do_not_annotate
PHIPO:0000236 qc_do_not_annotate
PHIPO:0000236 qc_do_not_manually_annotate
PHIPO:0000237 qc_do_not_manually_annotate
PHIPO:0000237 qc_do_not_annotate
PHIPO:0000238 qc_do_not_manually_annotate
PHIPO:0000238 qc_do_not_annotate
PHIPO:0000249 qc_do_not_annotate
PHIPO:0000249 qc_do_not_manually_annotate
PHIPO:0000250 qc_do_not_manually_annotate
PHIPO:0000250 qc_do_not_annotate
PHIPO:0000255 qc_do_not_annotate
PHIPO:0000255 qc_do_not_manually_annotate
PHIPO:0000256 qc_do_not_manually_annotate
PHIPO:0000256 qc_do_not_annotate
PHIPO:0000280 qc_do_not_annotate
PHIPO:0000280 qc_do_not_manually_annotate
PHIPO:0000289 host_phenotype
PHIPO:0000290 host_phenotype
PHIPO:0000407 qc_do_not_manually_annotate
PHIPO:0000407 qc_do_not_annotate
PHIPO:0000430 qc_do_not_annotate
PHIPO:0000430 qc_do_not_manually_annotate
PHIPO:0000432 qc_do_not_annotate
PHIPO:0000432 qc_do_not_manually_annotate
PHIPO:0000445 qc_do_not_annotate
PHIPO:0000445 qc_do_not_manually_annotate
PHIPO:0000446 host_phenotype
PHIPO:0000464 qc_do_not_manually_annotate
PHIPO:0000464 qc_do_not_annotate
PHIPO:0000466 qc_do_not_manually_annotate
PHIPO:0000466 qc_do_not_annotate
PHIPO:0000467 host_phenotype
PHIPO:0000507 qc_do_not_manually_annotate
PHIPO:0000507 qc_do_not_annotate
PHIPO:0000509 qc_do_not_annotate
PHIPO:0000509 qc_do_not_manually_annotate
PHIPO:0000510 qc_do_not_manually_annotate
PHIPO:0000510 qc_do_not_annotate
PHIPO:0000511 qc_do_not_manually_annotate
PHIPO:0000511 qc_do_not_annotate
PHIPO:0000512 qc_do_not_manually_annotate
PHIPO:0000512 qc_do_not_annotate
PHIPO:0000514 qc_do_not_annotate
PHIPO:0000514 qc_do_not_manually_annotate
PHIPO:0000929 qc_do_not_annotate
PHIPO:0000929 qc_do_not_manually_annotate
PHIPO:0000930 qc_do_not_annotate
PHIPO:0000930 qc_do_not_manually_annotate
PHIPO:0000932 qc_do_not_annotate
PHIPO:0000932 qc_do_not_manually_annotate
PHIPO:0000948 qc_do_not_annotate
PHIPO:0000964 qc_do_not_annotate
PHIPO:0000965 qc_extension_only
PHIPO:0000966 pathogen_phenotype
PHIPO:0000967 pathogen_phenotype
PHIPO:0000968 pathogen_phenotype
PHIPO:0000969 pathogen_phenotype
PHIPO:0000987 qc_do_not_manually_annotate
PHIPO:0000987 qc_do_not_annotate
PHIPO:0001025 qc_do_not_manually_annotate
PHIPO:0001025 qc_do_not_annotate
PHIPO:0001060 qc_do_not_annotate
PHIPO:0001060 qc_do_not_manually_annotate
PHIPO:0001163 qc_do_not_annotate
PHIPO:0001163 qc_do_not_manually_annotate
PHIPO:0001167 qc_do_not_manually_annotate
PHIPO:0001167 qc_do_not_annotate
PHIPO:0001179 qc_do_not_manually_annotate
PHIPO:0001179 qc_do_not_annotate
PHIPO:0001180 host_phenotype
PHIPO:0001183 qc_do_not_manually_annotate
PHIPO:0001183 qc_do_not_annotate
PHIPO:0001184 qc_do_not_annotate
PHIPO:0001185 qc_do_not_annotate
PHIPO:0001186 qc_do_not_annotate
PHIPO:0001187 qc_do_not_annotate
PHIPO:0001188 qc_do_not_manually_annotate
PHIPO:0001188 qc_do_not_annotate
PHIPO:0001189 qc_extension_only
PHIPO:0001190 qc_extension_only
PHIPO:0001198 qc_do_not_manually_annotate
PHIPO:0001198 qc_do_not_annotate
PHIPO:0001199 qc_extension_only
PHIPO:0001200 qc_extension_only
PHIPO:0001201 qc_do_not_annotate
PHIPO:0001201 qc_do_not_manually_annotate
PHIPO:0001202 qc_do_not_annotate
PHIPO:0001203 qc_do_not_annotate
PHIPO:0001214 qc_do_not_manually_annotate
PHIPO:0001214 qc_do_not_annotate
PHIPO:0001216 qc_do_not_manually_annotate
PHIPO:0001216 qc_do_not_annotate
PHIPO:0001217 qc_do_not_annotate
PHIPO:0001217 qc_do_not_manually_annotate
PHIPO:0001218 qc_do_not_annotate
PHIPO:0001218 qc_do_not_manually_annotate