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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 6287d89), 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
The text was updated successfully, but these errors were encountered:
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 6287d89), 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.
The text was updated successfully, but these errors were encountered: