Open kevinschaper opened 1 year ago
Here's the output I'm getting right now:
INVALID_NODE_PROPERTY_VALUE_TYPE
Multi-valued node property 'xref' is expected to be of type '<class 'list'>'
PomBase:SPAC1002.01 element count 56336
PomBase:SPAC1002.02 element count 56336
PomBase:SPAC1002.03c element count 56336
PomBase:SPAC1002.04c element count 56336
PomBase:SPAC1002.05c element count 56336
PomBase:SPAC1002.06c element count 56336
...
Multi-valued node property 'type' is expected to be of type '<class 'list'>'
PomBase:SPAC1002.01 element count 314203
PomBase:SPAC1002.02 element count 314203
PomBase:SPAC1002.03c element count 314203
PomBase:SPAC1002.04c element count 314203
PomBase:SPAC1002.05c element count 314203
PomBase:SPAC1002.06c element count 314203
...
Single-valued node property 'description' is expected to be of type '<class 'str'>'
MONDO:0014160 element count 1
INVALID_NODE_PROPERTY_VALUE
Node property 'id' has a value 'PomBase:SPAC1002.01' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.01 element count 1
Node property 'id' has a value 'PomBase:SPAC1002.02' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.02 element count 1
Node property 'id' has a value 'PomBase:SPAC1002.03c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.03c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.04c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.04c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.05c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.05c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.06c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.06c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.07c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.07c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.08c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.08c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.09c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.09c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.10c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.10c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.11' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.11 element count 1
Node property 'id' has a value 'PomBase:SPAC1002.12c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.12c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.13c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.13c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.14' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.14 element count 1
Node property 'id' has a value 'PomBase:SPAC1002.15c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.15c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.16c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.16c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.17c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.17c element count 1
Node property 'id' has a value 'PomBase:SPAC1002.18' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.18 element count 1
Node property 'id' has a value 'PomBase:SPAC1002.19' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.19 element count 1
Node property 'id' has a value 'PomBase:SPAC1002.20' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1002.20 element count 1
Node property 'id' has a value 'PomBase:SPAC1006.01' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.01 element count 1
Node property 'id' has a value 'PomBase:SPAC1006.02' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.02 element count 1
Node property 'id' has a value 'PomBase:SPAC1006.03c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.03c element count 1
Node property 'id' has a value 'PomBase:SPAC1006.04c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.04c element count 1
Node property 'id' has a value 'PomBase:SPAC1006.05c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.05c element count 1
Node property 'id' has a value 'PomBase:SPAC1006.06' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.06 element count 1
Node property 'id' has a value 'PomBase:SPAC1006.07' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.07 element count 1
Node property 'id' has a value 'PomBase:SPAC1006.08' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.08 element count 1
Node property 'id' has a value 'PomBase:SPAC1006.09' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1006.09 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.01' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.01 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.02' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.02 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.03' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.03 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.04' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.04 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.05c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.05c element count 1
Node property 'id' has a value 'PomBase:SPAC1039.06' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.06 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.07c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.07c element count 1
Node property 'id' has a value 'PomBase:SPAC1039.08' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.08 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.09' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.09 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.10' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.10 element count 1
Node property 'id' has a value 'PomBase:SPAC1039.11c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1039.11c element count 1
Node property 'id' has a value 'PomBase:SPAC105.01c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC105.01c element count 1
Node property 'id' has a value 'PomBase:SPAC105.02c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC105.02c element count 1
Node property 'id' has a value 'PomBase:SPAC105.03c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC105.03c element count 1
Node property 'id' has a value 'PomBase:SPAC1071.01c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1071.01c element count 1
Node property 'id' has a value 'PomBase:SPAC1071.02' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1071.02 element count 1
Node property 'id' has a value 'PomBase:SPAC1071.03c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1071.03c element count 1
Node property 'id' has a value 'PomBase:SPAC1071.04c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1071.04c element count 1
Node property 'id' has a value 'PomBase:SPAC1071.05' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1071.05 element count 1
Node property 'id' has a value 'PomBase:SPAC1071.06' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1071.06 element count 1
Node property 'id' has a value 'PomBase:SPAC1071.07c' with a CURIE prefix 'PomBase' is not represented in Biolink Model JSON-LD context
PomBase:SPAC1071.07c element count 1
...
INVALID_CATEGORY
Category 'biological_role_mixin' is not in CamelCase form
CHEBI:130181 element count 379
CHEBI:131699 element count 379
CHEBI:136651 element count 379
CHEBI:138880 element count 379
CHEBI:139492 element count 379
CHEBI:139512 element count 379
...
Category 'biological_role_mixin' is a mixin in the Biolink Model
CHEBI:130181 element count 379
CHEBI:131699 element count 379
CHEBI:136651 element count 379
CHEBI:138880 element count 379
CHEBI:139492 element count 379
CHEBI:139512 element count 379
...
Category 'is_metabolite_of' is not in CamelCase form
CHEBI:131604 element count 42
CHEBI:137684 element count 42
CHEBI:25212 element count 42
CHEBI:25442 element count 42
CHEBI:26115 element count 42
CHEBI:27026 element count 42
...
Category 'is_metabolite_of' is unknown in the current Biolink Model
CHEBI:131604 element count 42
CHEBI:137684 element count 42
CHEBI:25212 element count 42
CHEBI:25442 element count 42
CHEBI:26115 element count 42
CHEBI:27026 element count 42
...
Category 'chemical_role_mixin' is not in CamelCase form
CHEBI:13193 element count 40
CHEBI:138103 element count 40
CHEBI:15022 element count 40
CHEBI:15339 element count 40
CHEBI:17499 element count 40
CHEBI:17654 element count 40
...
Category 'chemical_role_mixin' is a mixin in the Biolink Model
CHEBI:13193 element count 40
CHEBI:138103 element count 40
CHEBI:15022 element count 40
CHEBI:15339 element count 40
CHEBI:17499 element count 40
CHEBI:17654 element count 40
...
Category 'RNAProduct' is not in CamelCase form
CHEBI:18111 element count 3
CHEBI:33697 element count 3
CHEBI:33699 element count 3
Category 'RNAProduct' is unknown in the current Biolink Model
CHEBI:18111 element count 3
CHEBI:33697 element count 3
CHEBI:33699 element count 3
Category 'derives_from' is not in CamelCase form
CHEBI:has_functional_parent element count 1
Category 'derives_from' is unknown in the current Biolink Model
CHEBI:has_functional_parent element count 1
Category 'subclass_of' is not in CamelCase form
CHEBI:has_parent_hydride element count 2
GO:isa element count 2
Category 'subclass_of' is unknown in the current Biolink Model
CHEBI:has_parent_hydride element count 2
GO:isa element count 2
Category 'related_to' is not in CamelCase form
CHEBI:is_conjugate_acid_of element count 6
CHEBI:is_conjugate_base_of element count 6
GOREL:0002005 element count 6
GOREL:0012006 element count 6
MONDO:disease_shares_features_of element count 6
UBERON:synapsed_by element count 6
...
Category 'related_to' is unknown in the current Biolink Model
CHEBI:is_conjugate_acid_of element count 6
CHEBI:is_conjugate_base_of element count 6
GOREL:0002005 element count 6
GOREL:0012006 element count 6
MONDO:disease_shares_features_of element count 6
UBERON:synapsed_by element count 6
...
Category 'close_match' is not in CamelCase form
CHEBI:is_enantiomer_of element count 2
CHEBI:is_tautomer_of element count 2
Category 'close_match' is unknown in the current Biolink Model
CHEBI:is_enantiomer_of element count 2
CHEBI:is_tautomer_of element count 2
Category 'part_of' is not in CamelCase form
CHEBI:is_substituent_group_from element count 3
MONDO:part_of_progression_of_disease element count 3
UBERON:subdivision_of element count 3
Category 'part_of' is unknown in the current Biolink Model
CHEBI:is_substituent_group_from element count 3
MONDO:part_of_progression_of_disease element count 3
UBERON:subdivision_of element count 3
Category 'causes' is not in CamelCase form
GOREL:0000040 element count 3
MONDO:disease_causes_feature element count 3
MONDO:disease_triggers element count 3
Category 'causes' is unknown in the current Biolink Model
GOREL:0000040 element count 3
MONDO:disease_causes_feature element count 3
MONDO:disease_triggers element count 3
Category 'located_in' is not in CamelCase form
GOREL:0001004 element count 1
Category 'located_in' is unknown in the current Biolink Model
GOREL:0001004 element count 1
Category 'affects' is not in CamelCase form
GOREL:0001006 element count 1
Category 'affects' is unknown in the current Biolink Model
GOREL:0001006 element count 1
Category 'affects_localization_of' is not in CamelCase form
GOREL:0002003 element count 1
Category 'affects_localization_of' is unknown in the current Biolink Model
GOREL:0002003 element count 1
Category 'increases_degradation_of' is not in CamelCase form
GOREL:0002004 element count 1
Category 'increases_degradation_of' is unknown in the current Biolink Model
GOREL:0002004 element count 1
Category 'Occurrent' is a mixin in the Biolink Model
GO:0000001 element count 38565
GO:0000002 element count 38565
GO:0000003 element count 38565
GO:0000006 element count 38565
GO:0000007 element count 38565
GO:0000009 element count 38565
...
Category 'MacromolecularComplexMixin' is unknown in the current Biolink Model
GO:0000015 element count 2100
GO:0000109 element count 2100
GO:0000110 element count 2100
GO:0000111 element count 2100
GO:0000112 element count 2100
GO:0000113 element count 2100
...
Category 'superclass_of' is not in CamelCase form
GO:inverse_isa element count 2
OMIM:has_manifestation element count 2
Category 'superclass_of' is unknown in the current Biolink Model
GO:inverse_isa element count 2
OMIM:has_manifestation element count 2
Category 'disease_has_basis_in' is not in CamelCase form
MONDO:disease_has_basis_in_accumulation_of element count 2
MONDO:disease_has_basis_in_development_of element count 2
Category 'disease_has_basis_in' is unknown in the current Biolink Model
MONDO:disease_has_basis_in_accumulation_of element count 2
MONDO:disease_has_basis_in_development_of element count 2
Category 'disease_has_location' is not in CamelCase form
MONDO:disease_has_location element count 1
Category 'disease_has_location' is unknown in the current Biolink Model
MONDO:disease_has_location element count 1
Category 'has_part' is not in CamelCase form
MONDO:disease_has_major_feature element count 1
Category 'has_part' is unknown in the current Biolink Model
MONDO:disease_has_major_feature element count 1
Category 'treated_by' is not in CamelCase form
MONDO:disease_responds_to element count 1
Category 'treated_by' is unknown in the current Biolink Model
MONDO:disease_responds_to element count 1
Category 'same_as' is not in CamelCase form
MONDO:equivalentTo element count 1
Category 'same_as' is unknown in the current Biolink Model
MONDO:equivalentTo element count 1
Category 'contributes_to' is not in CamelCase form
MONDO:predisposes_towards element count 1
Category 'contributes_to' is unknown in the current Biolink Model
MONDO:predisposes_towards element count 1
Category 'PathologicalEntityMixin' is a mixin in the Biolink Model
MPATH:0 element count 839
MPATH:1 element count 839
MPATH:10 element count 839
MPATH:100 element count 839
MPATH:101 element count 839
MPATH:102 element count 839
...
Category 'has_attribute' is not in CamelCase form
OMIM:has_inheritance_type element count 1
Category 'has_attribute' is unknown in the current Biolink Model
OMIM:has_inheritance_type element count 1
Category 'manifestation_of' is not in CamelCase form
OMIM:manifestation_of element count 1
Category 'manifestation_of' is unknown in the current Biolink Model
OMIM:manifestation_of element count 1
Category 'coexists_with' is not in CamelCase form
UBERON:anastomoses_with element count 18
UBERON:anteriorly_connected_to element count 18
UBERON:channel_for element count 18
UBERON:channels_from element count 18
UBERON:channels_into element count 18
UBERON:conduit_for element count 18
...
...
INVALID_EDGE_PROPERTY_VALUE_TYPE
Multi-valued edge property 'has_evidence' is expected to be of type 'list'
HGNC:11629->MGI:103180 element count 2579391
HGNC:11629->NCBIGene:514216 element count 2579391
HGNC:11629->NCBIGene:100152381 element count 2579391
HGNC:11629->Xenbase:XB-GENE-487230 element count 2579391
HGNC:11629->ZFIN:ZDB-GENE-060324-2 element count 2579391
HGNC:11629->WB:WBGene00007227 element count 2579391
...
INVALID_EDGE_PROPERTY_VALUE
Edge property 'subject' has a value 'EMAPA:0' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:0->UBERON:0000061 element count 1
Edge property 'subject' has a value 'EMAPA:16032' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16032->EMAPA:31859 element count 2
EMAPA:16032->EMAPA:36041 element count 2
Edge property 'object' has a value 'EMAPA:31859' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16032->EMAPA:31859 element count 6
EMAPA:16034->EMAPA:31859 element count 6
MGI:1920958->EMAPA:31859 element count 6
MGI:1924378->EMAPA:31859 element count 6
MGI:96285->EMAPA:31859 element count 6
MGI:95305->EMAPA:31859 element count 6
...
Edge property 'object' has a value 'EMAPA:36041' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16032->EMAPA:36041 element count 624
EMAPA:16033->EMAPA:36041 element count 624
EMAPA:16034->EMAPA:36041 element count 624
EMAPA:16035->EMAPA:36041 element count 624
MGI:88354->EMAPA:36041 element count 624
MGI:95755->EMAPA:36041 element count 624
...
Edge property 'subject' has a value 'EMAPA:16033' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16033->EMAPA:36032 element count 2
EMAPA:16033->EMAPA:36041 element count 2
Edge property 'object' has a value 'EMAPA:36032' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16033->EMAPA:36032 element count 14
EMAPA:16036->EMAPA:36032 element count 14
EMAPA:16037->EMAPA:36032 element count 14
EMAPA:16040->EMAPA:36032 element count 14
MGI:97797->EMAPA:36032 element count 14
MGI:97798->EMAPA:36032 element count 14
...
Edge property 'subject' has a value 'EMAPA:16034' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16034->EMAPA:31859 element count 7
EMAPA:16034->EMAPA:36041 element count 7
EMAPA:16034->EMAPA:36042 element count 7
EMAPA:16034->EMAPA:36043 element count 7
EMAPA:16034->EMAPA:36044 element count 7
EMAPA:16034->EMAPA:36045 element count 7
...
Edge property 'object' has a value 'EMAPA:36042' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16034->EMAPA:36042 element count 1173
EMAPA:16035->EMAPA:36042 element count 1173
EMAPA:16036->EMAPA:36042 element count 1173
MGI:88354->EMAPA:36042 element count 1173
MGI:101950->EMAPA:36042 element count 1173
MGI:105384->EMAPA:36042 element count 1173
...
Edge property 'object' has a value 'EMAPA:36043' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16034->EMAPA:36043 element count 779
EMAPA:16035->EMAPA:36043 element count 779
EMAPA:31864->EMAPA:36043 element count 779
MGI:88354->EMAPA:36043 element count 779
MGI:95298->EMAPA:36043 element count 779
MGI:106906->EMAPA:36043 element count 779
...
Edge property 'object' has a value 'EMAPA:36044' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16034->EMAPA:36044 element count 829
EMAPA:16035->EMAPA:36044 element count 829
EMAPA:31865->EMAPA:36044 element count 829
MGI:88354->EMAPA:36044 element count 829
MGI:101950->EMAPA:36044 element count 829
MGI:106924->EMAPA:36044 element count 829
...
Edge property 'object' has a value 'EMAPA:36045' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16034->EMAPA:36045 element count 1012
EMAPA:16035->EMAPA:36045 element count 1012
EMAPA:16040->EMAPA:36045 element count 1012
MGI:96601->EMAPA:36045 element count 1012
MGI:96610->EMAPA:36045 element count 1012
MGI:97073->EMAPA:36045 element count 1012
...
Edge property 'object' has a value 'EMAPA:36046' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16034->EMAPA:36046 element count 1500
EMAPA:16035->EMAPA:36046 element count 1500
EMAPA:36035->EMAPA:36046 element count 1500
MGI:88354->EMAPA:36046 element count 1500
MGI:95755->EMAPA:36046 element count 1500
MGI:101950->EMAPA:36046 element count 1500
...
Edge property 'subject' has a value 'EMAPA:16035' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16035->UBERON:0000086 element count 7
EMAPA:16035->EMAPA:36041 element count 7
EMAPA:16035->EMAPA:36042 element count 7
EMAPA:16035->EMAPA:36043 element count 7
EMAPA:16035->EMAPA:36044 element count 7
EMAPA:16035->EMAPA:36045 element count 7
...
Edge property 'subject' has a value 'EMAPA:16036' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16036->EMAPA:36032 element count 3
EMAPA:16036->UBERON:0019249 element count 3
EMAPA:16036->EMAPA:36042 element count 3
Edge property 'subject' has a value 'EMAPA:16037' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16037->EMAPA:36032 element count 3
EMAPA:16037->UBERON:0019250 element count 3
EMAPA:16037->EMAPA:36063 element count 3
Edge property 'object' has a value 'EMAPA:36063' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16037->EMAPA:36063 element count 100
EMAPA:36043->EMAPA:36063 element count 100
EMAPA:36044->EMAPA:36063 element count 100
MGI:97171->EMAPA:36063 element count 100
MGI:97172->EMAPA:36063 element count 100
MGI:108515->EMAPA:36063 element count 100
...
Edge property 'subject' has a value 'EMAPA:16039' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16039->UBERON:0000922 element count 2
EMAPA:16039->EMAPA:36040 element count 2
Edge property 'object' has a value 'EMAPA:36040' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16039->EMAPA:36040 element count 261
EMAPA:31859->EMAPA:36040 element count 261
EMAPA:36473->EMAPA:36040 element count 261
EMAPA:36699->EMAPA:36040 element count 261
MGI:95661->EMAPA:36040 element count 261
MGI:96683->EMAPA:36040 element count 261
...
Edge property 'subject' has a value 'EMAPA:16040' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16040->EMAPA:36032 element count 2
EMAPA:16040->EMAPA:36045 element count 2
Edge property 'subject' has a value 'EMAPA:16041' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16041->EMAPA:16039 element count 3
EMAPA:16041->UBERON:0000087 element count 3
EMAPA:16041->EMAPA:36035 element count 3
Edge property 'object' has a value 'EMAPA:16039' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16041->EMAPA:16039 element count 5506
EMAPA:16050->EMAPA:16039 element count 5506
EMAPA:16060->EMAPA:16039 element count 5506
EMAPA:16062->EMAPA:16039 element count 5506
EMAPA:16069->EMAPA:16039 element count 5506
EMAPA:16071->EMAPA:16039 element count 5506
...
Edge property 'object' has a value 'EMAPA:36035' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16041->EMAPA:36035 element count 306
EMAPA:16044->EMAPA:36035 element count 306
EMAPA:16046->EMAPA:36035 element count 306
EMAPA:16050->EMAPA:36035 element count 306
EMAPA:16051->EMAPA:36035 element count 306
EMAPA:16053->EMAPA:36035 element count 306
...
Edge property 'subject' has a value 'EMAPA:16042' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16042->UBERON:0016887 element count 2
EMAPA:16042->EMAPA:36119 element count 2
Edge property 'object' has a value 'EMAPA:36119' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16042->EMAPA:36119 element count 14
EMAPA:16050->EMAPA:36119 element count 14
EMAPA:16051->EMAPA:36119 element count 14
MGI:96787->EMAPA:36119 element count 14
MGI:96788->EMAPA:36119 element count 14
MGI:96560->EMAPA:36119 element count 14
...
Edge property 'subject' has a value 'EMAPA:16043' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16043->EMAPA:36037 element count 1
Edge property 'object' has a value 'EMAPA:36037' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16043->EMAPA:36037 element count 4
EMAPA:16054->EMAPA:36037 element count 4
EMAPA:16060->EMAPA:36037 element count 4
EMAPA:36038->EMAPA:36037 element count 4
Edge property 'subject' has a value 'EMAPA:16044' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16044->EMAPA:16043 element count 3
EMAPA:16044->UBERON:0000090 element count 3
EMAPA:16044->EMAPA:36035 element count 3
Edge property 'object' has a value 'EMAPA:16043' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16044->EMAPA:16043 element count 1
Edge property 'subject' has a value 'EMAPA:16046' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16046->UBERON:0004345 element count 3
EMAPA:16046->EMAPA:16042 element count 3
EMAPA:16046->EMAPA:36035 element count 3
Edge property 'object' has a value 'EMAPA:16042' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16046->EMAPA:16042 element count 860
EMAPA:16052->EMAPA:16042 element count 860
EMAPA:16054->EMAPA:16042 element count 860
EMAPA:16065->EMAPA:16042 element count 860
EMAPA:16076->EMAPA:16042 element count 860
EMAPA:16085->EMAPA:16042 element count 860
...
Edge property 'subject' has a value 'EMAPA:16047' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16047->UBERON:0006265 element count 2
EMAPA:16047->EMAPA:16046 element count 2
Edge property 'object' has a value 'EMAPA:16046' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16047->EMAPA:16046 element count 358
EMAPA:16048->EMAPA:16046 element count 358
EMAPA:31876->EMAPA:16046 element count 358
EMAPA:31877->EMAPA:16046 element count 358
EMAPA:31878->EMAPA:16046 element count 358
EMAPA:38205->EMAPA:16046 element count 358
...
Edge property 'subject' has a value 'EMAPA:16048' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16048->UBERON:0006280 element count 2
EMAPA:16048->EMAPA:16046 element count 2
Edge property 'subject' has a value 'EMAPA:16050' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16050->EMAPA:16039 element count 4
EMAPA:16050->UBERON:0008780 element count 4
EMAPA:16050->EMAPA:36035 element count 4
EMAPA:16050->EMAPA:36119 element count 4
Edge property 'subject' has a value 'EMAPA:16051' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16051->UBERON:0008776 element count 4
EMAPA:16051->EMAPA:35986 element count 4
EMAPA:16051->EMAPA:36035 element count 4
EMAPA:16051->EMAPA:36119 element count 4
Edge property 'object' has a value 'EMAPA:35986' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16051->EMAPA:35986 element count 18
EMAPA:16052->EMAPA:35986 element count 18
EMAPA:16056->EMAPA:35986 element count 18
EMAPA:16062->EMAPA:35986 element count 18
MGI:107191->EMAPA:35986 element count 18
MGI:1352738->EMAPA:35986 element count 18
...
Edge property 'subject' has a value 'EMAPA:16052' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16052->EMAPA:35986 element count 3
EMAPA:16052->UBERON:0008945 element count 3
EMAPA:16052->EMAPA:16042 element count 3
Edge property 'subject' has a value 'EMAPA:16053' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16053->UBERON:0008800 element count 3
EMAPA:16053->EMAPA:16052 element count 3
EMAPA:16053->EMAPA:36035 element count 3
Edge property 'object' has a value 'EMAPA:16052' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16053->EMAPA:16052 element count 51
EMAPA:16058->EMAPA:16052 element count 51
EMAPA:16086->EMAPA:16052 element count 51
MGI:95713->EMAPA:16052 element count 51
MGI:103577->EMAPA:16052 element count 51
MGI:103580->EMAPA:16052 element count 51
...
Edge property 'subject' has a value 'EMAPA:16054' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16054->EMAPA:36037 element count 3
EMAPA:16054->UBERON:0012466 element count 3
EMAPA:16054->EMAPA:16042 element count 3
Edge property 'subject' has a value 'EMAPA:16055' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16055->EMAPA:16054 element count 2
EMAPA:16055->UBERON:0005251 element count 2
Edge property 'object' has a value 'EMAPA:16054' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16055->EMAPA:16054 element count 9
EMAPA:16064->EMAPA:16054 element count 9
EMAPA:16079->EMAPA:16054 element count 9
EMAPA:16080->EMAPA:16054 element count 9
EMAPA:16081->EMAPA:16054 element count 9
EMAPA:16082->EMAPA:16054 element count 9
...
Edge property 'subject' has a value 'EMAPA:16056' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16056->UBERON:0003064 element count 2
EMAPA:16056->EMAPA:35986 element count 2
Edge property 'subject' has a value 'EMAPA:16057' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16057->EMAPA:38030 element count 3
EMAPA:16057->UBERON:0004369 element count 3
EMAPA:16057->EMAPA:16053 element count 3
Edge property 'object' has a value 'EMAPA:38030' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16057->EMAPA:38030 element count 25
EMAPA:38031->EMAPA:38030 element count 25
MGI:1328314->EMAPA:38030 element count 25
MGI:97527->EMAPA:38030 element count 25
MGI:97530->EMAPA:38030 element count 25
MGI:97342->EMAPA:38030 element count 25
...
Edge property 'object' has a value 'EMAPA:16053' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16057->EMAPA:16053 element count 60
EMAPA:35928->EMAPA:16053 element count 60
MGI:97073->EMAPA:16053 element count 60
MGI:104328->EMAPA:16053 element count 60
MGI:95517->EMAPA:16053 element count 60
MGI:95586->EMAPA:16053 element count 60
...
Edge property 'subject' has a value 'EMAPA:16058' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16058->UBERON:0004877 element count 2
EMAPA:16058->EMAPA:16052 element count 2
Edge property 'subject' has a value 'EMAPA:16059' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16059->UBERON:0004364 element count 2
EMAPA:16059->EMAPA:16048 element count 2
Edge property 'object' has a value 'EMAPA:16048' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16059->EMAPA:16048 element count 33
MGI:88180->EMAPA:16048 element count 33
MGI:88105->EMAPA:16048 element count 33
MGI:88108->EMAPA:16048 element count 33
MGI:1201683->EMAPA:16048 element count 33
MGI:97845->EMAPA:16048 element count 33
...
Edge property 'subject' has a value 'EMAPA:16060' with a CURIE prefix 'EMAPA' that is not represented in Biolink Model JSON-LD context
EMAPA:16060->EMAPA:36037 element count 3
EMAPA:16060->UBERON:0005906 element count 3
EMAPA:16060->EMAPA:16039 element count 3
...
We'd like to get additional insight from @amc-corey-cox & @cmungall during an upcoming Data Call. @sagehrke 👀 👆
I found myself going down a validation rabbit hole this week that wasn't represented in an issue, so I wanted to get it written down and try to nail down for myself what we can achieve and what "done" will look like in the short term.
I've been exploring kgx validation, and I think we can benefit from it, but we need to work around existing limitations.
Too much output
This will likely improve over time, for now kgx is enumerating each and every node or edge with the same problem. @bgood had a nice suggestion in https://github.com/biolink/kgx/issues/354 that I slightly tweaked:
This produces pretty good output, but, for example, it still floods with too many examples of the same prefix complaint, which hides other prefix complaints that won't be visible unless the others are fixed, which is something like a 16 hour round trip because it's....
Too slow
kgx validate on the current monarch-kg is taking 10 hours, which is way too long to add to our existing pipeline that is unfortunately ballooning into the 6 hour range. I'm sure this could be massively improved on the kgx side, but even without that, could probably mitigate by putting the validation in it's own Jenkins job that runs after a kg build.