GORULE violations assigned by ARUK-UCL

Contents

gorule-0000001 GAF lines are parsed according to GAF 2.2 specifications

gorule-0000013 Taxon-appropriate annotation check

gorule-0000020 Automatic repair of annotations to merged or obsoleted terms

gorule-0000046 The ‘with’ field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to ‘self-binding’ terms.

MESSAGES

gorule-0000001

GAF lines are parsed according to GAF 2.2 specifications

• total: 8

messages

• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 acts_upstream_of GO:0051897 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606 20200821 ARUK-UCL occurs_in(CL:0000182) `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 acts_upstream_of GO:1900017 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606 20200821 ARUK-UCL has_input(UniProtKB:P01579),occurs_in(CL:0000182)|has_input(UniProtKB:P05231),occurs_in(CL:0000182)|has_input(UniProtKB:Q14116),occurs_in(CL:0000182) `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 acts_upstream_of GO:1903428 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606 20200821 ARUK-UCL occurs_in(CL:0000182) `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 acts_upstream_of GO:1903945 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606 20200821 ARUK-UCL `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 acts_upstream_of GO:2000378 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606 20230717 ARUK-UCL occurs_in(CL:0000182) `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 acts_upstream_of GO:2001170 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606 20200821 ARUK-UCL occurs_in(CL:0000182) `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 involved_in GO:0035196 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606 20200821 ARUK-UCL has_input(RNAcentral:URS00004E5112_9606),occurs_in(CL:0000182) `
• WARNING - Invalid subject type:defaulting to 'gene_product'--`RNAcentral URS0000812128_9606 URS0000812128_9606 involved_in GO:0098586 PMID:31574452 IMP P Homo sapiens (human) H19 imprinted maternally expressed transcript sRNA taxon:9606|taxon:10407 20200821 ARUK-UCL occurs_in(CL:0000182) `

gorule-0000013

Taxon-appropriate annotation check

• total: 6

messages

• WARNING - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`UniProtKB Q29599 OAS1 involved_in GO:1904188 PMID:20844035 IDA P 2'-5'-oligoadenylate synthase 1 OAS1 protein taxon:9823|taxon:10310 20230314 ARUK-UCL UniProtKB:Q29599 `
• WARNING - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`UniProtKB Q29599 OAS1 involved_in GO:1904188 PMID:20844035 IDA P 2'-5'-oligoadenylate synthase 1 OAS1 protein taxon:9823|taxon:11276 20230314 ARUK-UCL UniProtKB:Q29599 `
• WARNING - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`UniProtKB Q07869 PPARA acts_upstream_of_or_within GO:1904189 PMID:22479552 IMP P Peroxisome proliferator-activated receptor alpha PPARA|NR1C1|PPAR protein taxon:9606|taxon:10407 20230314 ARUK-UCL UniProtKB:Q07869 `
• WARNING - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`RNAcentral URS000003E1A9_9606 URS000003E1A9_9606 acts_upstream_of GO:1904188 PMID:22479552 IDA P Homo sapiens (human) hsa-miR-141-3p miRNA taxon:9606|taxon:10407 20230314 ARUK-UCL `
• WARNING - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`RNAcentral URS000019907A_9606 URS000019907A_9606 acts_upstream_of GO:1904188 PMID:23418453 IMP P Homo sapiens (human) hsa-miR-30c-5p miRNA taxon:9606|taxon:11103 20230314 ARUK-UCL `
• WARNING - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`RNAcentral URS0000315338_9606 URS0000315338_9606 acts_upstream_of GO:1904187 PMID:23418453 IMP P Homo sapiens (human) hsa-miR-130a-3p miRNA taxon:9606|taxon:11103 20230314 ARUK-UCL `

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

• total: 2

messages

• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`RNAcentral URS0000DB8B87_9606 URS0000DB8B87_9606 enables GO:0140463 PMID:31048766 TAS F Homo sapiens (human) X inactive specific transcript lncRNA taxon:9606 20241116 ARUK-UCL part_of(GO:0060816)|part_of(GO:0051303) `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`RNAcentral URS0000DB8B87_9606 URS0000DB8B87_9606 involved_in GO:0051303 PMID:31048766 TAS P Homo sapiens (human) X inactive specific transcript lncRNA taxon:9606 20230530 ARUK-UCL `

gorule-0000046

The ‘with’ field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to ‘self-binding’ terms.

• total: 17

messages

• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`MGI MGI:1196458 Scarb2 enables GO:0042803 PMID:29199275 IPI UniProtKB:O35114 F Lysosome membrane protein 2 Scarb2 protein taxon:10090 20181031 ARUK-UCL `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`MGI MGI:1196458 mSCARB2 enables GO:0042803 PMID:29199275 IPI UniProtKB:O35114 F lysosome membrane protein 2 (mouse) 85 kDa lysosomal membrane sialoglycoprotein (mouse)|LGP85 (mouse)|LIMP II (mouse)|lysosome membrane protein II (mouse)|mSCARB2|scavenger receptor class B member 2 (mouse) protein taxon:10090 20181031 ARUK-UCL `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`MGI MGI:894311 Pirb enables GO:0042803 PMID:24052308 IPI UniProtKB:P97484 F Paired immunoglobulin-like receptor B Lilrb3|Pirb protein taxon:10090 20230314 ARUK-UCL causally_upstream_of(GO:0001540) `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`MGI MGI:894311 mPirb enables GO:0042803 PMID:24052308 IPI UniProtKB:P97484 F paired immunoglobulin-like receptor B (mouse) LIR-3 (mouse)|PIR-B (mouse)|cell-surface glycoprotein p91 (mouse)|leukocyte immunoglobulin-like receptor 3 (mouse)|leukocyte immunoglobulin-like receptor subfamily B member 3 (mouse)|mPirb protein taxon:10090 20230314 ARUK-UCL causally_upstream_of(GO:0001540) `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`MGI MGI:97275 Myod1 enables GO:0042803 PMID:10652346 IPI UniProtKB:P10085 F Myoblast determination protein 1 Myod|Myod1 protein taxon:10090 20230314 ARUK-UCL `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`MGI MGI:97275 mMYOD1 enables GO:0042803 PMID:10652346 IPI UniProtKB:P10085 F myoblast determination protein 1 (mouse) mMYOD1 protein taxon:10090 20230314 ARUK-UCL `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP enables GO:0042803 PMID:15447668 IPI UniProtKB:P05067-PRO_0000000092 F Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL UniProtKB:P05067-PRO_0000000092 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP enables GO:0042803 PMID:15447668 IPI UniProtKB:P05067-PRO_0000000093 F Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL UniProtKB:P05067-PRO_0000000093 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP enables GO:0042803 PMID:18568035 IPI UniProtKB:P05067-PRO_0000000092 F Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20170213 ARUK-UCL UniProtKB:P05067-PRO_0000000092 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP enables GO:0042803 PMID:22179788 IPI UniProtKB:P05067-PRO_0000000093 F Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL UniProtKB:P05067-PRO_0000000093 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP enables GO:0042803 PMID:23386614 IPI UniProtKB:P05067-PRO_0000000092 F Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL UniProtKB:P05067-PRO_0000000092 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP involved_in GO:0051260 PMID:15447668 IPI UniProtKB:P05067-PRO_0000000092 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL UniProtKB:P05067-PRO_0000000092 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP involved_in GO:0051260 PMID:15447668 IPI UniProtKB:P05067-PRO_0000000093 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL has_input(UniProtKB:P05067-PRO_0000000093) UniProtKB:P05067-PRO_0000000093 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP involved_in GO:0051260 PMID:18602473 IPI UniProtKB:P05067-PRO_0000000093 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL UniProtKB:P05067-PRO_0000000093 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P05067 APP involved_in GO:0051260 PMID:23386614 IPI UniProtKB:P05067-PRO_0000000092 P Amyloid-beta precursor protein APP|A4|AD1 protein taxon:9606 20230314 ARUK-UCL has_input(UniProtKB:P05067) UniProtKB:P05067-PRO_0000000092 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P10636 MAPT involved_in GO:0051260 PMID:26704708 IPI UniProtKB:P10636-8 P Microtubule-associated protein tau MAPT|MAPTL|MTBT1|TAU protein taxon:9606 20230314 ARUK-UCL happens_during(UBERON:0000112),happens_during(GO:0018105),occurs_in(UBERON:0002421),regulates(GO:0007611)|happens_during(UBERON:0018241),happens_during(GO:0018105),occurs_in(UBERON:0002421),regulates(GO:0007611) UniProtKB:P10636-8 `
• WARNING - Violates GO Rule:GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms--`UniProtKB P15172 MYOD1 enables GO:0042803 GO_REF:0000024 ISS UniProtKB:P10085 F Myoblast determination protein 1 MYOD1|BHLHC1|MYF3|MYOD protein taxon:9606 20230314 ARUK-UCL UniProtKB:P15172 `