GORULE violations assigned by ARUK-UCL

Contents

gorule-0000008 No annotations should be made to uninformative high level terms

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.

gorule-0000061 Allowed gene product to term relations (gp2term)

MESSAGES

gorule-0000008

No annotations should be made to uninformative high level terms

• total: 4

messages

• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`MGI MGI:97321 Ngf involved_in GO:0043388 PMID:10362258 IMP P Beta-nerve growth factor protein taxon:10090 20180124 ARUK-UCL has_input(UniProtKB:B2RWS6),has_input(UniProtKB:P38936),has_input(CHEBI:4705)|has_input(UniProtKB:O89090),has_input(UniProtKB:P38936),has_input(CHEBI:4705)|has_input(UniProtKB:O70494),has_input(UniProtKB:P38936),has_input(CHEBI:4705) `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`MGI MGI:95629 Slc6a13 enables GO:0005368 PMID:22896705 IMP F Sodium- and chloride-dependent GABA transporter 2 protein taxon:10090 20200605 ARUK-UCL part_of(UBERON:0002107) `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`MGI MGI:87904 Actb involved_in GO:0032091 PMID:19118186 IDA P Actin, cytoplasmic 1 protein taxon:10090 20171103 ARUK-UCL has_input(UniProtKB:P61809),has_input(UniProtKB:P49615) `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`MGI MGI:1341865 Mark3 involved_in GO:0032092 PMID:9543386 ISS UniProtKB:P27448 P MAP/microtubule affinity-regulating kinase 3 protein taxon:10090 20180328 ARUK-UCL has_input(UniProtKB:P48967),has_input(UniProtKB:P63101) `

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

• total: 6

messages

• ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`MGI MGI:97810 Ptprc involved_in GO:0044855 PMID:15661907 IGI UniProtKB:P05480 P Receptor-type tyrosine-protein phosphatase C protein taxon:10090 20180724 ARUK-UCL occurs_in(CL:0000084),has_end_location(GO:0042101),part_of(GO:0031668),occurs_in(GO:0098857) `
• ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`MGI MGI:894311 Lilrb3 involved_in GO:0035307 PMID:24052308 IGI ComplexPortal:CPX-1134 P Leukocyte immunoglobulin-like receptor subfamily B member 3 protein taxon:10090 20170725 ARUK-UCL occurs_in(CL:0010012),has_input(UniProtKB:P18760) `
• ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`MGI MGI:1196625 Fzd1 involved_in GO:0036520 PMID:21752258 IMP P Frizzled-1 protein taxon:10090 20190918 ARUK-UCL occurs_in(CL:2000097),causally_upstream_of(GO:1903204) `
• ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`MGI MGI:1196625 Fzd1 involved_in GO:0060070 PMID:21752258 IMP P Frizzled-1 protein taxon:10090 20190918 ARUK-UCL occurs_in(CL:2000097),part_of(GO:0036520),part_of(GO:1903204) `
• ERROR - Obsolete class with no replacement:Violates GORULE:0000020--`MGI MGI:98953 Wnt1 involved_in GO:0060070 PMID:21752258 IMP P Proto-oncogene Wnt-1 protein taxon:10090 20190918 ARUK-UCL occurs_in(CL:2000097),part_of(GO:0036520),part_of(GO:1903204) `
• WARNING - Obsolete class:Violates GORULE:0000020, but was repaired--`MGI MGI:95665 Gba1 acts_upstream_of_or_within GO:1904925 PMID:23707074 IMP P Lysosomal acid glucosylceramidase protein taxon:10090 20230704 ARUK-UCL occurs_in(UBERON:0001891),occurs_in(CL:0000540)|occurs_in(UBERON:0001891),occurs_in(CL:0000127) `

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: 3

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 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:97275 Myod1 enables GO:0042803 PMID:10652346 IPI UniProtKB:P10085 F Myoblast determination protein 1 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:894311 Lilrb3 enables GO:0042803 PMID:24052308 IPI UniProtKB:P97484 F Leukocyte immunoglobulin-like receptor subfamily B member 3 protein taxon:10090 20230314 ARUK-UCL causally_upstream_of(GO:0001540) `

gorule-0000061

Allowed gene product to term relations (gp2term)

• total: 2

messages

• WARNING - Violates GO Rule:GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: RO:0002432 should be one of BFO:0000050. Repaired to BFO:0000050--`MGI MGI:96247 Hsp90ab1 is_active_in GO:0101031 PMID:17517623 IMP C Heat shock protein HSP 90-beta protein taxon:10090 20240320 ARUK-UCL `
• WARNING - Violates GO Rule:GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: RO:0002432 should be one of BFO:0000050. Repaired to BFO:0000050--`MGI MGI:2442926 Mettl14 is_active_in GO:0036396 PMID:29290617 IDA C N6-adenosine-methyltransferase non-catalytic subunit protein taxon:10090 20240206 ARUK-UCL `