GORULE violations assigned by xenbase

gorule-0000006 IEP and HEP usage is restricted to terms from the Biological Process ontology

gorule-0000013 Taxon-appropriate annotation check

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

gorule-0000065 Annotations to term that are candidates for obsoletion should be produce a warning

MESSAGES

IEP and HEP usage is restricted to terms from the Biological Process ontology

ERROR - Violates GO Rule:GORULE:0000006: IEP and HEP usage is restricted to terms from the Biological Process ontology--`Xenbase XB-GENE-1017281 trim36 is_active_in GO:0005938 PMID:23615278 IEP C tripartite motif containing 36 Haprin protein taxon:8364 20220222 Xenbase `
ERROR - Violates GO Rule:GORULE:0000006: IEP and HEP usage is restricted to terms from the Biological Process ontology--`Xenbase XB-GENE-1034769 sox9 enables GO:0003714 PMID:22927467 IEP F SRY-box 9 cmd1|cmpd1|sox-9|sox9-a|sox9-b|sra1 protein taxon:8364 20220222 Xenbase part_of(GO:0014029) `
ERROR - Violates GO Rule:GORULE:0000006: IEP and HEP usage is restricted to terms from the Biological Process ontology--`Xenbase XB-GENE-1034769 sox9 enables GO:0003714 PMID:22927467 IEP F SRY-box 9 cmd1|cmpd1|sox-9|sox9-a|sox9-b|sra1 protein taxon:8364 20220222 Xenbase part_of(GO:0048839) `
ERROR - Violates GO Rule:GORULE:0000006: IEP and HEP usage is restricted to terms from the Biological Process ontology--`Xenbase XB-GENE-6486303 kmt2d.L is_active_in GO:0005737 PMID:31813957 IEP C lysine methyltransferase 2D L homeolog mll2 protein taxon:8355 20200626 Xenbase `

Taxon-appropriate annotation check

WARNING - Violates GO Rule:GORULE:0000013: Taxon-appropriate annotation check--`Xenbase XB-GENE-17342057 notch1.L acts_upstream_of_or_within GO:1905275 PMID:31899211 IMP P notch 1 receptor L homeolog notch|notch-1|xnotch|x-notch-1|xnotch1|xotch protein taxon:8355 20200626 Xenbase `

Allowed gene product to term relations (gp2term)

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--`Xenbase XB-GENE-6251797 vangl2.L is_active_in GO:0098797 PMID:34806749 IDA C VANGL planar cell polarity protein 2 L homeolog lpp1|ltap|stb1|stbm|stbm1|strabismus|vang|vangl2-a|vangl2-b|vang-like 2|Van Gogh|van gogh-like2|Xstrabismus protein taxon:8355 20230509 Xenbase `
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--`Xenbase XB-GENE-940037 prickle3.L is_active_in GO:0098797 PMID:34806749 IDA C prickle homolog 3 L homeolog LOC108699981|pk3|prickle-3 protein taxon:8355 20230509 Xenbase `

Annotations to term that are candidates for obsoletion should be produce a warning

WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`Xenbase XB-GENE-17340943 ccdc88c.L acts_upstream_of_or_within GO:0007258 PMID:16026968 IMP P coiled-coil domain containing 88C L homeolog daple|LOC108698716|LOC108699825|XDal protein taxon:8355 20181026 Xenbase `
WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`Xenbase XB-GENE-483735 fzd7.L acts_upstream_of_or_within GO:0007258 PMID:16026968 IMP P frizzled class receptor 7 L homeolog frizzled 7|frizzled-7|frizzled7|frz-7|frz7|fz7|Fz-7|Xfz7 protein taxon:8355 20190411 Xenbase `
WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`Xenbase XB-GENE-6488002 pnhd.L acts_upstream_of_or_within_negative_effect GO:0006468 PMID:32859582 IDA P pinhead L homeolog pinhead protein taxon:8355 20230711 Xenbase has_input(Xenbase:XB-GENE-17332607) `