GORULE violations assigned by TIGR

Contents

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

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

gorule-0000027 Each identifier in GAF is valid

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

gorule-0000065 Annotations to term that are candidates for obsoletion should be removed

MESSAGES

gorule-0000001

GAF lines are parsed according to GAF 2.2 specifications

• total: 2

messages

• WARNING - Invalid subject type:has been repaired--`AGI_LocusCode AT2G23040 AT2G23040 enables GO:0003674 TAIR:Communication:1345790 ND F AT2G23040 AT2G23040|F21P24.10|F21P24_10 lnc_RNA taxon:3702 20031004 TIGR TAIR:locus:2045304`
• WARNING - Invalid subject type:has been repaired--`AGI_LocusCode AT5G49410 R8 enables GO:0003674 TAIR:Communication:1345790 ND F AT5G49410 AT5G49410|R8|K7J8.8|K7J8_8 lnc_RNA taxon:3702 20031004 TIGR TAIR:locus:2158034`

gorule-0000008

No annotations should be made to uninformative high level terms

• total: 16

messages

• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT4G29010 AIM1 acts_upstream_of_or_within GO:0007275 TAIR:Publication:1097|PMID:10521521 IMP P AT4G29010 AT4G29010|AIM1|ABNORMAL INFLORESCENCE MERISTEM|F19B15.40|F19B15_40 protein taxon:3702 20030512 TIGR TAIR:locus:2119891 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G17520 RCP1 acts_upstream_of_or_within GO:0007275 TAIR:Publication:1060|PMID:10536027 IMP P AT5G17520 AT5G17520|RCP1|MEX1|ROOT CAP 1|MALTOSE EXCESS 1|K3M16.90|K3M16_90 protein taxon:3702 20030417 TIGR TAIR:locus:2157492 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT2G27250 CLV3 acts_upstream_of_or_within GO:0016043 TAIR:Publication:202|PMID:10915624 IMP P AT2G27250 AT2G27250|CLV3|AtCLV3|CLAVATA3|f12k2.17|f12k2_17 protein taxon:3702 20030417 TIGR TAIR:locus:2005502 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT3G20740 FIE acts_upstream_of_or_within GO:0022414 TAIR:Publication:501680858|PMID:11148284 IMP P AT3G20740 AT3G20740|FIE|FIS3|FIE1|FERTILIZATION-INDEPENDENT ENDOSPERM|FERTILIZATION-INDEPENDENT ENDOSPERM 1|MOE17.5 protein taxon:3702 20240326 TIGR TAIR:locus:2091876 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G07510 GRP14 acts_upstream_of_or_within GO:0019953 TAIR:Publication:501680645|PMID:11431566 IMP P AT5G07510 AT5G07510|GRP14|ATGRP14|GRP-4|ATGRP-4|glycine-rich protein 14|ARABIDOPSIS THALIANA GLYCINE-RICH PROTEIN 14|GLYCINE-RICH PROTEIN 4|ARABIDOPSIS THALIANA GLYCINE-RICH PROTEIN 4|T2I1.220|T2I1_220 protein taxon:3702 20030417 TIGR TAIR:locus:2183354 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G07520 GRP18 acts_upstream_of_or_within GO:0019953 TAIR:Publication:501680645|PMID:11431566 IMP P AT5G07520 AT5G07520|GRP18|ATGRP18|ATGRP-8|glycine-rich protein 18|T2I1.230|T2I1_230 protein taxon:3702 20030417 TIGR TAIR:locus:2183369 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G07530 GRP17 acts_upstream_of_or_within GO:0019953 TAIR:Publication:501680645|PMID:11431566 IMP P AT5G07530 AT5G07530|GRP17|ATGRP17|ATGRP-7|glycine rich protein 17|ARABIDOPSIS THALIANA GLYCINE RICH PROTEIN 17|ARABIDOPSIS THALIANA GLYCINE RICH PROTEIN 7|T2I1.240|T2I1_240 protein taxon:3702 20030417 TIGR TAIR:locus:2183384 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G07540 GRP16 acts_upstream_of_or_within GO:0019953 TAIR:Publication:501680645|PMID:11431566 IMP P AT5G07540 AT5G07540|GRP16|ATGRP16|ATGRP-6|glycine-rich protein 16|T2I1.250|T2I1_250 protein taxon:3702 20030417 TIGR TAIR:locus:2183399 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G07550 GRP19 acts_upstream_of_or_within GO:0019953 TAIR:Publication:501680645|PMID:11431566 IMP P AT5G07550 AT5G07550|GRP19|ATGRP19|glycine-rich protein 19|T2I1.260|T2I1_260 protein taxon:3702 20030417 TIGR TAIR:locus:2183414 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT1G43850 SEU acts_upstream_of_or_within GO:0007275 TAIR:Publication:1546142|PMID:11782418 IMP P AT1G43850 AT1G43850|SEU|seuss|F28H19.10|F28H19_10 protein taxon:3702 20031004 TIGR TAIR:locus:2029137 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT4G27760 FEY acts_upstream_of_or_within GO:0007275 TAIR:Publication:4636|PMID:7849756 IMP P AT4G27760 AT4G27760|FEY|FEY3|FOREVER YOUNG|T27E11.1 protein taxon:3702 20030512 TIGR TAIR:locus:2137772 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G61790 CNX1 located_in GO:0043231 TAIR:Publication:5225|PMID:8454626 IDA C AT5G61790 AT5G61790|CNX1|ATCNX1|calnexin 1|MAC9.15|MAC9_15 protein taxon:3702 20120820 TIGR TAIR:locus:2159223 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT3G27170 CLC-B located_in GO:0005622 TAIR:Publication:3512|PMID:8969232 TAS C AT3G27170 AT3G27170|CLC-B|ATCLC-B|chloride channel B|MYF5.4 protein taxon:3702 20030417 TIGR TAIR:locus:2095123 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G26240 CLC-D located_in GO:0005622 TAIR:Publication:3512|PMID:8969232 IC GO:0005247 C AT5G26240 AT5G26240|CLC-D|ATCLC-D|CLCd|AtCLCd|chloride channel D|T19G15.90|T19G15_90|chloride channel d protein taxon:3702 20030512 TIGR TAIR:locus:2179724 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT5G49890 CLC-C located_in GO:0005622 TAIR:Publication:3512|PMID:8969232 TAS C AT5G49890 AT5G49890|CLC-C|ATCLC-C|chloride channel C|K9P8.3|K9P8_3|chloride channel c protein taxon:3702 20030417 TIGR TAIR:locus:2158809 `
• WARNING - Violates GO Rule:GORULE:0000008: No annotations should be made to uninformatively high level terms--`AGI_LocusCode AT4G36920 AP2 acts_upstream_of_or_within GO:0019953 TAIR:Publication:3195|PMID:9192694 TAS P AT4G36920 AT4G36920|AP2|FLO2|FL1|AtAP2|APETALA 2|FLORAL MUTANT 2|FLOWER 1|AP22.49|AP22_49|FLORAL HOMEOTIC PROTEIN APETALA 2 protein taxon:3702 20030417 TIGR TAIR:locus:2005493 `

gorule-0000027

Each identifier in GAF is valid

• total: 1

messages

• WARNING - Invalid identifier:GORULE:0000027: INTERPRO not found in list of database names in dbxrefs--`AGI_LocusCode AT5G16840 BPA1 enables GO:0003676 TAIR:Communication:501714663 ISS INTERPRO:IPR000504 F AT5G16840 AT5G16840|BPA1|binding partner of acd11 1|F5E19.180|F5E19_180|BPA1 protein taxon:3702 20190814 TIGR TAIR:locus:2148970 `

gorule-0000061

Allowed gene product to term relations (gp2term)

• total: 11

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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT5G64040 PSAN located_in GO:0030093 TAIR:Publication:834|PMID:10631267 IPI SWISS-PROT:Q96299 C AT5G64040 AT5G64040|PSAN|MHJ24.2|MHJ24_2|PSI-N protein taxon:3702 20030512 TIGR TAIR:locus:2164371 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT1G02090 FUS5 located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT1G02090 AT1G02090|FUS5|CSN7|COP15|ATCSN7|FUSCA 5|COP9 SIGNALOSOME SUBUNIT 7|CONSTITUTIVE PHOTOMORPHOGENIC 15|ARABIDOPSIS THALIANA COP9 SIGNALOSOME SUBUNIT 7|T7I23.25|T7I23_25 protein taxon:3702 20030417 TIGR TAIR:locus:2205593 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT1G22920 CSN5A located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT1G22920 AT1G22920|CSN5A|AJH1|COP9 signalosome 5A|ARABIDOPSIS JAB1 HOMOLOG 1|F19G10.12|F19G10_12|PUTATIVE JUN KINASE ACTIVATOR|CSN5 protein taxon:3702 20030417 TIGR TAIR:locus:2017764 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT1G71230 CSN5B located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT1G71230 AT1G71230|CSN5B|CSN5|AJH2|COP9-signalosome 5B|F3I17.12|F3I17_12 protein taxon:3702 20030417 TIGR TAIR:locus:2032288 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT2G26990 FUS12 located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT2G26990 AT2G26990|FUS12|ATCSN2|COP12|CSN2|FUSCA 12|CONSTITUTIVE PHOTOMORPHOGENIC 12|T20P8.4|T20P8_4|CSN2 protein taxon:3702 20030417 TIGR TAIR:locus:2059289 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT3G61140 FUS6 located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT3G61140 AT3G61140|FUS6|ATFUS6|CSN1|COP11|EMB78|ATSK31|SK31|AtCSN1|FUSCA 6|ARABIDOPSIS THALIANA FUSCA 6|COP9 SIGNALOSOME SUBUNIT 1|CONSTITUTIVE PHOTOMORPHOGENIC 11|EMBRYO DEFECTIVE 78|SHAGGY-LIKE KINASE 31|T20K12.40 protein taxon:3702 20030417 TIGR TAIR:locus:2098851 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT4G14110 COP9 located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT4G14110 AT4G14110|COP9|CSN8|FUS7|EMB143|CONSTITUTIVE PHOTOMORPHOGENIC 9|COP9 SIGNALOSOME SUBUNIT 8|FUSCA 7|EMBRYO DEFECTIVE 143|DL3095C|FCAALL.131|FUSCA PROTEIN FUS7 protein taxon:3702 20030417 TIGR TAIR:locus:2129435 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT5G14250 COP13 located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT5G14250 AT5G14250|COP13|CSN3|FUS11|CONSTITUTIVE PHOTOMORPHOGENIC 13|COP9 SIGNALOSOME SUBUNIT 3|FUSCA 11|F18O22.40|F18O22_40|CSN3 protein taxon:3702 20030417 TIGR TAIR:locus:2145638 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT5G42970 COP8 located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT5G42970 AT5G42970|COP8|FUS4|EMB134|COP14|CSN4|FUS8|ATS4|CONSTITUTIVE PHOTOMORPHOGENIC 8|FUSCA 4|EMBRYO DEFECTIVE 134|CONSTITUTIVE PHOTOMORPHOGENIC 14|COP9 SIGNALOSOME SUBUNIT 4|FUSCA 8|MBD2.17|MBD2_17 protein taxon:3702 20030417 TIGR TAIR:locus:2159961 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT5G56280 CSN6A located_in GO:0008180 TAIR:Publication:5839|PMID:11019806 TAS C AT5G56280 AT5G56280|CSN6A|COP9 signalosome subunit 6A|MXK23.2|MXK23_2 protein taxon:3702 20030512 TIGR TAIR:locus:2177601 `
• 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:0001025 should be one of BFO:0000050. Repaired to BFO:0000050--`AGI_LocusCode AT1G08550 NPQ1 located_in GO:0030095 TAIR:Publication:501683128|PMID:11058750 TAS C AT1G08550 AT1G08550|NPQ1|AVDE1|non-photochemical quenching 1|ARABIDOPSIS VIOLAXANTHIN DE-EPOXIDASE 1|F22O13.3|F22O13_3|VIOLAXANTHIN DE-EPOXIDASE PRECURSOR protein taxon:3702 20030417 TIGR TAIR:locus:2025510 `

gorule-0000065

Annotations to term that are candidates for obsoletion should be removed

• total: 5

messages

• WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`AGI_LocusCode AT2G39550 PGGT-I acts_upstream_of_or_within GO:0018344 TAIR:Publication:501680612|PMID:11500541 IDA P AT2G39550 AT2G39550|ATGGT-IB|GGB|PGGT-I|GERANYLGERANYLTRANSFERASE-I BETA SUBUNIT protein taxon:3702 20030417 TIGR TAIR:locus:2039752 `
• WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`AGI_LocusCode AT3G05840 ATSK12 acts_upstream_of_or_within GO:0016310 TAIR:Publication:4961|PMID:7509023 IDA P AT3G05840 AT3G05840|ATSK12|SK12|SHAGGY-like kinase 12|F10A16.14|F10A16_14|ASKGAMMA protein taxon:3702 20030417 TIGR TAIR:locus:2074464 `
• WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`AGI_LocusCode AT5G26751 SK 11 acts_upstream_of_or_within GO:0016310 TAIR:Publication:4961|PMID:7509023 IDA P AT5G26751 AT5G26751|ATSK11|SK 11|ASKalpha|ARABIDOPSIS THALIANA SHAGGY-RELATED KINASE 11|shaggy-related kinase 11|Arabidopsis GSK alpha|F2P16.21|F2P16_21|ASKALPHA protein taxon:3702 20030417 TIGR TAIR:locus:2832141 `
• WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`AGI_LocusCode AT4G26080 ABI1 acts_upstream_of_or_within GO:0006470 TAIR:Publication:1918|PMID:9869399 TAS P AT4G26080 AT4G26080|ABI1|AtABI1|ABA INSENSITIVE 1|F20B18.190|F20B18_190|PROTEIN PHOSPHATASE 2C ABI1 protein taxon:3702 20030417 TIGR TAIR:locus:2005488 `
• WARNING - Violates GO Rule:GORULE:0000065: Annotations to term that are candidates for obsoletion should be removed--`AGI_LocusCode AT5G57050 ABI2 acts_upstream_of_or_within GO:0006470 TAIR:Publication:1918|PMID:9869399 TAS P AT5G57050 AT5G57050|ABI2|AtABI2|ABA INSENSITIVE 2|MHM17.19|MHM17_19|PROTEIN PHOSPHATASE 2C protein taxon:3702 20030417 TIGR TAIR:locus:2164610 `