From 8f2e2cebbf9cf33a928a6aca28d65f61d1e7d35f Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 17 Jul 2024 17:11:25 +0200 Subject: [PATCH 01/42] Update ecocyc.yaml For #2344 --- metadata/datasets/ecocyc.yaml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/metadata/datasets/ecocyc.yaml b/metadata/datasets/ecocyc.yaml index c0b5fc1f..e8f669c4 100644 --- a/metadata/datasets/ecocyc.yaml +++ b/metadata/datasets/ecocyc.yaml @@ -21,3 +21,18 @@ datasets: species_code: Ecol taxa: - NCBITaxon:83333 +- + id: ecocyc.gpi + label: "ecocyc gpi file" + description: "gpi file for Escherichia coli from EcoCyc" + url: + type: gpi + dataset: ecocyc + submitter: ecocyc + compression: gzip + source: https://www.ai.sri.com/~kr/go/latest/ecocyc.gpi + entity_type: + status: active + species_code: Ecol + taxa: + - NCBITaxon:83333 From 2652f352a6175e4753da643c42fb962114b25eac Mon Sep 17 00:00:00 2001 From: Seth Carbon Date: Mon, 22 Jul 2024 14:37:02 -0700 Subject: [PATCH 02/42] fixes for #2344 --- metadata/datasets/ecocyc.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/metadata/datasets/ecocyc.yaml b/metadata/datasets/ecocyc.yaml index e8f669c4..02274256 100644 --- a/metadata/datasets/ecocyc.yaml +++ b/metadata/datasets/ecocyc.yaml @@ -21,16 +21,16 @@ datasets: species_code: Ecol taxa: - NCBITaxon:83333 -- +- id: ecocyc.gpi label: "ecocyc gpi file" description: "gpi file for Escherichia coli from EcoCyc" - url: + url: https://current.geneontology.org/annotations/ecocyc.gpi.gz type: gpi dataset: ecocyc submitter: ecocyc compression: gzip - source: https://www.ai.sri.com/~kr/go/latest/ecocyc.gpi + source: https://www.ai.sri.com/~kr/go/latest/ecocyc.gpi.gz entity_type: status: active species_code: Ecol From e88c40e62b7490539e11694170014a2aa889ad47 Mon Sep 17 00:00:00 2001 From: Seth Carbon Date: Mon, 22 Jul 2024 14:39:48 -0700 Subject: [PATCH 03/42] tabs for #2344 --- metadata/datasets/ecocyc.yaml | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/metadata/datasets/ecocyc.yaml b/metadata/datasets/ecocyc.yaml index 02274256..384c1cac 100644 --- a/metadata/datasets/ecocyc.yaml +++ b/metadata/datasets/ecocyc.yaml @@ -21,18 +21,17 @@ datasets: species_code: Ecol taxa: - NCBITaxon:83333 -- - id: ecocyc.gpi - label: "ecocyc gpi file" - description: "gpi file for Escherichia coli from EcoCyc" - url: https://current.geneontology.org/annotations/ecocyc.gpi.gz - type: gpi - dataset: ecocyc - submitter: ecocyc - compression: gzip - source: https://www.ai.sri.com/~kr/go/latest/ecocyc.gpi.gz - entity_type: - status: active - species_code: Ecol - taxa: - - NCBITaxon:83333 + - id: ecocyc.gpi + label: "ecocyc gpi file" + description: "gpi file for Escherichia coli from EcoCyc" + url: https://current.geneontology.org/annotations/ecocyc.gpi.gz + type: gpi + dataset: ecocyc + submitter: ecocyc + compression: gzip + source: https://www.ai.sri.com/~kr/go/latest/ecocyc.gpi.gz + entity_type: + status: active + species_code: Ecol + taxa: + - NCBITaxon:83333 From e523005037c4a8508ec2ab21e5d7c8e664aa1685 Mon Sep 17 00:00:00 2001 From: Seth Carbon Date: Mon, 22 Jul 2024 14:42:18 -0700 Subject: [PATCH 04/42] okay, tested fix for ecocyc tabs. for #2344 --- metadata/datasets/ecocyc.yaml | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/metadata/datasets/ecocyc.yaml b/metadata/datasets/ecocyc.yaml index 384c1cac..4522435c 100644 --- a/metadata/datasets/ecocyc.yaml +++ b/metadata/datasets/ecocyc.yaml @@ -7,20 +7,19 @@ project_url: "http://ecocyc.org" funding_source: "NIH/NIGMS GM077678" email_report: "biocyc-support@ai.sri.com" datasets: - - - id: ecocyc.gaf - label: "ecocyc gaf file" - description: "gaf file for ecocyc from Encyclopedia of E. coli metabolism" - url: https://current.geneontology.org/annotations/ecocyc.gaf.gz - type: gaf - dataset: ecocyc - submitter: ecocyc - source: https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/18.E_coli_MG1655.goa - entity_type: - status: active - species_code: Ecol - taxa: - - NCBITaxon:83333 + - id: ecocyc.gaf + label: "ecocyc gaf file" + description: "gaf file for ecocyc from Encyclopedia of E. coli metabolism" + url: https://current.geneontology.org/annotations/ecocyc.gaf.gz + type: gaf + dataset: ecocyc + submitter: ecocyc + source: https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/18.E_coli_MG1655.goa + entity_type: + status: active + species_code: Ecol + taxa: + - NCBITaxon:83333 - id: ecocyc.gpi label: "ecocyc gpi file" description: "gpi file for Escherichia coli from EcoCyc" From 5ce88074c531aa51d73b0c5c1d075369df7f2e92 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 25 Jul 2024 15:40:30 +0200 Subject: [PATCH 05/42] Update gorules_test_errors.gaf for #2063 --- docs/gorules_test_errors.gaf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 5d1d79a6..214b4e1b 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -65,8 +65,10 @@ UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TE UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-26 other taxon:318586 20230427 GO_Central ! FAILS GORULE:0000001 - TEST 27 - entity type missing UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-27 taxon:318586 20230427 GO_Central -! FAILS GORULE:0000001 - TEST 27 - bad entity type -UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-27 misc_RNA taxon:318586 20230427 GO_Central +! FAILS GORULE:0000001 - TEST 28 - bad entity type +UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-28 misc_RNA taxon:318586 20230427 GO_Central +! FAILS GORULE:0000001 - TEST 29 - Bad referencesyntax +UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID: IDA P GORULE_TEST:0000001-29 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000002 - TEST 1 - has a 'NOT' annotations to 'protein binding ; GO:0005515 UniProtKB O76187 darA NOT|enables GO:0005515 PMID:9802899 IPI UniProtKB:P34149 F GORULE_TEST:0000002-1 Darlin darA protein taxon:44689 20100205 GO_Central ! FAILS GORULE:0000002 - TEST 2 - has a 'NOT' annotations to 'binding ; GO:0005515 @@ -157,10 +159,8 @@ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA P GORULE_TEST: UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:PMID:14561399 IDA P GORULE_TEST:0000027-3 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000027 - TEST 4 - Bad reference syntax UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:unpublished IDA P GORULE_TEST:0000027-4 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central -! FAILS GORULE:0000027 - TEST 5 - Bad referencesyntax -UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID: IDA P GORULE_TEST:0000027-5 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central -! FAILS GORULE:0000027 - TEST 6 - Bad reference syntax -UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P GORULE_TEST:0000027-6 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central +! FAILS GORULE:0000027 - TEST 5 - Bad reference syntax +UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P GORULE_TEST:0000027-5 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From 7864cf8d2a7228d0e32b788c2f056f045831616e Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 25 Jul 2024 15:49:55 +0200 Subject: [PATCH 06/42] Update gorules_test_errors.gpad for #2063 --- docs/gorules_test_errors.gpad | 224 +++++++++++++++++----------------- 1 file changed, 111 insertions(+), 113 deletions(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index d38514d8..1d15b548 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -4,231 +4,229 @@ ! Dummy GPAD file containing deliberate errors to test that GO rules are correctly implemented. ! Should be equivalent to https://github.com/geneontology/go-site/blob/master/docs/gorules_test_errors.gaf when the rule applies. ! FAILS GORULE:0000002 - TEST 1 - has a 'NOT' annotations to 'protein binding ; GO:0005515 -UniProtKB:O76187 NOT RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST=0000002-1 Darlin +UniProtKB:O76187 NOT RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-1 Darlin ! FAILS GORULE:0000002 - TEST 2 - has a 'NOT' annotations to 'binding ; GO:0005515 -UniProtKB:O76187 NOT RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST=0000002-1 Darlin +UniProtKB:O76187 NOT RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-1 Darlin ! SHOULD PASS GORULE:0000003 - TEST 3 - has a 'NOT' annotations to GO:0005509, a child of 'binding ; GO:0005515 -UniProtKB:O76187 NOT RO:0002327 GO:0005509 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST=0000002-3-PASS Darlin +UniProtKB:O76187 NOT RO:0002327 GO:0005509 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-3-PASS Darlin ! TBC FAILS GORULE:0000005 - TEST 1 - incorrect evidence codes for 'protein binding ; GO:0005515' - ISS not allowed -UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000250 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST=0000005-1 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000250 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000005-1 Darlin ! TBC FAILS GORULE:0000005 - TEST 2 - incorrect evidence codes for 'protein binding ; GO:0005515' - IS0 not allowed -UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000266 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST=0000005-2 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000266 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000005-2 Darlin ! TBC FAILS GORULE:0000005 - TEST 3 - incorrect evidence codes for 'protein binding ; GO:0005515' - IBA not allowed -UniProtKB:O76187 RO:0002327 GO:0005515 GO_REF:0000033 ECO:0000318 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST=0000005-3 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 GO_REF:0000033 ECO:0000318 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000005-3 Darlin ! FAILS GORULE:0000006 - TEST 1 - fails because uses IEP with a molecular function term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST=0000006-1 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-1 subtilisin-like ! FAILS GORULE:0000006 - TEST 2 - fails because uses HEP with a molecular function term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0007007 2010-02-05 GO_Central GORULE_TEST=0000006-2 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0007007 2010-02-05 GO_Central GORULE_TEST:0000006-2 subtilisin-like ! FAILS GORULE:0000006 - TEST 3 - fails because uses IEP with a cellular component term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0005634 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST=0000006-3 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0005634 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-3 subtilisin-like ! SHOULD PASS GORULE:0000006 - TEST 4 - passes because uses assigned_by is GOC, even if there is an IEP with a molecular function term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GOC GORULE_TEST=0000006-4 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GOC GORULE_TEST:0000006-4 subtilisin-like ! SHOULD PASS GORULE:0000006 - TEST 5 - should pass because obsolete BP term should be ignored; GO:1901011 obsolete (S)-reticuline catabolic process -GeneDB:PF3D7_0507500 RO:0002327 GO:1901011 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST=0000006-5 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:1901011 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-5 subtilisin-like ! SHOULD PASS GORULE:0000006 - TEST 6 - should pass because alt_ids should be ignored, and GO:0006758 is an alt_id to GO:0006754 ATP biosynthetic process -GeneDB:PF3D7_0507500 RO:0002327 GO:0006758 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST=0000006-6 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0006758 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-6 subtilisin-like ! FAILS GORULE:0000007 - IPI used with GO:0003824 catalytic activity or descendents (GO:0004674 protein serine/threonine kinase activity) -UniProtKB:A0A078CGE6 RO:0002327 GO:0004674 PMID:11489177 ECO:0000021 UniProtKB:A0A078FEZ9 2010-02-05 GO_Central GORULE_TEST=0000007-1 +UniProtKB:A0A078CGE6 RO:0002327 GO:0004674 PMID:11489177 ECO:0000021 UniProtKB:A0A078FEZ9 2010-02-05 GO_Central GORULE_TEST:0000007-1 ! FAILS GORULE:0000008 - TEST 1 - GO:0005622 is in the subset gocheck_do_not_annotate -UniProtKB:Q9DGE2 RO:0002432 GO:0005622 PMID:10995439 ECO:0000314 2018-01-29 GO_Central GORULE_TEST=0000008-1 Mitogen-activated protein kinase 14A +UniProtKB:Q9DGE2 RO:0002432 GO:0005622 PMID:10995439 ECO:0000314 2018-01-29 GO_Central GORULE_TEST:0000008-1 Mitogen-activated protein kinase 14A ! FAILS GORULE:0000008 - TEST 2 - GO:0007049 is in the subset gocheck_do_not_manually_annotate -UniProtKB:Q9WVH3 RO:0002331 GO:0007049 PMID:12048180 ECO:0000314 2018-01-29 GO_Central GORULE_TEST=0000008-2 Forkhead box protein O4 +UniProtKB:Q9WVH3 RO:0002331 GO:0007049 PMID:12048180 ECO:0000314 2018-01-29 GO_Central GORULE_TEST:0000008-2 Forkhead box protein O4 ! FAILS GORULE:0000008 - TEST 3 - also fails GORULE:0000051 - GO:0005488 is in the subset gocheck_do_not_manually_annotate -UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2018-01-29 GO_Central GORULE_TEST=0000008-3 Darlin +UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2018-01-29 GO_Central GORULE_TEST:0000008-3 Darlin ! FAILS GORULE:0000011 - TEST 1 - because the GO ID is not one of GO:0003674, GO:0008150 or GO:0005575 -UniProtKB:Q4KA26 RO:0002432 GO:0016020 GO_REF:0000015 ECO:0000307 2018-01-29 GO_Central GORULE_TEST=0000011-1 Putative membrane protein +UniProtKB:Q4KA26 RO:0002432 GO:0016020 GO_REF:0000015 ECO:0000307 2018-01-29 GO_Central GORULE_TEST:0000011-1 Putative membrane protein ! FAILS GORULE:0000011 - TEST 2 - fails because the evidence code is not ND, even if the GO ID one of GO:0003674, GO:0008150 or GO:0005575. -UniProtKB:Q4KA26 RO:0002432 GO:0005575 GO_REF:0000015 ECO:0000314 2018-01-29 GO_Central GORULE_TEST=0000011-2 Putative membrane protein +UniProtKB:Q4KA26 RO:0002432 GO:0005575 GO_REF:0000015 ECO:0000314 2018-01-29 GO_Central GORULE_TEST:0000011-2 Putative membrane protein ! SHOULD PASS GORULE:0000011 - TEST 3 -UniProtKB:Q6UW15 RO:0002331 GO:0050689 PMID:16931762 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000011-3 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0050689 PMID:16931762 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000011-3 Regenerating islet-derived protein 3-gamma ! FAILS GORULE:0000013 - fails because GO:0075342 should not be annotated for human gene products - cannot be tested in ontobio parser (not a line-by-line check) -UniProtKB:P67870 RO:0002331 GO:0075342 PMID:20719947 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000013-1 Casein kinase II subunit beta +UniProtKB:P67870 RO:0002331 GO:0075342 PMID:20719947 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000013-1 Casein kinase II subunit beta ! FAILS GORULE:0000015 - TEST 1 - GO:0005886 plasma membrane is not a child of "GO:0018995 host cellular component" -UniProtKB:O56786 RO:0002432 GO:0005886 PMID:10419939 ECO:0000314 taxon:9696 2022-06-06 GO_Central GORULE_TEST=0000015-1 Holin protein Hol187 +UniProtKB:O56786 RO:0002432 GO:0005886 PMID:10419939 ECO:0000314 taxon:9696 2022-06-06 GO_Central GORULE_TEST:0000015-1 Holin protein Hol187 ! FAILS GORULE:0000015 - TEST 2 - "neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" -UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:55511 2022-06-06 GO_Central GORULE_TEST=0000015-2 Protein CD300H +UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:55511 2022-06-06 GO_Central GORULE_TEST:0000015-2 Protein CD300H ! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall -UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606 2022-06-06 GO_Central GORULE_TEST=0000015-3 Holin protein Hol187 +UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606 2022-06-06 GO_Central GORULE_TEST:0000015-3 Holin protein Hol187 ! PASSES GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID -UniProtKB:O56786 RO:0002432 GO:0042025 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000015-4 Holin protein Hol187 +UniProtKB:O56786 RO:0002432 GO:0042025 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 ! PASSES GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID -UniProtKB:O56786 RO:0002331 GO:0010363 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000015-4 Holin protein Hol187 +UniProtKB:O56786 RO:0002331 GO:0010363 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 ! PASSES GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID -UniProtKB:O56786 RO:0002331 GO:0141062 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000015-4 Holin protein Hol187 +UniProtKB:O56786 RO:0002331 GO:0141062 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 ! SHOULD PASS GORULE:0000015 - TEST 4 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction -UniProtKB:Q6UW15 RO:0002331 GO:0010363 PMID:16931762 ECO:0000314 taxon:1334565 2022-06-06 GO_Central GORULE_TEST=0000015-4 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0010363 PMID:16931762 ECO:0000314 taxon:1334565 2022-06-06 GO_Central GORULE_TEST:0000015-4 Regenerating islet-derived protein 3-gamma ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 2022-06-06 GO_Central GORULE_TEST=0000016-1 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 2022-06-06 GO_Central GORULE_TEST:0000016-1 Calpain-10 ! FAILS GORULE:0000016 - TEST 2 - column 8 (with/from) is has a non-GOID -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 UBERON:0002048 2022-06-06 GO_Central GORULE_TEST=0000016-2 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 UBERON:0002048 2022-06-06 GO_Central GORULE_TEST:0000016-2 Calpain-10 ! FAILS GORULE:0000016 - TEST 3 - column 8 (with/from) is the same GOID as column 5 -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 GO:0006921 2022-06-06 GO_Central GORULE_TEST=0000016-3 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 GO:0006921 2022-06-06 GO_Central GORULE_TEST:0000016-3 Calpain-10 ! SHOULD PASS GORULE:0000016 - TEST 4 - column 8 (with/from) is has a valid GO ID -UniProtKB:Q9HC96 RO:0002432 GO:0005886 GO_REF:0000036 ECO:0000305 GO:0001591 2022-06-06 GO_Central GORULE_TEST=0000016-4 Calpain-10 +UniProtKB:Q9HC96 RO:0002432 GO:0005886 GO_REF:0000036 ECO:0000305 GO:0001591 2022-06-06 GO_Central GORULE_TEST:0000016-4 Calpain-10 ! FAILS GORULE:0000017 - TEST 1 - IDA annotations must not have a with/from entry (column 8) -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000314 GO:0004198|GO:0008092 2022-06-06 GO_Central GORULE_TEST=0000017-1 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000314 GO:0004198|GO:0008092 2022-06-06 GO_Central GORULE_TEST:0000017-1 Calpain-10 ! FAILS GORULE:0000018 - TEST 1 - column 8 (with/from) is null for IPI annotation to 'protein binding ; GO:0005515' -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central GORULE_TEST=0000018-1 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central GORULE_TEST:0000018-1 Mitogen-activated protein kinase kinase kinase mlk-1 ! FAILS GORULE:0000018 - TEST 2 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central GORULE_TEST=0000018-2 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central GORULE_TEST:0000018-2 Mitogen-activated protein kinase kinase kinase mlk-1 ! FAILS GORULE:0000018 - TEST 3 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' -UniProtKB:O76187 RO:0002331 GO:0005488 PMID:9802899 ECO:0000021 2022-06-06 GO_Central GORULE_TEST=0000018-3 +UniProtKB:O76187 RO:0002331 GO:0005488 PMID:9802899 ECO:0000021 2022-06-06 GO_Central GORULE_TEST:0000018-3 ! FAILS GORULE:0000020 - TEST 1 - obsolete term with no replacement -UniProtKB:P04995 RO:0002331 GO:0090503 GO_REF:0000108 ECO:0000501 GO:0000175 2022-06-06 GO_Central GORULE_TEST=0000020-1 Exodeoxyribonuclease I +UniProtKB:P04995 RO:0002331 GO:0090503 GO_REF:0000108 ECO:0000501 GO:0000175 2022-06-06 GO_Central GORULE_TEST:0000020-1 Exodeoxyribonuclease I ! FAILS GORULE:0000020 - TEST 2 - obsolete term with a replacement term -TriTrypDB:Tb11.02.5420b RO:0001025 GO:0016021 GO_REF:0000002 ECO:0000266 GeneDB:Tb11.02.5420 2022-06-06 GO_Central GORULE_TEST=0000020-2 NADPH-cytochrome p450 reductase, putative +TriTrypDB:Tb11.02.5420b RO:0001025 GO:0016021 GO_REF:0000002 ECO:0000266 GeneDB:Tb11.02.5420 2022-06-06 GO_Central GORULE_TEST:0000020-2 NADPH-cytochrome p450 reductase, putative ! FAILS GORULE:0000020 - TEST 3 - obsolete term in 'with' (column 8) with no replacement -MGI:1100518:Smad7 RO:0002331 GO:0017015 MGI:MGI:3836072|PMID:18952608 ECO:0000305 GO:0060389 2022-06-06 GO_Central GORULE_TEST=0000020-3 +MGI:1100518:Smad7 RO:0002331 GO:0017015 MGI:MGI:3836072|PMID:18952608 ECO:0000305 GO:0060389 2022-06-06 GO_Central GORULE_TEST:0000020-3 ! FAILS GORULE:0000020 - TEST 4 - obsolete term in 'extension' (column 16) with no replacement -UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0090503) GORULE_TEST=0000020-4 Darlin +UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0090503) GORULE_TEST:0000020-4 Darlin ! FAILS GORULE:0000020 - TEST 5 - obsolete term in 'extension' (column 16) with a replacement -UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0014067) GORULE_TEST=0000020-5 Darlin +UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0014067) GORULE_TEST:0000020-5 Darlin ! FAILS GORULE:0000022 - TEST 1 - retracted paper UniProtKB:O76187 RO:0002327 GO:0004672 PMID:37278189 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000022-1 ! FAILS GORULE:0000027 - TEST 1 - Prefix not in /db-xrefs.yaml -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000027-1 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000027-1 Calpain-10 ! FAILS GORULE:0000027 - TEST 2 - Assigned_by not in /groups.yaml -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 SGDDB GORULE_TEST=0000027-2 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 SGDDB GORULE_TEST:0000027-2 Calpain-10 ! FAILS GORULE:0000027 - TEST 3 - Bad reference syntax -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:PMID:14561399 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000027-3 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:PMID:14561399 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000027-3 Calpain-10 ! FAILS GORULE:0000027 - TEST 4 - Bad reference syntax -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:unpublished ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000027-4 Calpain-10 -! FAILS GORULE:0000027 - TEST 5 - Bad referencesyntax -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID: ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000027-5 Calpain-10 -! FAILS GORULE:0000027 - TEST 6 - Bad reference syntax -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:0. ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000027-6 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:unpublished ECO:0000314 2022-06-06 GO_Central GORULE_TEST0000027-4 Calpain-10 +! FAILS GORULE:0000027 - TEST 5 - Bad reference syntax +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:0. ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000027-5 Calpain-10 ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000028-1 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-1 Calpain-10 ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000028-2 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-2 Calpain-10 ! FAILS GORULE:0000028 - TEST 3 - Bad GO aspect, P instead of F -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000028-3 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-3 Mitogen-activated protein kinase kinase kinase mlk-1 ! FAILS GORULE:0000028 - TEST 4 - GO aspect missing -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000028-4 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-4 Mitogen-activated protein kinase kinase kinase mlk-1 ! FAILS GORULE:0000029 - TEST 1 - IEA older than 1 year -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2023-05-06 GO_Central GORULE_TEST=0000029-1 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2023-05-06 GO_Central GORULE_TEST:0000029-1 ! FAILS GORULE:0000029 - TEST 2 - IEA older than 3 years -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2020-06-06 GO_Central GORULE_TEST=0000029-2 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2020-06-06 GO_Central GORULE_TEST:0000029-2 ! FAILS GORULE:0000030 - TEST 1 - Deprecated GO_REF -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000045 ECO:0000501 UniProtKB-SubCell:SL-0375 2022-06-06 GO_Central GORULE_TEST=0000030-1 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000045 ECO:0000501 UniProtKB-SubCell:SL-0375 2022-06-06 GO_Central GORULE_TEST:0000030-1 ! SHOULD PASS GORULE:0000030 - TEST 2 - Valid GO_REF -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000033 ECO:0000318 FB:FBgn0032677|PANTHER:PTN005196447 2022-06-06 GO_Central GORULE_TEST=0000030-2 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000033 ECO:0000318 FB:FBgn0032677|PANTHER:PTN005196447 2022-06-06 GO_Central GORULE_TEST:0000030-2 ! FAILS GORULE:0000037 - TEST 1 - IBA with Assigned_by other than GO_Central -UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:21873635 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 PomBase GORULE_TEST=0000037-1 +UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:21873635 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 PomBase GORULE_TEST:0000037-1 ! FAILS GORULE:0000037 - TEST 2 - IBA with reference other than GO_REF:0000033 -UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:26221034 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 GO_Central GORULE_TEST=0000037-2 +UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:26221034 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 GO_Central GORULE_TEST:0000037-2 ! FAILS GORULE:0000039 - TEST 1 - Protein complex annotated to GO:0032991 protein-containing complex -ComplexPortal:CPX-102 BFO:0000050 GO:0032991 PMID:10629061 ECO:0000315 2022-06-06 GO_Central GORULE_TEST=0000039-1 +ComplexPortal:CPX-102 BFO:0000050 GO:0032991 PMID:10629061 ECO:0000315 2022-06-06 GO_Central GORULE_TEST:0000039-1 ! FAILS GORULE:0000039 - TEST 2 - Protein complex annotated to an is_a descendant of GO:0032991 protein-containing complex -ComplexPortal:CPX-102 BFO:0000050 GO:0043020 PMID:10629061 ECO:0000315 2022-06-06 GO_Central GORULE_TEST=0000039-2 +ComplexPortal:CPX-102 BFO:0000050 GO:0043020 PMID:10629061 ECO:0000315 2022-06-06 GO_Central GORULE_TEST:0000039-2 ! FAILS GORULE:0000042 - TEST 1 - IKR evidence, no negation (NOT) in column 4 -UniProtKB:A0A0B4JCV5 RO:0002327 GO:0004252 PMID:30367934 ECO:0000320 2022-06-06 GO_Central GORULE_TEST=0000042-1 +UniProtKB:A0A0B4JCV5 RO:0002327 GO:0004252 PMID:30367934 ECO:0000320 2022-06-06 GO_Central GORULE_TEST:0000042-1 ! FAILS GORULE:0000046 - TEST 1 - self-binding’ term, no data in Column 8 -UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000046-1 +UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000046-1 ! FAILS GORULE:0000046 - TEST 2 - self-binding’ term, annotated to a protein other than 'self' -UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000021 UniProtKB:P35555 2022-06-06 GO_Central GORULE_TEST=0000046-2 +UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000021 UniProtKB:P35555 2022-06-06 GO_Central GORULE_TEST:0000046-2 ! FAILS GORULE:0000050 - TEST 1 - self-referential ISS annotations -UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000250 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST=0000050-1 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 +UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000250 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-1 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 ! FAILS GORULE:0000050 - TEST 2 - self-referential ISO annotations -UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000266 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST=0000050-2 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 +UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000266 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-2 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 ! FAILS GORULE:0000050 - TEST 3 - self-referential ISA annotations -UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000247 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST=0000050-3 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 +UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000247 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-3 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 ! SHOULD PASS GORULE:0000051 - Pass RULE 51 - Annotation extension for certain GO terms - protein binding; GO:0005515 -UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central RO:0002233(GO:0003674)|BFO:0000066(CL:123456) GORULE_TEST=0000051-PASS1 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central RO:0002233(GO:0003674)|BFO:0000066(CL:123456) GORULE_TEST:0000051-PASS1 Darlin ! FAILS GORULE:0000051 - TEST 1 - also fails GORULE:0000008 - Annotation extension is required for certain terms - binding GO:0005488 -UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central GORULE_TEST=0000051-1 Darlin +UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central GORULE_TEST:0000051-1 Darlin ! FAILS GORULE:0000055 - TEST 1 - Two references in the same ID space - PMID -PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 PMID:12477793|PMID:15961998 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000055-1 +PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 PMID:12477793|PMID:15961998 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000055-1 ! FAILS GORULE:0000055 - TEST 2 - Two references in the same ID space - GO_REF -PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 GO_REF:0000044|GO_REF:0000003 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000055-2 +PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 GO_REF:0000044|GO_REF:0000003 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000055-2 ! SHOULD PASS GORULE:0000061 - TEST 1 - the part_of GP2term relation is allowed for GO:0008023 (CC complex) -FB:FBgn0011273 BFO:0000050 GO:0008023 FB:FBrf0193169|PMID:16790438 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000061-1 Androcam +FB:FBgn0011273 BFO:0000050 GO:0008023 FB:FBrf0193169|PMID:16790438 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-1 Androcam ! SHOULD PASS GORULE:0000061 - TEST 2- 'enables' is allowed for a GO MF -UniProtKB:A1B2F4 RO:0002327 GO:0003909 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000061-2 +UniProtKB:A1B2F4 RO:0002327 GO:0003909 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-2 ! FAILS GORULE:0000061 - TEST 3 the 'part_of' GP2term relation is not allowed for GO:0070864 (CC cellular anatomical entity) -FB:FBgn0011273 BFO:0000050 GO:0070864 PMID:12432073 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000061-3 Dynamin +FB:FBgn0011273 BFO:0000050 GO:0070864 PMID:12432073 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-3 Dynamin ! FAILS GORULE:0000061 - TEST 4 - the 'part_of' GP2term relation is not allowed for GO:0140827 (MF) -UniProtKB:A1B2F4 BFO:0000050 GO:0140827 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000061-4 +UniProtKB:A1B2F4 BFO:0000050 GO:0140827 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-4 ! FAILS GORULE:0000061 - TEST 5 - the 'enables' GP2term relation is not allowed for GO:0005856 (CC) -UniProtKB:A1B2F4 RO:0002327 GO:0005856 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST=0000061-5 +UniProtKB:A1B2F4 RO:0002327 GO:0005856 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-5 ! FAILS GORULE:0000061 - TEST 6 - the 'located in' GP2term relation is not allowed for GO:0005575 (root CC) -UniProtKB:A1B2F4 RO:0001025 GO:0005575 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST=0000061-6 +UniProtKB:A1B2F4 RO:0001025 GO:0005575 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST:0000061-6 ! FAILS GORULE:0000061 - TEST 7 - the 'contributes_to' GP2term relation is not allowed for GO:0003674 (root MF) -UniProtKB:A1B2F4 RO:0002326 GO:0003674 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST=0000061-7 +UniProtKB:A1B2F4 RO:0002326 GO:0003674 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST:0000061-7 ! FAILS GORULE:0000061 - TEST 8 - the 'acts upstream of or within' GP2term relation is not allowed for GO:0008150 (root BP) -UniProtKB:A1B2F4 RO:0002264 GO:0008150 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST=0000061-8 +UniProtKB:A1B2F4 RO:0002264 GO:0008150 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST:0000061-8 ! FAILS GORULE:0000061 - TEST 9 - 'enables' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002327 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-9 +UniProtKB:A1B2F4 RO:0002327 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-9 ! FAILS GORULE:0000061 - TEST 10 - 'contributes_to' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002326 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-10 +UniProtKB:A1B2F4 RO:0002326 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-10 ! FAILS GORULE:0000061 - TEST 11 - 'enables' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002327 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-11 +UniProtKB:A1B2F4 RO:0002327 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-11 ! FAILS GORULE:0000061 - TEST 12 - 'contributes_to' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002326 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-12 +UniProtKB:A1B2F4 RO:0002326 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-12 ! FAILS GORULE:0000061 - TEST 13 - 'involved_in' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002331 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-13 +UniProtKB:A1B2F4 RO:0002331 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-13 ! FAILS GORULE:0000061 - TEST 14 - 'acts_upstream_of_or_within' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002264 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-14 +UniProtKB:A1B2F4 RO:0002264 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-14 ! FAILS GORULE:0000061 - TEST 15 - 'acts_upstream_of_or_within_positive_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004032 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-15 +UniProtKB:A1B2F4 RO:0004032 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-15 ! FAILS GORULE:0000061 - TEST 16 - 'acts_upstream_of_or_within_negative_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-16 +UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-16 ! FAILS GORULE:0000061 - TEST 17 - 'acts_upstream_of' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002263 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-17 +UniProtKB:A1B2F4 RO:0002263 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-17 ! FAILS GORULE:0000061 - TEST 18 - acts_upstream_of_positive_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004034 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-18 +UniProtKB:A1B2F4 RO:0004034 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-18 ! FAILS GORULE:0000061 - TEST 19 - 'acts_upstream_of_negative_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-19 +UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-19 ! FAILS GORULE:0000061 - TEST 20 - 'involved_in' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002331 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-20 +UniProtKB:A1B2F4 RO:0002331 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-20 ! FAILS GORULE:0000061 - TEST 21 - 'acts_upstream_of_or_within' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002264 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-21 +UniProtKB:A1B2F4 RO:0002264 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-21 ! FAILS GORULE:0000061 - TEST 22 - 'acts_upstream_of_or_within_positive_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004032 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-22 +UniProtKB:A1B2F4 RO:0004032 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-22 ! FAILS GORULE:0000061 - TEST 23 - 'acts_upstream_of_or_within_negative_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-23 +UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-23 ! FAILS GORULE:0000061 - TEST 24 - 'acts_upstream_of' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002263 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-24 +UniProtKB:A1B2F4 RO:0002263 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-24 ! FAILS GORULE:0000061 - TEST 25 - 'acts_upstream_of_positive_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004034 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-25 +UniProtKB:A1B2F4 RO:0004034 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-25 ! FAILS GORULE:0000061 - TEST 26 - 'acts_upstream_of_negative_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-26 +UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-26 ! FAILS GORULE:0000061 - TEST 27 - 'is_active_in' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002432 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-27 +UniProtKB:A1B2F4 RO:0002432 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-27 ! FAILS GORULE:0000061 - TEST 28 - 'part_of' is not allowed for a GO MF -UniProtKB:A1B2F4 BFO:0000050 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-28 +UniProtKB:A1B2F4 BFO:0000050 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-28 ! FAILS GORULE:0000061 - TEST 29 - 'located_in' is not allowed for a GO MF UniProtKB:A1B2F4 RO:0001025 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TES=0000061-29 ! FAILS GORULE:0000061 - TEST 30 - 'colocalizes_with' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002325 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-30 +UniProtKB:A1B2F4 RO:0002325 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-30 ! FAILS GORULE:0000061 - TEST 31 - 'is_active_in' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002432 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-31 +UniProtKB:A1B2F4 RO:0002432 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-31 ! FAILS GORULE:0000061 - TEST 32 - 'part_of' is not allowed for a GO BP -UniProtKB:A1B2F4 BFO:0000050 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-32 +UniProtKB:A1B2F4 BFO:0000050 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-32 ! FAILS GORULE:0000061 - TEST 33 - 'located_in' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0001025 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-33 +UniProtKB:A1B2F4 RO:0001025 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-33 ! FAILS GORULE:0000061 - TEST 34 - 'colocalizes_with' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002325 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-34 +UniProtKB:A1B2F4 RO:0002325 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-34 ! FAILS GORULE:0000061 - TEST 35 - 'is_active_in' is not allowed for a GO CC - complex -UniProtKB:A1B2F4 RO:0002432 GO:0000124 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-34 +UniProtKB:A1B2F4 RO:0002432 GO:0000124 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-34 ! FAILS GORULE:0000061 - TEST 36 - 'located_in' is not allowed for a GO CC - complex -UniProtKB:A1B2F4 RO:0001025 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-36 +UniProtKB:A1B2F4 RO:0001025 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-36 ! FAILS GORULE:0000061 - TEST 37 - 'colocalizes_with' is not allowed for a GO CC - complex -UniProtKB:A1B2F4 RO:0002325 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-37 +UniProtKB:A1B2F4 RO:0002325 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-37 ! FAILS GORULE:0000061 - TEST 38 - 'part_of' is not allowed for a GO CC - cellular anatomical entity -UniProtKB:A1B2F4 BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-38 +UniProtKB:A1B2F4 BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-38 ! FAILS GORULE:0000061 - TEST 39 - 'part_of' is not allowed for GO CC - cellular anatomical entity -UniProtKB:A1B2F4 NOT BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-39 +UniProtKB:A1B2F4 NOT BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-39 ! FAILS GORULE:0000061 - TEST 40 - 'part_of' is not allowed for GO CC - cell plate descendent of cellular anatomical entity -UniProtKB:A1B2F4 BFO:0000050 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-40 +UniProtKB:A1B2F4 BFO:0000050 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-40 ! FAILS GORULE:0000061 - TEST 41 - 'part_of' is not allowed for GO CC cellular anatomical entity (GO:0005739 mitochondrion) -UniProtKB:A1B2F4 BFO:0000050 GO:0005739 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-41 +UniProtKB:A1B2F4 BFO:0000050 GO:0005739 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-41 ! FAILS GORULE:0000061 - TEST 42 - 'part_of' is not allowed for GO CC virion component -UniProtKB:A1B2F4 BFO:0000050 GO:0044423 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-42 +UniProtKB:A1B2F4 BFO:0000050 GO:0044423 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-42 ! FAILS GORULE:0000061 - TEST 43 - 'part_of' is not allowed for a GO CC icosahedral viral capsid, neck descendant of virion component -UniProtKB:A1B2F4 BFO:0000050 GO:0098030 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-43 +UniProtKB:A1B2F4 BFO:0000050 GO:0098030 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-43 ! SHOULD PASS GORULE:0000061 - TEST 45 - 'is_active_in' is allowed for GO CC - 'cell plate' descendent of cellular anatomical entity -UniProtKB:A1B2F4 RO:0002432 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST=0000061-45 +UniProtKB:A1B2F4 RO:0002432 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-45 ! SHOULD PASS GORULE:0000063 - TEST 1 PomBase:SPAC25B8.17 RO:0002432 GO:0005634 GO_REF:0000024 ECO:0000266 SGD:S000001583 2023-04-27 GO_Central GORULE_TEST:0000063-1 ! FAILS GORULE:0000063 - TEST 2 - no data in 'with' field (column 7) From aa919d7ffb021fdb08f81130b9cc502e1d43cae6 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 25 Jul 2024 16:17:41 +0200 Subject: [PATCH 07/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 214b4e1b..1a8d33c8 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -73,8 +73,6 @@ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID: IDA P GORULE_TEST:0000001- UniProtKB O76187 darA NOT|enables GO:0005515 PMID:9802899 IPI UniProtKB:P34149 F GORULE_TEST:0000002-1 Darlin darA protein taxon:44689 20100205 GO_Central ! FAILS GORULE:0000002 - TEST 2 - has a 'NOT' annotations to 'binding ; GO:0005515 UniProtKB O76187 darA NOT|enables GO:0005488 PMID:9802899 IPI UniProtKB:P34149 F GORULE_TEST:0000002-2 Darlin darA protein taxon:44689 20100205 GO_Central -! SHOULD PASS GORULE:0000003 - TEST 3 - has a 'NOT' annotations to GO:0005509, a child of 'binding ; GO:0005515 -UniProtKB O76187 darA NOT|enables GO:0005509 PMID:9802899 IPI UniProtKB:P34149 F GORULE_TEST:0000002-3-PASS Darlin darA protein taxon:44689 20100205 GO_Central ! TBC FAILS GORULE:0000005 - TEST 1 - incorrect evidence codes for 'protein binding ; GO:0005515' - ISS not allowed UniProtKB O76187 darA enables GO:0005515 PMID:9802899 ISS UniProtKB:P34149 F GORULE_TEST:0000005-1 Darlin darA protein taxon:44689 20100205 GO_Central ! TBC FAILS GORULE:0000005 - TEST 2 - incorrect evidence codes for 'protein binding ; GO:0005515' - IS0 not allowed From e7e60c19e07d4331925608f3770c062ab90f0b0b Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 25 Jul 2024 16:18:30 +0200 Subject: [PATCH 08/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index 1d15b548..aba4d2cb 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -7,8 +7,6 @@ UniProtKB:O76187 NOT RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-1 Darlin ! FAILS GORULE:0000002 - TEST 2 - has a 'NOT' annotations to 'binding ; GO:0005515 UniProtKB:O76187 NOT RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-1 Darlin -! SHOULD PASS GORULE:0000003 - TEST 3 - has a 'NOT' annotations to GO:0005509, a child of 'binding ; GO:0005515 -UniProtKB:O76187 NOT RO:0002327 GO:0005509 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-3-PASS Darlin ! TBC FAILS GORULE:0000005 - TEST 1 - incorrect evidence codes for 'protein binding ; GO:0005515' - ISS not allowed UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000250 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000005-1 Darlin ! TBC FAILS GORULE:0000005 - TEST 2 - incorrect evidence codes for 'protein binding ; GO:0005515' - IS0 not allowed From 0e1b63c5ce88ede209c339367aa2edbb18bb0c88 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 25 Jul 2024 18:12:36 +0200 Subject: [PATCH 09/42] Update gorule-0000031.md fixes #2352 --- metadata/rules/gorule-0000031.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/metadata/rules/gorule-0000031.md b/metadata/rules/gorule-0000031.md index 0c7b0a01..a180ad71 100644 --- a/metadata/rules/gorule-0000031.md +++ b/metadata/rules/gorule-0000031.md @@ -1,10 +1,10 @@ --- layout: rule id: GORULE:0000031 -title: "Annotation relations are replaced when not provided by source" +title: "DEPRECATED. Annotation relations are replaced when not provided by source" type: repair fail_mode: hard -status: implemented +status: deprecated contact: "go-quality@lists.stanford.edu" implementations: - language: python @@ -17,3 +17,5 @@ For Biological Process: relation = 'involved_in' For Molecular Function: relation = 'enables' ##This seems to be only exported in GPAD for now. + +##Now covered by GORULE-0000059 and GORULE-0000061. This was not being reported in rule reports as og 2024-07. From 9aa71ec21e28be78545014d3b0c92401bc65b417 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 25 Jul 2024 16:12:52 +0000 Subject: [PATCH 10/42] refreshing rules README.md file --- metadata/rules/README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/metadata/rules/README.md b/metadata/rules/README.md index e3754744..26f3d12d 100644 --- a/metadata/rules/README.md +++ b/metadata/rules/README.md @@ -37,7 +37,7 @@ For more details for GOC members on how to create rules, see [SOP.md](SOP.md) * GORULE:0000028 GO aspect should match the term's namespace; otherwise it is repaired to the appropriate aspect * GORULE:0000029 IEAs should be less than one year old. * GORULE:0000030 Obsolete GO_REFs are not allowed - * GORULE:0000031 Annotation relations are replaced when not provided by source + * GORULE:0000031 DEPRECATED. Annotation relations are replaced when not provided by source * GORULE:0000032 DEPRECATED Allowed References for each ECO. * GORULE:0000033 DEPRECATED. Public Reference IDs (PMID, PMC, doi, or GO_REF) should be preferred over group specific Reference IDs * GORULE:0000035 DEPRECATED - Colocalizes_with' qualifier not allowed with protein-containing complex (GO:0032991)' and children. @@ -679,10 +679,10 @@ References for which is_obsolete: `true` should not be allowed as a reference (G -## Annotation relations are replaced when not provided by source +## DEPRECATED. Annotation relations are replaced when not provided by source * id: [GORULE:0000031](https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000031.md) - * status: implemented + * status: deprecated In GAFs, relation is overloaded into qualifier. @@ -693,6 +693,8 @@ For Molecular Function: relation = 'enables' ##This seems to be only exported in GPAD for now. +##Now covered by GORULE-0000059 and GORULE-0000061. This was not being reported in rule reports as og 2024-07. + ## DEPRECATED Allowed References for each ECO. From 3cb098224bfb929a934bdb52a7f40f64015605cc Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 11:57:14 +0200 Subject: [PATCH 11/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 1a8d33c8..636d9d00 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -159,6 +159,8 @@ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:PMID:14561399 IDA P GORULE_ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:unpublished IDA P GORULE_TEST:0000027-4 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000027 - TEST 5 - Bad reference syntax UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P GORULE_TEST:0000027-5 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central +! FAILS GORULE:0000027 - TEST 6 - Prefix is a synonyms in /db-xrefs.yaml is REPAIRED +WormBase WBGene00000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C F27C8.1 gene taxon:6239 20131022 WB ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From bfddae026d409b57a72885b6e623608f0fd6e217 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 12:06:55 +0200 Subject: [PATCH 12/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 636d9d00..6eb52178 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -159,8 +159,10 @@ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:PMID:14561399 IDA P GORULE_ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:unpublished IDA P GORULE_TEST:0000027-4 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000027 - TEST 5 - Bad reference syntax UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P GORULE_TEST:0000027-5 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central -! FAILS GORULE:0000027 - TEST 6 - Prefix is a synonyms in /db-xrefs.yaml is REPAIRED -WormBase WBGene00000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C F27C8.1 gene taxon:6239 20131022 WB +! FAILS GORULE:0000027 - TEST 6 - Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED +WormBase WBGene00000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-6 F27C8.1 gene taxon:6239 20131022 WB +! FAILS GORULE:0000027 - TEST 7 - bad id syntax: WB needs 8 digits, has only 7 +WormBase WBGene0000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-7 F27C8.1 gene taxon:6239 20131022 WB ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From 75c8c8fecee4391a21b6b94fdc7d6b93a2995d45 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 12:07:35 +0200 Subject: [PATCH 13/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 6eb52178..2323f395 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -160,9 +160,9 @@ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:unpublished IDA P GORULE_TE ! FAILS GORULE:0000027 - TEST 5 - Bad reference syntax UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P GORULE_TEST:0000027-5 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000027 - TEST 6 - Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED -WormBase WBGene00000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-6 F27C8.1 gene taxon:6239 20131022 WB +WormBase WBGene00000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-6 F27C8.1 gene taxon:6239 20131022 GO_Central ! FAILS GORULE:0000027 - TEST 7 - bad id syntax: WB needs 8 digits, has only 7 -WormBase WBGene0000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-7 F27C8.1 gene taxon:6239 20131022 WB +WormBase WBGene0000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-7 F27C8.1 gene taxon:6239 20131022 GO_Central ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From 969e48504219162f85b8f370d70fa4f0dd1b9f71 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 12:07:48 +0200 Subject: [PATCH 14/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 2323f395..4957c07d 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -1,6 +1,6 @@ !gaf-version: 2.2 !generated-by: GOC -!date-generated: 2024-07-14 +!date-generated: 2024-07-26 ! Dummy GAF file containing deliberate errors to test that GO rules are correctly implemented. ! Should be equivalent to https://github.com/geneontology/go-site/blob/master/docs/gorules_test_errors.gpad when the rule applies. ! FAILS GORULE:0000001 - empty col1 and col2 From 41a955c7e45a7cd10ad9132c75a40b21ac9cd6d7 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 12:10:48 +0200 Subject: [PATCH 15/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 4957c07d..c19e99ce 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -163,6 +163,8 @@ UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P GORULE_TEST:000002 WormBase WBGene00000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-6 F27C8.1 gene taxon:6239 20131022 GO_Central ! FAILS GORULE:0000027 - TEST 7 - bad id syntax: WB needs 8 digits, has only 7 WormBase WBGene0000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-7 F27C8.1 gene taxon:6239 20131022 GO_Central +! FAILS GORULE:0000027 - TEST 8 - caolumn 2 cardinality should be 1 +WormBase WBGene00000002|WBGene00000003 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-8 F27C8.1 gene taxon:6239 20131022 GO_Central ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From 5b6a56a3be5a8b8be06206b7c89c8ecf5f9e1079 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 13:32:48 +0200 Subject: [PATCH 16/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index c19e99ce..918bc5f6 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -165,6 +165,12 @@ WormBase WBGene00000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:146 WormBase WBGene0000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-7 F27C8.1 gene taxon:6239 20131022 GO_Central ! FAILS GORULE:0000027 - TEST 8 - caolumn 2 cardinality should be 1 WormBase WBGene00000002|WBGene00000003 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-8 F27C8.1 gene taxon:6239 20131022 GO_Central +! SHOULD PASS GORULE:0000027 - TEST 9 - 2 values in with field, pipe-separated +UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniProtKB:P77335|UniProtKB:A0A0K3AV08 P GORULE_TEST:0000027-9 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central +! FAILS GORULE:0000027 - TEST 10 - 2 values in with field, comma-separated +UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniProtKB:P77335,UniProtKB:A0A0K3AV08 P GORULE_TEST:0000027-10 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central +! FAILS GORULE:0000027 - TEST 11 - 2 values in with field, second namespace missing +UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniProtKB:P77335|A0A0K3AV08 P GORULE_TEST:0000027-11 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From ea1d4af8ad5196c4b70b8db475bc97ecf095b531 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 13:43:06 +0200 Subject: [PATCH 17/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 918bc5f6..98f2aa9b 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -167,10 +167,16 @@ WormBase WBGene0000002 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:1466 WormBase WBGene00000002|WBGene00000003 aat-1 part_of GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 IPI WB:WBGene00000225 C GORULE_TEST:0000027-8 F27C8.1 gene taxon:6239 20131022 GO_Central ! SHOULD PASS GORULE:0000027 - TEST 9 - 2 values in with field, pipe-separated UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniProtKB:P77335|UniProtKB:A0A0K3AV08 P GORULE_TEST:0000027-9 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central -! FAILS GORULE:0000027 - TEST 10 - 2 values in with field, comma-separated +! FAILS GORULE:0000027 - TEST 10 - 2 values in 'with' field, comma-separated UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniProtKB:P77335,UniProtKB:A0A0K3AV08 P GORULE_TEST:0000027-10 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central -! FAILS GORULE:0000027 - TEST 11 - 2 values in with field, second namespace missing +! FAILS GORULE:0000027 - TEST 11 - 2 values in 'with' field, second namespace missing UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniProtKB:P77335|A0A0K3AV08 P GORULE_TEST:0000027-11 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central +! FAILS GORULE:0000027 - TEST 12 - 'with' prefix not in /db-xrefs.yaml +UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniPotKB:P77335 P GORULE_TEST:0000027-12 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central +! FAILS GORULE:0000027 - TEST 13 - 'with' Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED +FB FBgn0020238 14-3-3epsilon involved_in GO:0006401 PMID:16931762 IGI FLYBASE:FBgn0004907 P GORULE_TEST:0000027-13 14-3-3epsilon 14-3-3|14-3-3 epsilon|14-3-3 protein epsilon protein taxon:7227 20220606 GO_Central +! FAILS GORULE:0000027 - TEST 14 - 'bad with' id syntax - should have 7 digits, has 8 +FB FBgn0020238 14-3-3epsilon involved_in GO:0006401 PMID:16931762 IGI FLYBASE:FBgn10004907 P GORULE_TEST:0000027-13 14-3-3epsilon 14-3-3|14-3-3 epsilon|14-3-3 protein epsilon protein taxon:7227 20220606 GO_Central ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From ad5acecd40dcd32c674d6e12a2c36ef099bdc554 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 13:54:53 +0200 Subject: [PATCH 18/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 98f2aa9b..b0be04ca 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -176,7 +176,13 @@ UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IGI UniPotKB:P77335 ! FAILS GORULE:0000027 - TEST 13 - 'with' Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED FB FBgn0020238 14-3-3epsilon involved_in GO:0006401 PMID:16931762 IGI FLYBASE:FBgn0004907 P GORULE_TEST:0000027-13 14-3-3epsilon 14-3-3|14-3-3 epsilon|14-3-3 protein epsilon protein taxon:7227 20220606 GO_Central ! FAILS GORULE:0000027 - TEST 14 - 'bad with' id syntax - should have 7 digits, has 8 -FB FBgn0020238 14-3-3epsilon involved_in GO:0006401 PMID:16931762 IGI FLYBASE:FBgn10004907 P GORULE_TEST:0000027-13 14-3-3epsilon 14-3-3|14-3-3 epsilon|14-3-3 protein epsilon protein taxon:7227 20220606 GO_Central +FB FBgn0020238 14-3-3epsilon involved_in GO:0006401 PMID:16931762 IGI FLYBASE:FBgn10004907 P GORULE_TEST:0000027-14 14-3-3epsilon 14-3-3|14-3-3 epsilon|14-3-3 protein epsilon protein taxon:7227 20220606 GO_Central +! SHOULD PASS GORULE:0000027 - TEST 15 - Two references in different ID spaces, space separated (instead of pipe-separated) +FB FBgn0024811 Crk involved_in GO:0048010 FB:FBrf0180198|PMID:15457211 IMP P GORULE_TEST:0000027-15 Crk oncogene CED-2|CG1587|CRK|D-CRK|D-Crk|DCrk|Dcrk|crk|dCRK|dCrk protein taxon:7227 20180912 GO_Central +! FAILS GORULE:0000027 - TEST 16 - Two references in different ID spaces +FB FBgn0024811 Crk involved_in GO:0048010 FB:FBrf0180198 PMID:15457211 IMP P GORULE_TEST:0000027-16 Crk oncogene CED-2|CG1587|CRK|D-CRK|D-Crk|DCrk|Dcrk|crk|dCRK|dCrk protein taxon:7227 20180912 GO_Central +! FAILS GORULE:0000027 - TEST 17 - bad PMID ID syntax +FB FBgn0024811 Crk involved_in GO:0048010 FB:FBrf0180198|PMID:1545721X IMP P GORULE_TEST:0000027-17 Crk oncogene CED-2|CG1587|CRK|D-CRK|D-Crk|DCrk|Dcrk|crk|dCRK|dCrk protein taxon:7227 20180912 GO_Central ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From 87cd1ba81a8ec96dd745e8937ae2b4a0b3cf37e6 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 14:02:24 +0200 Subject: [PATCH 19/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index b0be04ca..6d67cbda 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -183,6 +183,10 @@ FB FBgn0024811 Crk involved_in GO:0048010 FB:FBrf0180198|PMID:15457211 IMP P GO FB FBgn0024811 Crk involved_in GO:0048010 FB:FBrf0180198 PMID:15457211 IMP P GORULE_TEST:0000027-16 Crk oncogene CED-2|CG1587|CRK|D-CRK|D-Crk|DCrk|Dcrk|crk|dCRK|dCrk protein taxon:7227 20180912 GO_Central ! FAILS GORULE:0000027 - TEST 17 - bad PMID ID syntax FB FBgn0024811 Crk involved_in GO:0048010 FB:FBrf0180198|PMID:1545721X IMP P GORULE_TEST:0000027-17 Crk oncogene CED-2|CG1587|CRK|D-CRK|D-Crk|DCrk|Dcrk|crk|dCRK|dCrk protein taxon:7227 20180912 GO_Central +! SHOULD PASS GORULE:0000027 - TEST 18 - 'Assigned by' is in groups.yaml (but not in dbxref.yaml) +UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IDA P GORULE_TEST:0000027-18 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 LBL +! FAILS GORULE:0000027 - TEST 19 - 'Assigned by' is in dbxref.yaml but not in groups.yaml +UniProtKB Q6UW15 REG3G involved_in GO:0006401 PMID:16931762 IDA P GORULE_TEST:0000027-18 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 PO ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE_TEST:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From f9d884ee949b28408a4dd5ca9893e4fba673a98b Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 14:14:20 +0200 Subject: [PATCH 20/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 6d67cbda..8c9ee040 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -116,11 +116,11 @@ UniProtKB O56786 hol187 is_active_in GO:0018995 PMID:10419939 IDA C GORULE_TEST ! PASSES GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID UniProtKB O56786 hol187 is_active_in GO:0042025 PMID:10419939 IDA C GORULE_TEST:0000015-4 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! PASSES GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID -UniProtKB O56786 hol187 involved_in GO:0010363 PMID:10419939 IDA C GORULE_TEST:0000015-4 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central +UniProtKB O56786 hol187 involved_in GO:0010363 PMID:10419939 IDA C GORULE_TEST:0000015-5 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! PASSES GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID -UniProtKB O56786 hol187 involved_in GO:0141062 PMID:10419939 IDA C GORULE_TEST:0000015-4 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central -! SHOULD PASS GORULE:0000015 - TEST 4 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction -UniProtKB Q6UW15 REG3G involved_in GO:0010363 PMID:16931762 IDA P GORULE_TEST:0000015-4 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606|taxon:1334565 20220606 GO_Central +UniProtKB O56786 hol187 involved_in GO:0141062 PMID:10419939 IDA C GORULE_TEST:0000015-6 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central +! SHOULD PASS GORULE:0000015 - TEST 7 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction +UniProtKB Q6UW15 REG3G involved_in GO:0010363 PMID:16931762 IDA P GORULE_TEST:0000015-7 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606|taxon:1334565 20220606 GO_Central ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 GO_REF:0000036 IC P GORULE_TEST:0000016-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000016 - TEST 2 - column 8 (with/from) is has a non-GOID From e5b8302c73d3a95efd1b03b9de9ce3ba1ffb4313 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 14:14:51 +0200 Subject: [PATCH 21/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index aba4d2cb..17086eb2 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -50,11 +50,11 @@ UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606 20 ! PASSES GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID UniProtKB:O56786 RO:0002432 GO:0042025 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 ! PASSES GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID -UniProtKB:O56786 RO:0002331 GO:0010363 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 +UniProtKB:O56786 RO:0002331 GO:0010363 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-5 Holin protein Hol187 ! PASSES GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID -UniProtKB:O56786 RO:0002331 GO:0141062 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 -! SHOULD PASS GORULE:0000015 - TEST 4 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction -UniProtKB:Q6UW15 RO:0002331 GO:0010363 PMID:16931762 ECO:0000314 taxon:1334565 2022-06-06 GO_Central GORULE_TEST:0000015-4 Regenerating islet-derived protein 3-gamma +UniProtKB:O56786 RO:0002331 GO:0141062 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-6 Holin protein Hol187 +! SHOULD PASS GORULE:0000015 - TEST 7 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction +UniProtKB:Q6UW15 RO:0002331 GO:0010363 PMID:16931762 ECO:0000314 taxon:1334565 2022-06-06 GO_Central GORULE_TEST:0000015-7 Regenerating islet-derived protein 3-gamma ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 2022-06-06 GO_Central GORULE_TEST:0000016-1 Calpain-10 ! FAILS GORULE:0000016 - TEST 2 - column 8 (with/from) is has a non-GOID From 3e6d07261aae35a78c58b260322aebb269a0f7a0 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 14:58:17 +0200 Subject: [PATCH 22/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 8c9ee040..519e09b6 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -113,13 +113,13 @@ UniProtKB O56786 hol187 is_active_in GO:0005886 PMID:10419939 IDA C GORULE_TEST UniProtKB A0A0K2S4Q6 CD300H involved_in GO:0030593 PMID:26221034 IDA P GORULE_TEST:0000015-2 Protein CD300H CD300H protein taxon:9606|taxon:55511 20160428 GO_Central ! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall UniProtKB O56786 hol187 is_active_in GO:0018995 PMID:10419939 IDA C GORULE_TEST:0000015-3 Holin protein Hol187 hol187 protein taxon:9606|taxon:9606 20170423 GO_Central -! PASSES GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID +! SHOULD PASS GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID UniProtKB O56786 hol187 is_active_in GO:0042025 PMID:10419939 IDA C GORULE_TEST:0000015-4 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central -! PASSES GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID +! SHOULD PASS GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID UniProtKB O56786 hol187 involved_in GO:0010363 PMID:10419939 IDA C GORULE_TEST:0000015-5 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central -! PASSES GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID +! SHOULD PASS GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID UniProtKB O56786 hol187 involved_in GO:0141062 PMID:10419939 IDA C GORULE_TEST:0000015-6 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central -! SHOULD PASS GORULE:0000015 - TEST 7 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction +! FAILS GORULE:0000015 - TEST 7 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction UniProtKB Q6UW15 REG3G involved_in GO:0010363 PMID:16931762 IDA P GORULE_TEST:0000015-7 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606|taxon:1334565 20220606 GO_Central ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 GO_REF:0000036 IC P GORULE_TEST:0000016-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central From 884927553af68e66a5577c892df6dac0d276f17c Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:00:09 +0200 Subject: [PATCH 23/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 519e09b6..830a4bdf 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -107,9 +107,9 @@ UniProtKB Q4KA26 PFL_3807 is_active_in GO:0005575 GO_REF:0000015 IDA C GORULE_T UniProtKB Q6UW15 REG3G involved_in GO:0050689 PMID:16931762 IDA P GORULE_TEST:0000011-3 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606 20220606 GO_Central ! FAILS GORULE:0000013 - fails because GO:0075342 should not be annotated for human gene products - cannot be tested in ontobio parser (not a line-by-line check) UniProtKB P67870 CSNK2B involved_in GO:0075342 PMID:20719947 IDA P GORULE_TEST:0000013-1 Casein kinase II subunit beta CSNK2B|CK2N|G5A protein taxon:9606 20230307 GO_Central -! FAILS GORULE:0000015 - TEST 1 - GO:0005886 plasma membrane is not a child of "GO:0018995 host cellular component" +! FAILS GORULE:0000015 - TEST 1 - "GO:0005886 plasma membrane" is not a child of "GO:0018995 host cellular component" UniProtKB O56786 hol187 is_active_in GO:0005886 PMID:10419939 IDA C GORULE_TEST:0000015-1 Holin protein Hol187 hol187 protein taxon:55511|taxon:9696 20170423 GO_Central -! FAILS GORULE:0000015 - TEST 2 - "neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" +! FAILS GORULE:0000015 - TEST 2 - "GO:0030593 neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" UniProtKB A0A0K2S4Q6 CD300H involved_in GO:0030593 PMID:26221034 IDA P GORULE_TEST:0000015-2 Protein CD300H CD300H protein taxon:9606|taxon:55511 20160428 GO_Central ! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall UniProtKB O56786 hol187 is_active_in GO:0018995 PMID:10419939 IDA C GORULE_TEST:0000015-3 Holin protein Hol187 hol187 protein taxon:9606|taxon:9606 20170423 GO_Central From f0c27cd19ab90d9ce89ca836def4609d4cbbade6 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:01:16 +0200 Subject: [PATCH 24/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index 17086eb2..b0ae43ed 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -41,17 +41,17 @@ UniProtKB:Q4KA26 RO:0002432 GO:0005575 GO_REF:0000015 ECO:0000314 2018-01-29 UniProtKB:Q6UW15 RO:0002331 GO:0050689 PMID:16931762 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000011-3 Regenerating islet-derived protein 3-gamma ! FAILS GORULE:0000013 - fails because GO:0075342 should not be annotated for human gene products - cannot be tested in ontobio parser (not a line-by-line check) UniProtKB:P67870 RO:0002331 GO:0075342 PMID:20719947 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000013-1 Casein kinase II subunit beta -! FAILS GORULE:0000015 - TEST 1 - GO:0005886 plasma membrane is not a child of "GO:0018995 host cellular component" +! FAILS GORULE:0000015 - TEST 1 - "GO:0005886 plasma membrane" is not a child of "GO:0018995 host cellular component" UniProtKB:O56786 RO:0002432 GO:0005886 PMID:10419939 ECO:0000314 taxon:9696 2022-06-06 GO_Central GORULE_TEST:0000015-1 Holin protein Hol187 -! FAILS GORULE:0000015 - TEST 2 - "neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" +! FAILS GORULE:0000015 - TEST 2 - "GO:0030593 neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:55511 2022-06-06 GO_Central GORULE_TEST:0000015-2 Protein CD300H ! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606 2022-06-06 GO_Central GORULE_TEST:0000015-3 Holin protein Hol187 -! PASSES GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID +! SHOULD PASS GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID UniProtKB:O56786 RO:0002432 GO:0042025 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 -! PASSES GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID +! SHOULD PASS GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID UniProtKB:O56786 RO:0002331 GO:0010363 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-5 Holin protein Hol187 -! PASSES GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID +! SHOULD PASS GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID UniProtKB:O56786 RO:0002331 GO:0141062 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-6 Holin protein Hol187 ! SHOULD PASS GORULE:0000015 - TEST 7 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction UniProtKB:Q6UW15 RO:0002331 GO:0010363 PMID:16931762 ECO:0000314 taxon:1334565 2022-06-06 GO_Central GORULE_TEST:0000015-7 Regenerating islet-derived protein 3-gamma From 870757fea1bf483389bb2a50c2002fd977ec40cb Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:07:19 +0200 Subject: [PATCH 25/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 830a4bdf..33ff4764 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -119,8 +119,8 @@ UniProtKB O56786 hol187 is_active_in GO:0042025 PMID:10419939 IDA C GORULE_TEST UniProtKB O56786 hol187 involved_in GO:0010363 PMID:10419939 IDA C GORULE_TEST:0000015-5 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! SHOULD PASS GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID UniProtKB O56786 hol187 involved_in GO:0141062 PMID:10419939 IDA C GORULE_TEST:0000015-6 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central -! FAILS GORULE:0000015 - TEST 7 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction -UniProtKB Q6UW15 REG3G involved_in GO:0010363 PMID:16931762 IDA P GORULE_TEST:0000015-7 Regenerating islet-derived protein 3-gamma REG3G|PAP1B|UNQ429/PRO162 protein taxon:9606|taxon:1334565 20220606 GO_Central +! SHOULD PASS GORULE:0000015 - TEST 7 - "GO:0034053 symbiont-mediated perturbation of host defense-related programmed cell death" with two taxon ID +UniProtKB P16971 recA involved_in GO:0034053 PMID:26221034 IDA P GORULE_TEST:0000015-7 Protein CD300H CD300H protein taxon:9606|taxon:224308 20160428 GO_Central ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 GO_REF:0000036 IC P GORULE_TEST:0000016-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000016 - TEST 2 - column 8 (with/from) is has a non-GOID From db81044558d50214cc0fde1eda8b0ec8ac7c4938 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:25:07 +0200 Subject: [PATCH 26/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index b0ae43ed..86167f76 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -41,20 +41,16 @@ UniProtKB:Q4KA26 RO:0002432 GO:0005575 GO_REF:0000015 ECO:0000314 2018-01-29 UniProtKB:Q6UW15 RO:0002331 GO:0050689 PMID:16931762 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000011-3 Regenerating islet-derived protein 3-gamma ! FAILS GORULE:0000013 - fails because GO:0075342 should not be annotated for human gene products - cannot be tested in ontobio parser (not a line-by-line check) UniProtKB:P67870 RO:0002331 GO:0075342 PMID:20719947 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000013-1 Casein kinase II subunit beta -! FAILS GORULE:0000015 - TEST 1 - "GO:0005886 plasma membrane" is not a child of "GO:0018995 host cellular component" -UniProtKB:O56786 RO:0002432 GO:0005886 PMID:10419939 ECO:0000314 taxon:9696 2022-06-06 GO_Central GORULE_TEST:0000015-1 Holin protein Hol187 -! FAILS GORULE:0000015 - TEST 2 - "GO:0030593 neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" -UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:55511 2022-06-06 GO_Central GORULE_TEST:0000015-2 Protein CD300H -! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall -UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606 2022-06-06 GO_Central GORULE_TEST:0000015-3 Holin protein Hol187 -! SHOULD PASS GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID -UniProtKB:O56786 RO:0002432 GO:0042025 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 -! SHOULD PASS GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID -UniProtKB:O56786 RO:0002331 GO:0010363 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-5 Holin protein Hol187 -! SHOULD PASS GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID -UniProtKB:O56786 RO:0002331 GO:0141062 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-6 Holin protein Hol187 -! SHOULD PASS GORULE:0000015 - TEST 7 - GO:0010363 regulation of plant-type hypersensitive response is_ GO:0043903 regulation of biological process involved in symbiotic interaction -UniProtKB:Q6UW15 RO:0002331 GO:0010363 PMID:16931762 ECO:0000314 taxon:1334565 2022-06-06 GO_Central GORULE_TEST:0000015-7 Regenerating islet-derived protein 3-gamma +! FAILS GORULE:0000015 - TEST 1 - "GO:0005886 plasma membrane" is not a child of "GO:0018995 host cellular component" +UniProtKB:O56786 RO:0002432 GO:0005886 PMID:10419939 ECO:0000314 taxon:9696 2022-06-06 GO_Central GORULE_TEST:0000015-1 Holin protein Hol187 +! FAILS GORULE:0000015 - TEST 2 - "GO:0030593 neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" +UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:55511 2022-06-06 GO_Central GORULE_TEST:0000015-2 Protein CD300H +! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall +UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606|taxon:9606 2022-06-06 GO_Central GORULE_TEST:0000015-3 Holin protein Hol187 +! SHOULD PASS GORULE:0000015 - GPAD TEST 4 - "GO:0042025 host cell nucleus" with no interacting taxon +UniProtKB:O56786 RO:0002331 GO:0034053 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-5 Holin protein Hol187 +! DO NOT APPLY TO GPAD GORULE:0000015 - TEST 5 - "GO:0141062 disruption of tissue in another organism" with single taxon ID +! DO NOT APPLY TO GPAD GORULE:0000015 - TEST 6 - "GO:0010363 regulation of plant-type hypersensitive response" is_a "GO:0043903 regulation of biological process involved in symbiotic interaction" ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 2022-06-06 GO_Central GORULE_TEST:0000016-1 Calpain-10 ! FAILS GORULE:0000016 - TEST 2 - column 8 (with/from) is has a non-GOID From 40f87a4b23146b751e7de742a4af3dbce67424c7 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:25:40 +0200 Subject: [PATCH 27/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index 86167f76..2f2eaca9 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -48,7 +48,7 @@ UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:555 ! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606|taxon:9606 2022-06-06 GO_Central GORULE_TEST:0000015-3 Holin protein Hol187 ! SHOULD PASS GORULE:0000015 - GPAD TEST 4 - "GO:0042025 host cell nucleus" with no interacting taxon -UniProtKB:O56786 RO:0002331 GO:0034053 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-5 Holin protein Hol187 +UniProtKB:O56786 RO:0002331 GO:0034053 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 ! DO NOT APPLY TO GPAD GORULE:0000015 - TEST 5 - "GO:0141062 disruption of tissue in another organism" with single taxon ID ! DO NOT APPLY TO GPAD GORULE:0000015 - TEST 6 - "GO:0010363 regulation of plant-type hypersensitive response" is_a "GO:0043903 regulation of biological process involved in symbiotic interaction" ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null From fde85684a9c40e691d07b702d7e14fbaa2515e3d Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:31:25 +0200 Subject: [PATCH 28/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index 2f2eaca9..31a2add8 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -125,9 +125,9 @@ UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000250 UniProtKB:F1N UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000266 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-2 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 ! FAILS GORULE:0000050 - TEST 3 - self-referential ISA annotations UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000247 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-3 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 -! SHOULD PASS GORULE:0000051 - Pass RULE 51 - Annotation extension for certain GO terms - protein binding; GO:0005515 +! PROPOSED GORULE:0000051 - Pass RULE 51 - Annotation extension for certain GO terms - protein binding; GO:0005515 UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central RO:0002233(GO:0003674)|BFO:0000066(CL:123456) GORULE_TEST:0000051-PASS1 Darlin -! FAILS GORULE:0000051 - TEST 1 - also fails GORULE:0000008 - Annotation extension is required for certain terms - binding GO:0005488 +! PROPOSED GORULE:0000051 - TEST 1 - also fails GORULE:0000008 - Annotation extension is required for certain terms - binding GO:0005488 UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central GORULE_TEST:0000051-1 Darlin ! FAILS GORULE:0000055 - TEST 1 - Two references in the same ID space - PMID PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 PMID:12477793|PMID:15961998 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000055-1 From 944c4833eed4ade7bf192f2dc9d1f9955d7bc588 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:31:43 +0200 Subject: [PATCH 29/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 33ff4764..cf51081c 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -223,9 +223,9 @@ UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISS UniProtKB:F1N2N9 C G UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISO UniProtKB:F1N2N9 C GORULE_TEST:0000050-2 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 GO_Central ! FAILS GORULE:0000050 - TEST 3 - self-referential ISA annotations UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISA UniProtKB:F1N2N9 C GORULE_TEST:0000050-3 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 GO_Central -! SHOULD PASS GORULE:0000051 - Pass RULE 51 - Annotation extension for certain GO terms - protein binding; GO:0005515 +! PROPOSED RULE GORULE:0000051 - Pass RULE 51 - Annotation extension for certain GO terms - protein binding; GO:0005515 UniProtKB O76187 darA enables GO:0005515 PMID:9802899 IPI UniProtKB:P34149 F GORULE_TEST:0000051-PASS1 Darlin darA protein taxon:44689 20100205 GO_Central has_input(GO:0003674)|occurs_in(CL:1234567) -! FAILS GORULE:0000051 - TEST 1 - also fails GORULE:0000008 - Annotation extension is required for certain terms - binding GO:0005488 +! PROPOSED RULE GORULE:0000051 - TEST 1 - also fails GORULE:0000008 - Annotation extension is required for certain terms - binding GO:0005488 UniProtKB O76187 darA enables GO:0005488 PMID:9802899 IPI UniProtKB:P34149 F GORULE_TEST:0000051-1 Darlin darA protein taxon:44689 20100205 GO_Central ! FAILS GORULE:0000055 - TEST 1 - Two references in the same ID space - PMID PlasmoDB PF3D7_0200400 PF3D7_0200400 is_active_in GO:0020036 PMID:12477793|PMID:15961998 IDA C GORULE_TEST:0000055-1 stevor mRNA taxon:4896 20131007 GO_Central From 067db9d148767bc0b802a1b2dc8da4e82ee5d527 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 15:41:47 +0200 Subject: [PATCH 30/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index cf51081c..6ed41c77 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -67,7 +67,7 @@ UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TE UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-27 taxon:318586 20230427 GO_Central ! FAILS GORULE:0000001 - TEST 28 - bad entity type UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-28 misc_RNA taxon:318586 20230427 GO_Central -! FAILS GORULE:0000001 - TEST 29 - Bad referencesyntax +! FAILS GORULE:0000001 - TEST 29 - Bad reference syntax (has namespace but not value) UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID: IDA P GORULE_TEST:0000001-29 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000002 - TEST 1 - has a 'NOT' annotations to 'protein binding ; GO:0005515 UniProtKB O76187 darA NOT|enables GO:0005515 PMID:9802899 IPI UniProtKB:P34149 F GORULE_TEST:0000002-1 Darlin darA protein taxon:44689 20100205 GO_Central From e3d9d57e60984bd9a9732c2d876e75f92213cb72 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:07:49 +0200 Subject: [PATCH 31/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index 31a2add8..60cb5cbc 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -89,6 +89,34 @@ UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:PMID:14561399 ECO:0000314 2022-06- UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:unpublished ECO:0000314 2022-06-06 GO_Central GORULE_TEST0000027-4 Calpain-10 ! FAILS GORULE:0000027 - TEST 5 - Bad reference syntax UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:0. ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000027-5 Calpain-10 +! FAILS GORULE:0000027 - TEST 6 - Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED +WormBase:WBGene00000002 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central GORULE_TEST:0000027-6 F27C8.1 +! FAILS GORULE:0000027 - TEST 7 - bad id syntax: WB needs 8 digits, has only 7 +WormBase:WBGene00000002 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central GORULE_TEST:0000027-7 F27C8.1 +! FAILS GORULE:0000027 - TEST 8 - caolumn 2 cardinality should be 1 +WormBase:WBGene00000002|WBGene00000003 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central GORULE_TEST:0000027-8 F27C8.1 +! SHOULD PASS GORULE:0000027 - TEST 9 - 2 values in with field, pipe-separated +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-9 Regenerating islet-derived protein 3-gamma +! FAILS GORULE:0000027 - TEST 10 - 2 values in 'with' field, comma-separated +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-10 Regenerating islet-derived protein 3-gamma +! FAILS GORULE:0000027 - TEST 11 - 2 values in 'with' field, second namespace missing +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-11 Regenerating islet-derived protein 3-gamma +! FAILS GORULE:0000027 - TEST 12 - 'with' prefix not in /db-xrefs.yaml +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-12 Regenerating islet-derived protein 3-gamma +! FAILS GORULE:0000027 - TEST 13 - 'with' Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED +FB:FBgn0020238 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-13 14-3-3epsilon +! FAILS GORULE:0000027 - TEST 14 - 'bad with' id syntax - should have 7 digits, has 8 +FB:FBgn0020238 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-14 14-3-3epsilon +! SHOULD PASS GORULE:0000027 - TEST 15 - Two references in different ID spaces, space separated +FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198|PMID:15457211 ECO:0000315 2013-10-22 GO_Central GORULE_TEST:0000027-15 Crk oncogene +! FAILS GORULE:0000027 - TEST 16 - Two references in different ID spaces +FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198 PMID:15457211 ECO:0000315 2013-10-22 GO_Central GORULE_TEST:0000027-16 Crk oncogene +! FAILS GORULE:0000027 - TEST 17 - bad PMID ID syntax +FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198|PMID:1545721X ECO:0000315 2013-10-22 GO_Central GORULE_TEST:0000027-17 Crk oncogene +! SHOULD PASS GORULE:0000027 - TEST 18 - 'Assigned by' is in groups.yaml (but not in dbxref.yaml) +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000314 2013-10-22 LBL GORULE_TEST:0000027-18 Regenerating islet-derived protein 3-gamma +! FAILS GORULE:0000027 - TEST 19 - 'Assigned by' is in dbxref.yaml but not in groups.yaml +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000314 2013-10-22 PO GORULE_TEST:0000027-18 Regenerating islet-derived protein 3-gamma ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-1 Calpain-10 ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P From 73f619240629fc9e6ca4a81885cd9c62781e7f20 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:18:32 +0200 Subject: [PATCH 32/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 252 +++++++++++++++++----------------- 1 file changed, 126 insertions(+), 126 deletions(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index 60cb5cbc..cd1fae6f 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -4,256 +4,256 @@ ! Dummy GPAD file containing deliberate errors to test that GO rules are correctly implemented. ! Should be equivalent to https://github.com/geneontology/go-site/blob/master/docs/gorules_test_errors.gaf when the rule applies. ! FAILS GORULE:0000002 - TEST 1 - has a 'NOT' annotations to 'protein binding ; GO:0005515 -UniProtKB:O76187 NOT RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-1 Darlin +UniProtKB:O76187 NOT RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central comment=GORULE_TEST:0000002-1 ! FAILS GORULE:0000002 - TEST 2 - has a 'NOT' annotations to 'binding ; GO:0005515 -UniProtKB:O76187 NOT RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000002-1 Darlin +UniProtKB:O76187 NOT RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2010-02-05 GO_Central comment=GORULE_TEST:0000002-1 ! TBC FAILS GORULE:0000005 - TEST 1 - incorrect evidence codes for 'protein binding ; GO:0005515' - ISS not allowed -UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000250 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000005-1 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000250 UniProtKB:P34149 2010-02-05 GO_Central comment=GORULE_TEST:0000005-1 ! TBC FAILS GORULE:0000005 - TEST 2 - incorrect evidence codes for 'protein binding ; GO:0005515' - IS0 not allowed -UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000266 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000005-2 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000266 UniProtKB:P34149 2010-02-05 GO_Central comment=GORULE_TEST:0000005-2 ! TBC FAILS GORULE:0000005 - TEST 3 - incorrect evidence codes for 'protein binding ; GO:0005515' - IBA not allowed -UniProtKB:O76187 RO:0002327 GO:0005515 GO_REF:0000033 ECO:0000318 UniProtKB:P34149 2010-02-05 GO_Central GORULE_TEST:0000005-3 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 GO_REF:0000033 ECO:0000318 UniProtKB:P34149 2010-02-05 GO_Central comment=GORULE_TEST:0000005-3 ! FAILS GORULE:0000006 - TEST 1 - fails because uses IEP with a molecular function term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-1 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GO_Central comment=GORULE_TEST:0000006-1 ! FAILS GORULE:0000006 - TEST 2 - fails because uses HEP with a molecular function term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0007007 2010-02-05 GO_Central GORULE_TEST:0000006-2 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0007007 2010-02-05 GO_Central comment=GORULE_TEST:0000006-2 ! FAILS GORULE:0000006 - TEST 3 - fails because uses IEP with a cellular component term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0005634 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-3 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0005634 PMID:12764150 ECO:0000270 2010-02-05 GO_Central comment=GORULE_TEST:0000006-3 ! SHOULD PASS GORULE:0000006 - TEST 4 - passes because uses assigned_by is GOC, even if there is an IEP with a molecular function term. -GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GOC GORULE_TEST:0000006-4 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0004672 PMID:12764150 ECO:0000270 2010-02-05 GOC comment=GORULE_TEST:0000006-4 ! SHOULD PASS GORULE:0000006 - TEST 5 - should pass because obsolete BP term should be ignored; GO:1901011 obsolete (S)-reticuline catabolic process -GeneDB:PF3D7_0507500 RO:0002327 GO:1901011 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-5 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:1901011 PMID:12764150 ECO:0000270 2010-02-05 GO_Central comment=GORULE_TEST:0000006-5 ! SHOULD PASS GORULE:0000006 - TEST 6 - should pass because alt_ids should be ignored, and GO:0006758 is an alt_id to GO:0006754 ATP biosynthetic process -GeneDB:PF3D7_0507500 RO:0002327 GO:0006758 PMID:12764150 ECO:0000270 2010-02-05 GO_Central GORULE_TEST:0000006-6 subtilisin-like +GeneDB:PF3D7_0507500 RO:0002327 GO:0006758 PMID:12764150 ECO:0000270 2010-02-05 GO_Central comment=GORULE_TEST:0000006-6 ! FAILS GORULE:0000007 - IPI used with GO:0003824 catalytic activity or descendents (GO:0004674 protein serine/threonine kinase activity) -UniProtKB:A0A078CGE6 RO:0002327 GO:0004674 PMID:11489177 ECO:0000021 UniProtKB:A0A078FEZ9 2010-02-05 GO_Central GORULE_TEST:0000007-1 +UniProtKB:A0A078CGE6 RO:0002327 GO:0004674 PMID:11489177 ECO:0000021 UniProtKB:A0A078FEZ9 2010-02-05 GO_Central comment=GORULE_TEST:0000007-1 ! FAILS GORULE:0000008 - TEST 1 - GO:0005622 is in the subset gocheck_do_not_annotate -UniProtKB:Q9DGE2 RO:0002432 GO:0005622 PMID:10995439 ECO:0000314 2018-01-29 GO_Central GORULE_TEST:0000008-1 Mitogen-activated protein kinase 14A +UniProtKB:Q9DGE2 RO:0002432 GO:0005622 PMID:10995439 ECO:0000314 2018-01-29 GO_Central comment=GORULE_TEST:0000008-1 ! FAILS GORULE:0000008 - TEST 2 - GO:0007049 is in the subset gocheck_do_not_manually_annotate -UniProtKB:Q9WVH3 RO:0002331 GO:0007049 PMID:12048180 ECO:0000314 2018-01-29 GO_Central GORULE_TEST:0000008-2 Forkhead box protein O4 +UniProtKB:Q9WVH3 RO:0002331 GO:0007049 PMID:12048180 ECO:0000314 2018-01-29 GO_Central comment=GORULE_TEST:0000008-2 ! FAILS GORULE:0000008 - TEST 3 - also fails GORULE:0000051 - GO:0005488 is in the subset gocheck_do_not_manually_annotate -UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2018-01-29 GO_Central GORULE_TEST:0000008-3 Darlin +UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2018-01-29 GO_Central comment=GORULE_TEST:0000008-3 ! FAILS GORULE:0000011 - TEST 1 - because the GO ID is not one of GO:0003674, GO:0008150 or GO:0005575 -UniProtKB:Q4KA26 RO:0002432 GO:0016020 GO_REF:0000015 ECO:0000307 2018-01-29 GO_Central GORULE_TEST:0000011-1 Putative membrane protein +UniProtKB:Q4KA26 RO:0002432 GO:0016020 GO_REF:0000015 ECO:0000307 2018-01-29 GO_Central comment=GORULE_TEST:0000011-1 ! FAILS GORULE:0000011 - TEST 2 - fails because the evidence code is not ND, even if the GO ID one of GO:0003674, GO:0008150 or GO:0005575. -UniProtKB:Q4KA26 RO:0002432 GO:0005575 GO_REF:0000015 ECO:0000314 2018-01-29 GO_Central GORULE_TEST:0000011-2 Putative membrane protein +UniProtKB:Q4KA26 RO:0002432 GO:0005575 GO_REF:0000015 ECO:0000314 2018-01-29 GO_Central comment=GORULE_TEST:0000011-2 ! SHOULD PASS GORULE:0000011 - TEST 3 -UniProtKB:Q6UW15 RO:0002331 GO:0050689 PMID:16931762 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000011-3 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0050689 PMID:16931762 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000011-3 ! FAILS GORULE:0000013 - fails because GO:0075342 should not be annotated for human gene products - cannot be tested in ontobio parser (not a line-by-line check) -UniProtKB:P67870 RO:0002331 GO:0075342 PMID:20719947 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000013-1 Casein kinase II subunit beta +UniProtKB:P67870 RO:0002331 GO:0075342 PMID:20719947 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000013-1 ! FAILS GORULE:0000015 - TEST 1 - "GO:0005886 plasma membrane" is not a child of "GO:0018995 host cellular component" -UniProtKB:O56786 RO:0002432 GO:0005886 PMID:10419939 ECO:0000314 taxon:9696 2022-06-06 GO_Central GORULE_TEST:0000015-1 Holin protein Hol187 +UniProtKB:O56786 RO:0002432 GO:0005886 PMID:10419939 ECO:0000314 taxon:9696 2022-06-06 GO_Central comment=GORULE_TEST:0000015-1 ! FAILS GORULE:0000015 - TEST 2 - "GO:0030593 neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms" -UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:55511 2022-06-06 GO_Central GORULE_TEST:0000015-2 Protein CD300H +UniProtKB:A0A0K2S4Q6 RO:0002331 GO:0030593 PMID:26221034 ECO:0000314 taxon:55511 2022-06-06 GO_Central comment=GORULE_TEST:0000015-2 ! FAILS GORULE:0000015 - TEST 3 - same taxon in Column 13 for GO:0044158 host cell wall -UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606|taxon:9606 2022-06-06 GO_Central GORULE_TEST:0000015-3 Holin protein Hol187 +UniProtKB:O56786 RO:0002432 GO:0018995 PMID:10419939 ECO:0000314 taxon:9606|taxon:9606 2022-06-06 GO_Central comment=GORULE_TEST:0000015-3 ! SHOULD PASS GORULE:0000015 - GPAD TEST 4 - "GO:0042025 host cell nucleus" with no interacting taxon -UniProtKB:O56786 RO:0002331 GO:0034053 PMID:10419939 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000015-4 Holin protein Hol187 +UniProtKB:O56786 RO:0002331 GO:0034053 PMID:10419939 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000015-4 ! DO NOT APPLY TO GPAD GORULE:0000015 - TEST 5 - "GO:0141062 disruption of tissue in another organism" with single taxon ID ! DO NOT APPLY TO GPAD GORULE:0000015 - TEST 6 - "GO:0010363 regulation of plant-type hypersensitive response" is_a "GO:0043903 regulation of biological process involved in symbiotic interaction" ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 2022-06-06 GO_Central GORULE_TEST:0000016-1 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 2022-06-06 GO_Central comment=GORULE_TEST:0000016-1 ! FAILS GORULE:0000016 - TEST 2 - column 8 (with/from) is has a non-GOID -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 UBERON:0002048 2022-06-06 GO_Central GORULE_TEST:0000016-2 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 UBERON:0002048 2022-06-06 GO_Central comment=GORULE_TEST:0000016-2 ! FAILS GORULE:0000016 - TEST 3 - column 8 (with/from) is the same GOID as column 5 -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 GO:0006921 2022-06-06 GO_Central GORULE_TEST:0000016-3 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000305 GO:0006921 2022-06-06 GO_Central comment=GORULE_TEST:0000016-3 ! SHOULD PASS GORULE:0000016 - TEST 4 - column 8 (with/from) is has a valid GO ID -UniProtKB:Q9HC96 RO:0002432 GO:0005886 GO_REF:0000036 ECO:0000305 GO:0001591 2022-06-06 GO_Central GORULE_TEST:0000016-4 Calpain-10 +UniProtKB:Q9HC96 RO:0002432 GO:0005886 GO_REF:0000036 ECO:0000305 GO:0001591 2022-06-06 GO_Central comment=GORULE_TEST:0000016-4 ! FAILS GORULE:0000017 - TEST 1 - IDA annotations must not have a with/from entry (column 8) -UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000314 GO:0004198|GO:0008092 2022-06-06 GO_Central GORULE_TEST:0000017-1 Calpain-10 +UniProtKB:Q9HC96 RO:0002331 GO:0006921 GO_REF:0000036 ECO:0000314 GO:0004198|GO:0008092 2022-06-06 GO_Central comment=GORULE_TEST:0000017-1 ! FAILS GORULE:0000018 - TEST 1 - column 8 (with/from) is null for IPI annotation to 'protein binding ; GO:0005515' -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central GORULE_TEST:0000018-1 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central comment=GORULE_TEST:0000018-1 ! FAILS GORULE:0000018 - TEST 2 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central GORULE_TEST:0000018-2 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central comment=GORULE_TEST:0000018-2 ! FAILS GORULE:0000018 - TEST 3 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' -UniProtKB:O76187 RO:0002331 GO:0005488 PMID:9802899 ECO:0000021 2022-06-06 GO_Central GORULE_TEST:0000018-3 +UniProtKB:O76187 RO:0002331 GO:0005488 PMID:9802899 ECO:0000021 2022-06-06 GO_Central comment=GORULE_TEST:0000018-3 ! FAILS GORULE:0000020 - TEST 1 - obsolete term with no replacement -UniProtKB:P04995 RO:0002331 GO:0090503 GO_REF:0000108 ECO:0000501 GO:0000175 2022-06-06 GO_Central GORULE_TEST:0000020-1 Exodeoxyribonuclease I +UniProtKB:P04995 RO:0002331 GO:0090503 GO_REF:0000108 ECO:0000501 GO:0000175 2022-06-06 GO_Central comment=GORULE_TEST:0000020-1 ! FAILS GORULE:0000020 - TEST 2 - obsolete term with a replacement term -TriTrypDB:Tb11.02.5420b RO:0001025 GO:0016021 GO_REF:0000002 ECO:0000266 GeneDB:Tb11.02.5420 2022-06-06 GO_Central GORULE_TEST:0000020-2 NADPH-cytochrome p450 reductase, putative +TriTrypDB:Tb11.02.5420b RO:0001025 GO:0016021 GO_REF:0000002 ECO:0000266 GeneDB:Tb11.02.5420 2022-06-06 GO_Central comment=GORULE_TEST:0000020-2 ! FAILS GORULE:0000020 - TEST 3 - obsolete term in 'with' (column 8) with no replacement -MGI:1100518:Smad7 RO:0002331 GO:0017015 MGI:MGI:3836072|PMID:18952608 ECO:0000305 GO:0060389 2022-06-06 GO_Central GORULE_TEST:0000020-3 +MGI:1100518:Smad7 RO:0002331 GO:0017015 MGI:MGI:3836072|PMID:18952608 ECO:0000305 GO:0060389 2022-06-06 GO_Central comment=GORULE_TEST:0000020-3 ! FAILS GORULE:0000020 - TEST 4 - obsolete term in 'extension' (column 16) with no replacement -UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0090503) GORULE_TEST:0000020-4 Darlin +UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0090503) comment=GORULE_TEST:0000020-4 ! FAILS GORULE:0000020 - TEST 5 - obsolete term in 'extension' (column 16) with a replacement -UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0014067) GORULE_TEST:0000020-5 Darlin +UniProtKB:O76187 RO:0002327 GO:0004672 PMID:9802899 ECO:0000314 UniProtKB:P34149 2022-06-06 GO_Central RO:0002331(GO:0014067) comment=GORULE_TEST:0000020-5 ! FAILS GORULE:0000022 - TEST 1 - retracted paper -UniProtKB:O76187 RO:0002327 GO:0004672 PMID:37278189 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000022-1 +UniProtKB:O76187 RO:0002327 GO:0004672 PMID:37278189 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000022-1 ! FAILS GORULE:0000027 - TEST 1 - Prefix not in /db-xrefs.yaml -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000027-1 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000027-1 ! FAILS GORULE:0000027 - TEST 2 - Assigned_by not in /groups.yaml -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 SGDDB GORULE_TEST:0000027-2 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 SGDDB comment=GORULE_TEST:0000027-2 ! FAILS GORULE:0000027 - TEST 3 - Bad reference syntax -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:PMID:14561399 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000027-3 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:PMID:14561399 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000027-3 ! FAILS GORULE:0000027 - TEST 4 - Bad reference syntax -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:unpublished ECO:0000314 2022-06-06 GO_Central GORULE_TEST0000027-4 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:unpublished ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST0000027-4 ! FAILS GORULE:0000027 - TEST 5 - Bad reference syntax -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:0. ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000027-5 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:0. ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000027-5 ! FAILS GORULE:0000027 - TEST 6 - Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED -WormBase:WBGene00000002 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central GORULE_TEST:0000027-6 F27C8.1 +WormBase:WBGene00000002 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central comment=GORULE_TEST:0000027-6 ! FAILS GORULE:0000027 - TEST 7 - bad id syntax: WB needs 8 digits, has only 7 -WormBase:WBGene00000002 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central GORULE_TEST:0000027-7 F27C8.1 +WormBase:WBGene00000002 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central comment=GORULE_TEST:0000027-7 ! FAILS GORULE:0000027 - TEST 8 - caolumn 2 cardinality should be 1 -WormBase:WBGene00000002|WBGene00000003 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central GORULE_TEST:0000027-8 F27C8.1 +WormBase:WBGene00000002|WBGene00000003 BFO:0000050 GO:1990184 WB_REF:WBPaper00006408|PMID:14668347 ECO:0000021 2013-10-22 GO_Central comment=GORULE_TEST:0000027-8 ! SHOULD PASS GORULE:0000027 - TEST 9 - 2 values in with field, pipe-separated -UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-9 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central comment=GORULE_TEST:0000027-9 ! FAILS GORULE:0000027 - TEST 10 - 2 values in 'with' field, comma-separated -UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-10 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central comment=GORULE_TEST:0000027-10 ! FAILS GORULE:0000027 - TEST 11 - 2 values in 'with' field, second namespace missing -UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-11 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central comment=GORULE_TEST:0000027-11 ! FAILS GORULE:0000027 - TEST 12 - 'with' prefix not in /db-xrefs.yaml -UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-12 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central comment=GORULE_TEST:0000027-12 ! FAILS GORULE:0000027 - TEST 13 - 'with' Prefix is a synonyms in /db-xrefs.yaml and IS REPAIRED -FB:FBgn0020238 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-13 14-3-3epsilon +FB:FBgn0020238 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central comment=GORULE_TEST:0000027-13 ! FAILS GORULE:0000027 - TEST 14 - 'bad with' id syntax - should have 7 digits, has 8 -FB:FBgn0020238 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central GORULE_TEST:0000027-14 14-3-3epsilon +FB:FBgn0020238 RO:0002331 GO:0006401 PMID:16931762 ECO:0000316 2013-10-22 GO_Central comment=GORULE_TEST:0000027-14 ! SHOULD PASS GORULE:0000027 - TEST 15 - Two references in different ID spaces, space separated -FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198|PMID:15457211 ECO:0000315 2013-10-22 GO_Central GORULE_TEST:0000027-15 Crk oncogene +FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198|PMID:15457211 ECO:0000315 2013-10-22 GO_Central comment=GORULE_TEST:0000027-15 ! FAILS GORULE:0000027 - TEST 16 - Two references in different ID spaces -FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198 PMID:15457211 ECO:0000315 2013-10-22 GO_Central GORULE_TEST:0000027-16 Crk oncogene +FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198 PMID:15457211 ECO:0000315 2013-10-22 GO_Central comment=GORULE_TEST:0000027-16 ! FAILS GORULE:0000027 - TEST 17 - bad PMID ID syntax -FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198|PMID:1545721X ECO:0000315 2013-10-22 GO_Central GORULE_TEST:0000027-17 Crk oncogene +FB:FBgn0024811 RO:0002331 GO:0048010 FB:FBrf0180198|PMID:1545721X ECO:0000315 2013-10-22 GO_Central comment=GORULE_TEST:0000027-17 ! SHOULD PASS GORULE:0000027 - TEST 18 - 'Assigned by' is in groups.yaml (but not in dbxref.yaml) -UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000314 2013-10-22 LBL GORULE_TEST:0000027-18 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000314 2013-10-22 LBL comment=GORULE_TEST:0000027-18 ! FAILS GORULE:0000027 - TEST 19 - 'Assigned by' is in dbxref.yaml but not in groups.yaml -UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000314 2013-10-22 PO GORULE_TEST:0000027-18 Regenerating islet-derived protein 3-gamma +UniProtKB:Q6UW15 RO:0002331 GO:0006401 PMID:16931762 ECO:0000314 2013-10-22 PO comment=GORULE_TEST:0000027-18 ! FAILS GORULE:0000028 - TEST 1 - Bad GO aspect, C instead of P -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-1 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000028-1 ! FAILS GORULE:0000028 - TEST 2 - Bad GO aspect, F instead of P -UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-2 Calpain-10 +UniPotKB:Q9HC96 RO:0002331 GO:0006921 PMID:23072806 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000028-2 ! FAILS GORULE:0000028 - TEST 3 - Bad GO aspect, P instead of F -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-3 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000028-3 ! FAILS GORULE:0000028 - TEST 4 - GO aspect missing -UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000028-4 Mitogen-activated protein kinase kinase kinase mlk-1 +UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000028-4 ! FAILS GORULE:0000029 - TEST 1 - IEA older than 1 year -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2023-05-06 GO_Central GORULE_TEST:0000029-1 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2023-05-06 GO_Central comment=GORULE_TEST:0000029-1 ! FAILS GORULE:0000029 - TEST 2 - IEA older than 3 years -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2020-06-06 GO_Central GORULE_TEST:0000029-2 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2020-06-06 GO_Central comment=GORULE_TEST:0000029-2 ! FAILS GORULE:0000030 - TEST 1 - Deprecated GO_REF -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000045 ECO:0000501 UniProtKB-SubCell:SL-0375 2022-06-06 GO_Central GORULE_TEST:0000030-1 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000045 ECO:0000501 UniProtKB-SubCell:SL-0375 2022-06-06 GO_Central comment=GORULE_TEST:0000030-1 ! SHOULD PASS GORULE:0000030 - TEST 2 - Valid GO_REF -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000033 ECO:0000318 FB:FBgn0032677|PANTHER:PTN005196447 2022-06-06 GO_Central GORULE_TEST:0000030-2 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000033 ECO:0000318 FB:FBgn0032677|PANTHER:PTN005196447 2022-06-06 GO_Central comment=GORULE_TEST:0000030-2 ! FAILS GORULE:0000037 - TEST 1 - IBA with Assigned_by other than GO_Central -UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:21873635 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 PomBase GORULE_TEST:0000037-1 +UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:21873635 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 PomBase comment=GORULE_TEST:0000037-1 ! FAILS GORULE:0000037 - TEST 2 - IBA with reference other than GO_REF:0000033 -UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:26221034 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 GO_Central GORULE_TEST:0000037-2 +UniProtKB:A0A024BTL2 RO:0002432 GO:0005634 PMID:26221034 ECO:0000318 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 2022-06-06 GO_Central comment=GORULE_TEST:0000037-2 ! FAILS GORULE:0000039 - TEST 1 - Protein complex annotated to GO:0032991 protein-containing complex -ComplexPortal:CPX-102 BFO:0000050 GO:0032991 PMID:10629061 ECO:0000315 2022-06-06 GO_Central GORULE_TEST:0000039-1 +ComplexPortal:CPX-102 BFO:0000050 GO:0032991 PMID:10629061 ECO:0000315 2022-06-06 GO_Central comment=GORULE_TEST:0000039-1 ! FAILS GORULE:0000039 - TEST 2 - Protein complex annotated to an is_a descendant of GO:0032991 protein-containing complex -ComplexPortal:CPX-102 BFO:0000050 GO:0043020 PMID:10629061 ECO:0000315 2022-06-06 GO_Central GORULE_TEST:0000039-2 +ComplexPortal:CPX-102 BFO:0000050 GO:0043020 PMID:10629061 ECO:0000315 2022-06-06 GO_Central comment=GORULE_TEST:0000039-2 ! FAILS GORULE:0000042 - TEST 1 - IKR evidence, no negation (NOT) in column 4 -UniProtKB:A0A0B4JCV5 RO:0002327 GO:0004252 PMID:30367934 ECO:0000320 2022-06-06 GO_Central GORULE_TEST:0000042-1 +UniProtKB:A0A0B4JCV5 RO:0002327 GO:0004252 PMID:30367934 ECO:0000320 2022-06-06 GO_Central comment=GORULE_TEST:0000042-1 ! FAILS GORULE:0000046 - TEST 1 - self-binding’ term, no data in Column 8 -UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000046-1 +UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000046-1 ! FAILS GORULE:0000046 - TEST 2 - self-binding’ term, annotated to a protein other than 'self' -UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000021 UniProtKB:P35555 2022-06-06 GO_Central GORULE_TEST:0000046-2 +UniProtKB:A4D126 RO:0002327 GO:0042803 PMID:26687144 ECO:0000021 UniProtKB:P35555 2022-06-06 GO_Central comment=GORULE_TEST:0000046-2 ! FAILS GORULE:0000050 - TEST 1 - self-referential ISS annotations -UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000250 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-1 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 +UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000250 UniProtKB:F1N2N9 2022-06-06 GO_Central comment=GORULE_TEST:0000050-1 ! FAILS GORULE:0000050 - TEST 2 - self-referential ISO annotations -UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000266 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-2 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 +UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000266 UniProtKB:F1N2N9 2022-06-06 GO_Central comment=GORULE_TEST:0000050-2 ! FAILS GORULE:0000050 - TEST 3 - self-referential ISA annotations -UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000247 UniProtKB:F1N2N9 2022-06-06 GO_Central GORULE_TEST:0000050-3 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 +UniProtKB:F1N2N9 BFO:0000050 GO:0120228 PMID:34715025 ECO:0000247 UniProtKB:F1N2N9 2022-06-06 GO_Central comment=GORULE_TEST:0000050-3 ! PROPOSED GORULE:0000051 - Pass RULE 51 - Annotation extension for certain GO terms - protein binding; GO:0005515 -UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central RO:0002233(GO:0003674)|BFO:0000066(CL:123456) GORULE_TEST:0000051-PASS1 Darlin +UniProtKB:O76187 RO:0002327 GO:0005515 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central RO:0002233(GO:0003674)|BFO:0000066(CL:123456) comment=GORULE_TEST:0000051-PASS1 ! PROPOSED GORULE:0000051 - TEST 1 - also fails GORULE:0000008 - Annotation extension is required for certain terms - binding GO:0005488 -UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central GORULE_TEST:0000051-1 Darlin +UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 UniProtKB:P34149 2022-06-06 GO_Central comment=GORULE_TEST:0000051-1 ! FAILS GORULE:0000055 - TEST 1 - Two references in the same ID space - PMID -PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 PMID:12477793|PMID:15961998 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000055-1 +PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 PMID:12477793|PMID:15961998 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000055-1 ! FAILS GORULE:0000055 - TEST 2 - Two references in the same ID space - GO_REF -PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 GO_REF:0000044|GO_REF:0000003 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000055-2 +PlasmoDB:PF3D7_0200400 RO:0002432 GO:0020036 GO_REF:0000044|GO_REF:0000003 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000055-2 ! SHOULD PASS GORULE:0000061 - TEST 1 - the part_of GP2term relation is allowed for GO:0008023 (CC complex) -FB:FBgn0011273 BFO:0000050 GO:0008023 FB:FBrf0193169|PMID:16790438 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-1 Androcam +FB:FBgn0011273 BFO:0000050 GO:0008023 FB:FBrf0193169|PMID:16790438 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000061-1 ! SHOULD PASS GORULE:0000061 - TEST 2- 'enables' is allowed for a GO MF -UniProtKB:A1B2F4 RO:0002327 GO:0003909 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-2 +UniProtKB:A1B2F4 RO:0002327 GO:0003909 PMID:26468286 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000061-2 ! FAILS GORULE:0000061 - TEST 3 the 'part_of' GP2term relation is not allowed for GO:0070864 (CC cellular anatomical entity) -FB:FBgn0011273 BFO:0000050 GO:0070864 PMID:12432073 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-3 Dynamin +FB:FBgn0011273 BFO:0000050 GO:0070864 PMID:12432073 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000061-3 ! FAILS GORULE:0000061 - TEST 4 - the 'part_of' GP2term relation is not allowed for GO:0140827 (MF) -UniProtKB:A1B2F4 BFO:0000050 GO:0140827 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-4 +UniProtKB:A1B2F4 BFO:0000050 GO:0140827 PMID:26468286 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000061-4 ! FAILS GORULE:0000061 - TEST 5 - the 'enables' GP2term relation is not allowed for GO:0005856 (CC) -UniProtKB:A1B2F4 RO:0002327 GO:0005856 PMID:26468286 ECO:0000314 2022-06-06 GO_Central GORULE_TEST:0000061-5 +UniProtKB:A1B2F4 RO:0002327 GO:0005856 PMID:26468286 ECO:0000314 2022-06-06 GO_Central comment=GORULE_TEST:0000061-5 ! FAILS GORULE:0000061 - TEST 6 - the 'located in' GP2term relation is not allowed for GO:0005575 (root CC) -UniProtKB:A1B2F4 RO:0001025 GO:0005575 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST:0000061-6 +UniProtKB:A1B2F4 RO:0001025 GO:0005575 PMID:26468286 ECO:0000307 2023-04-27 GO_Central comment=GORULE_TEST:0000061-6 ! FAILS GORULE:0000061 - TEST 7 - the 'contributes_to' GP2term relation is not allowed for GO:0003674 (root MF) -UniProtKB:A1B2F4 RO:0002326 GO:0003674 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST:0000061-7 +UniProtKB:A1B2F4 RO:0002326 GO:0003674 PMID:26468286 ECO:0000307 2023-04-27 GO_Central comment=GORULE_TEST:0000061-7 ! FAILS GORULE:0000061 - TEST 8 - the 'acts upstream of or within' GP2term relation is not allowed for GO:0008150 (root BP) -UniProtKB:A1B2F4 RO:0002264 GO:0008150 PMID:26468286 ECO:0000307 2023-04-27 GO_Central GORULE_TEST:0000061-8 +UniProtKB:A1B2F4 RO:0002264 GO:0008150 PMID:26468286 ECO:0000307 2023-04-27 GO_Central comment=GORULE_TEST:0000061-8 ! FAILS GORULE:0000061 - TEST 9 - 'enables' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002327 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-9 +UniProtKB:A1B2F4 RO:0002327 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-9 ! FAILS GORULE:0000061 - TEST 10 - 'contributes_to' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002326 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-10 +UniProtKB:A1B2F4 RO:0002326 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-10 ! FAILS GORULE:0000061 - TEST 11 - 'enables' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002327 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-11 +UniProtKB:A1B2F4 RO:0002327 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-11 ! FAILS GORULE:0000061 - TEST 12 - 'contributes_to' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002326 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-12 +UniProtKB:A1B2F4 RO:0002326 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-12 ! FAILS GORULE:0000061 - TEST 13 - 'involved_in' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002331 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-13 +UniProtKB:A1B2F4 RO:0002331 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-13 ! FAILS GORULE:0000061 - TEST 14 - 'acts_upstream_of_or_within' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002264 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-14 +UniProtKB:A1B2F4 RO:0002264 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-14 ! FAILS GORULE:0000061 - TEST 15 - 'acts_upstream_of_or_within_positive_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004032 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-15 +UniProtKB:A1B2F4 RO:0004032 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-15 ! FAILS GORULE:0000061 - TEST 16 - 'acts_upstream_of_or_within_negative_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-16 +UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-16 ! FAILS GORULE:0000061 - TEST 17 - 'acts_upstream_of' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002263 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-17 +UniProtKB:A1B2F4 RO:0002263 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-17 ! FAILS GORULE:0000061 - TEST 18 - acts_upstream_of_positive_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004034 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-18 +UniProtKB:A1B2F4 RO:0004034 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-18 ! FAILS GORULE:0000061 - TEST 19 - 'acts_upstream_of_negative_effect' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-19 +UniProtKB:A1B2F4 RO:0004033 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-19 ! FAILS GORULE:0000061 - TEST 20 - 'involved_in' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002331 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-20 +UniProtKB:A1B2F4 RO:0002331 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-20 ! FAILS GORULE:0000061 - TEST 21 - 'acts_upstream_of_or_within' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002264 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-21 +UniProtKB:A1B2F4 RO:0002264 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-21 ! FAILS GORULE:0000061 - TEST 22 - 'acts_upstream_of_or_within_positive_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004032 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-22 +UniProtKB:A1B2F4 RO:0004032 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-22 ! FAILS GORULE:0000061 - TEST 23 - 'acts_upstream_of_or_within_negative_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-23 +UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-23 ! FAILS GORULE:0000061 - TEST 24 - 'acts_upstream_of' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0002263 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-24 +UniProtKB:A1B2F4 RO:0002263 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-24 ! FAILS GORULE:0000061 - TEST 25 - 'acts_upstream_of_positive_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004034 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-25 +UniProtKB:A1B2F4 RO:0004034 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-25 ! FAILS GORULE:0000061 - TEST 26 - 'acts_upstream_of_negative_effect' is not allowed for a GO CC -UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-26 +UniProtKB:A1B2F4 RO:0004033 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-26 ! FAILS GORULE:0000061 - TEST 27 - 'is_active_in' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002432 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-27 +UniProtKB:A1B2F4 RO:0002432 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-27 ! FAILS GORULE:0000061 - TEST 28 - 'part_of' is not allowed for a GO MF -UniProtKB:A1B2F4 BFO:0000050 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-28 +UniProtKB:A1B2F4 BFO:0000050 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-28 ! FAILS GORULE:0000061 - TEST 29 - 'located_in' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0001025 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TES=0000061-29 +UniProtKB:A1B2F4 RO:0001025 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST=0000061-29 ! FAILS GORULE:0000061 - TEST 30 - 'colocalizes_with' is not allowed for a GO MF -UniProtKB:A1B2F4 RO:0002325 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-30 +UniProtKB:A1B2F4 RO:0002325 GO:0004672 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-30 ! FAILS GORULE:0000061 - TEST 31 - 'is_active_in' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002432 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-31 +UniProtKB:A1B2F4 RO:0002432 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-31 ! FAILS GORULE:0000061 - TEST 32 - 'part_of' is not allowed for a GO BP -UniProtKB:A1B2F4 BFO:0000050 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-32 +UniProtKB:A1B2F4 BFO:0000050 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-32 ! FAILS GORULE:0000061 - TEST 33 - 'located_in' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0001025 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-33 +UniProtKB:A1B2F4 RO:0001025 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-33 ! FAILS GORULE:0000061 - TEST 34 - 'colocalizes_with' is not allowed for a GO BP -UniProtKB:A1B2F4 RO:0002325 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-34 +UniProtKB:A1B2F4 RO:0002325 GO:0043491 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-34 ! FAILS GORULE:0000061 - TEST 35 - 'is_active_in' is not allowed for a GO CC - complex -UniProtKB:A1B2F4 RO:0002432 GO:0000124 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-34 +UniProtKB:A1B2F4 RO:0002432 GO:0000124 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-34 ! FAILS GORULE:0000061 - TEST 36 - 'located_in' is not allowed for a GO CC - complex -UniProtKB:A1B2F4 RO:0001025 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-36 +UniProtKB:A1B2F4 RO:0001025 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-36 ! FAILS GORULE:0000061 - TEST 37 - 'colocalizes_with' is not allowed for a GO CC - complex -UniProtKB:A1B2F4 RO:0002325 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-37 +UniProtKB:A1B2F4 RO:0002325 GO:0042101 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-37 ! FAILS GORULE:0000061 - TEST 38 - 'part_of' is not allowed for a GO CC - cellular anatomical entity -UniProtKB:A1B2F4 BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-38 +UniProtKB:A1B2F4 BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-38 ! FAILS GORULE:0000061 - TEST 39 - 'part_of' is not allowed for GO CC - cellular anatomical entity -UniProtKB:A1B2F4 NOT BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-39 +UniProtKB:A1B2F4 NOT BFO:0000050 GO:0005634 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-39 ! FAILS GORULE:0000061 - TEST 40 - 'part_of' is not allowed for GO CC - cell plate descendent of cellular anatomical entity -UniProtKB:A1B2F4 BFO:0000050 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-40 +UniProtKB:A1B2F4 BFO:0000050 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-40 ! FAILS GORULE:0000061 - TEST 41 - 'part_of' is not allowed for GO CC cellular anatomical entity (GO:0005739 mitochondrion) -UniProtKB:A1B2F4 BFO:0000050 GO:0005739 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-41 +UniProtKB:A1B2F4 BFO:0000050 GO:0005739 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-41 ! FAILS GORULE:0000061 - TEST 42 - 'part_of' is not allowed for GO CC virion component -UniProtKB:A1B2F4 BFO:0000050 GO:0044423 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-42 +UniProtKB:A1B2F4 BFO:0000050 GO:0044423 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-42 ! FAILS GORULE:0000061 - TEST 43 - 'part_of' is not allowed for a GO CC icosahedral viral capsid, neck descendant of virion component -UniProtKB:A1B2F4 BFO:0000050 GO:0098030 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-43 +UniProtKB:A1B2F4 BFO:0000050 GO:0098030 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-43 ! SHOULD PASS GORULE:0000061 - TEST 45 - 'is_active_in' is allowed for GO CC - 'cell plate' descendent of cellular anatomical entity -UniProtKB:A1B2F4 RO:0002432 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central GORULE_TEST:0000061-45 +UniProtKB:A1B2F4 RO:0002432 GO:0009504 PMID:26468286 ECO:0000314 2023-04-27 GO_Central comment=GORULE_TEST:0000061-45 ! SHOULD PASS GORULE:0000063 - TEST 1 -PomBase:SPAC25B8.17 RO:0002432 GO:0005634 GO_REF:0000024 ECO:0000266 SGD:S000001583 2023-04-27 GO_Central GORULE_TEST:0000063-1 +PomBase:SPAC25B8.17 RO:0002432 GO:0005634 GO_REF:0000024 ECO:0000266 SGD:S000001583 2023-04-27 GO_Central comment=GORULE_TEST:0000063-1 ! FAILS GORULE:0000063 - TEST 2 - no data in 'with' field (column 7) -PomBase:SPAC25B8.17 RO:0002432 GO:0005634 GO_REF:0000024 ECO:0000266 2023-04-27 GO_Central GORULE_TEST:0000063-2 +PomBase:SPAC25B8.17 RO:0002432 GO:0005634 GO_REF:0000024 ECO:0000266 2023-04-27 GO_Central comment=GORULE_TEST:0000063-2 ! FAILS GORULE:0000064 - TEST 1 - human protein has TreeGrafter annotation -UniProtKB:A0A140VJL9 RO:0002331 GO:0006783 GO_REF:0000118 PANTHER:PTHR11458:SF0 2023-04-27 TreeGrafter GORULE_TEST:0000064-1 +UniProtKB:A0A140VJL9 RO:0002331 GO:0006783 GO_REF:0000118 PANTHER:PTHR11458:SF0 2023-04-27 TreeGrafter comment=GORULE_TEST:0000064-1 ! FAILS GORULE:0000064 - TEST 2 - Drosophila protein has TreeGrafter annotation -FB:FBgn0014191 RO:0002331 GO:0006783 GO_REF:0000118 PANTHER:PTHR11557:SF0 2023-04-27 TreeGrafter GORULE_TEST:0000064-1 +FB:FBgn0014191 RO:0002331 GO:0006783 GO_REF:0000118 PANTHER:PTHR11557:SF0 2023-04-27 TreeGrafter comment=GORULE_TEST:0000064-1 From 02a5643f16a9c187bc8d0c016840ba57da9aaa8f Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:19:20 +0200 Subject: [PATCH 33/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 6ed41c77..84f8ba52 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -4,7 +4,7 @@ ! Dummy GAF file containing deliberate errors to test that GO rules are correctly implemented. ! Should be equivalent to https://github.com/geneontology/go-site/blob/master/docs/gorules_test_errors.gpad when the rule applies. ! FAILS GORULE:0000001 - empty col1 and col2 - ypf1 is_active_in GO:0005634 GO_REF:0000024 ISO SGD:S000001583 C GORULE:0000001-1 intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase + ypf1 is_active_in GO:0005634 GO_REF:0000024 ISO SGD:S000001583 C intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase ! FAILS GORULE:0000001 - No gene symbol (Column 3) PomBase SPAC977.10 is_active_in GO:1990578 PMID:19171118 IDA C plasma membrane sodium ion/proton antiporter Nhe1/Sod2 sod2 protein taxon:4896 20151201 PomBase ! FAILS GORULE:0000001 - Blank lines From b95229f0fc088142bc32ab3de55de22b99d76d04 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:20:56 +0200 Subject: [PATCH 34/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 84f8ba52..641dab7c 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -116,7 +116,7 @@ UniProtKB O56786 hol187 is_active_in GO:0018995 PMID:10419939 IDA C GORULE_TEST ! SHOULD PASS GORULE:0000015 - TEST 4 - "GO:0042025 host cell nucleus" with single taxon ID UniProtKB O56786 hol187 is_active_in GO:0042025 PMID:10419939 IDA C GORULE_TEST:0000015-4 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! SHOULD PASS GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID -UniProtKB O56786 hol187 involved_in GO:0010363 PMID:10419939 IDA C GORULE_TEST:0000015-5 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central +UniProtKB O56786 hol187 involved_in GO:0010363 PMID:10419939 IDA P GORULE_TEST:0000015-5 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! SHOULD PASS GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID UniProtKB O56786 hol187 involved_in GO:0141062 PMID:10419939 IDA C GORULE_TEST:0000015-6 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! SHOULD PASS GORULE:0000015 - TEST 7 - "GO:0034053 symbiont-mediated perturbation of host defense-related programmed cell death" with two taxon ID From 0117023607cc69ca49f959968bc6ed78c85ca996 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:22:30 +0200 Subject: [PATCH 35/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 641dab7c..896569d4 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -118,7 +118,7 @@ UniProtKB O56786 hol187 is_active_in GO:0042025 PMID:10419939 IDA C GORULE_TEST ! SHOULD PASS GORULE:0000015 - TEST 5 - "GO:0010363 regulation of plant-type hypersensitive response" with single taxon ID UniProtKB O56786 hol187 involved_in GO:0010363 PMID:10419939 IDA P GORULE_TEST:0000015-5 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! SHOULD PASS GORULE:0000015 - TEST 6 - "GO:0141062 disruption of tissue in another organism" with single taxon ID -UniProtKB O56786 hol187 involved_in GO:0141062 PMID:10419939 IDA C GORULE_TEST:0000015-6 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central +UniProtKB O56786 hol187 involved_in GO:0141062 PMID:10419939 IDA P GORULE_TEST:0000015-6 Holin protein Hol187 hol187 protein taxon:55511 20170423 GO_Central ! SHOULD PASS GORULE:0000015 - TEST 7 - "GO:0034053 symbiont-mediated perturbation of host defense-related programmed cell death" with two taxon ID UniProtKB P16971 recA involved_in GO:0034053 PMID:26221034 IDA P GORULE_TEST:0000015-7 Protein CD300H CD300H protein taxon:9606|taxon:224308 20160428 GO_Central ! FAILS GORULE:0000016 - TEST 1 - column 8 (with/from) is null From f38da6ddf98e6c69005cd34808309d63ec84ee90 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:23:26 +0200 Subject: [PATCH 36/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index cd1fae6f..a8c78916 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -130,7 +130,7 @@ UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-Sub ! FAILS GORULE:0000029 - TEST 2 - IEA older than 3 years UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000044 ECO:0000501 UniProtKB-SubCell:SL-0375 2020-06-06 GO_Central comment=GORULE_TEST:0000029-2 ! FAILS GORULE:0000030 - TEST 1 - Deprecated GO_REF -UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000045 ECO:0000501 UniProtKB-SubCell:SL-0375 2022-06-06 GO_Central comment=GORULE_TEST:0000030-1 +UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000045 ECO:0000501 UniProtKB-SubCell:SL-0375 2024-07-06 GO_Central comment=GORULE_TEST:0000030-1 ! SHOULD PASS GORULE:0000030 - TEST 2 - Valid GO_REF UniProtKB:P77335 RO:0001025 GO:0020002 GO_REF:0000033 ECO:0000318 FB:FBgn0032677|PANTHER:PTN005196447 2022-06-06 GO_Central comment=GORULE_TEST:0000030-2 ! FAILS GORULE:0000037 - TEST 1 - IBA with Assigned_by other than GO_Central From ecb0cbf1629bab66c997377f8d8cd5713c36f272 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:23:55 +0200 Subject: [PATCH 37/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 896569d4..8ea7138e 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -200,7 +200,7 @@ UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000044 IEA UniProtKB-SubCell ! FAILS GORULE:0000029 - TEST 2 - IEA older than 3 years UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000044 IEA UniProtKB-SubCell:SL-0375 C GORULE_TEST:0000029-2 protein taxon:83333 20200507 GO_Central ! FAILS GORULE:0000030 - TEST 1 - Deprecated GO_REF -UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000045 IEA UniProtKB-SubCell:SL-0375 C GORULE_TEST:0000030-1 protein taxon:83333 20230607 GO_Central +UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000045 IEA UniProtKB-SubCell:SL-0375 C GORULE_TEST:0000030-1 protein taxon:83333 20240707 GO_Central ! SHOULD PASS GORULE:0000030 - TEST 2 - Valid GO_REF UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000033 IBA FB:FBgn0032677|PANTHER:PTN005196447 C GORULE_TEST:0000030-2 protein taxon:83333 20230607 GO_Central ! FAILS GORULE:0000037 - TEST 1 - IBA with Assigned_by other than GO_Central From 5f1d7af01bfbcef9df15b42d0d2eb79aa29930fc Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:27:49 +0200 Subject: [PATCH 38/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 8ea7138e..39a98e67 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -136,7 +136,7 @@ UniProtKB A0A0K3AV08 mlk-1 enables GO:0005080 PMID:23072806 IPI F GORULE_TEST:0 ! FAILS GORULE:0000018 - TEST 2 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' UniProtKB A0A0K3AV08 mlk-1 enables GO:0005080 PMID:23072806 IPI F GORULE_TEST:0000018-2 Mitogen-activated protein kinase kinase kinase mlk-1 mlk-1,K11D12.10 protein taxon:6239 20170322 GO_Central ! FAILS GORULE:0000018 - TEST 3 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' -UniProtKB O76187 darA involved_in GO:0005488 PMID:9802899 IPI F GORULE_TEST:0000018-3 protein taxon:44689 20230513 GO_Central +UniProtKB O76187 darA enables GO:0005488 PMID:9802899 IPI F GORULE_TEST:0000018-3 protein taxon:44689 20230513 GO_Central ! FAILS GORULE:0000020 - TEST 1 - obsolete term with no replacement UniProtKB P04995 sbcB involved_in GO:0090503 GO_REF:0000108 IEA GO:0000175 P GORULE_TEST:0000020-1 Exodeoxyribonuclease I sbcB|cpeA|xonA|JW1993|b2011 protein taxon:83333 20230509 GO_Central ! FAILS GORULE:0000020 - TEST 2 - obsolete term with a replacement term From 3bad814f378d4f02df75e25222acb1057a9415ed Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:28:29 +0200 Subject: [PATCH 39/42] Update gorules_test_errors.gpad --- docs/gorules_test_errors.gpad | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gpad b/docs/gorules_test_errors.gpad index a8c78916..9d7e7e5a 100644 --- a/docs/gorules_test_errors.gpad +++ b/docs/gorules_test_errors.gpad @@ -66,7 +66,7 @@ UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06- ! FAILS GORULE:0000018 - TEST 2 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' UniProtKB:A0A0K3AV08 RO:0002327 GO:0005080 PMID:23072806 ECO:0000021 2022-06-06 GO_Central comment=GORULE_TEST:0000018-2 ! FAILS GORULE:0000018 - TEST 3 - missing Column 8 data ('with' field) for 'binding ; GO:0005488' -UniProtKB:O76187 RO:0002331 GO:0005488 PMID:9802899 ECO:0000021 2022-06-06 GO_Central comment=GORULE_TEST:0000018-3 +UniProtKB:O76187 RO:0002327 GO:0005488 PMID:9802899 ECO:0000021 2022-06-06 GO_Central comment=GORULE_TEST:0000018-3 ! FAILS GORULE:0000020 - TEST 1 - obsolete term with no replacement UniProtKB:P04995 RO:0002331 GO:0090503 GO_REF:0000108 ECO:0000501 GO:0000175 2022-06-06 GO_Central comment=GORULE_TEST:0000020-1 ! FAILS GORULE:0000020 - TEST 2 - obsolete term with a replacement term From 4bcea5623738f181d2f6fe660ec9f4139fd55b4b Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:41:03 +0200 Subject: [PATCH 40/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 39a98e67..fc75465b 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -208,9 +208,9 @@ UniProtKB A0A024BTL2 PHKG1 is_active_in GO:0005634 PMID:21873635 IBA FB:FBgn0019 ! FAILS GORULE:0000037 - TEST 2 - IBA with reference other than GO_REF:0000033 UniProtKB A0A024BTL2 PHKG1 is_active_in GO:0005634 PMID:26221034 IBA FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 C GORULE_TEST:0000037-2 protein taxon:9823 20221009 GO_Central ! FAILS GORULE:0000039 - TEST 1 - Protein complex annotated to GO:0032991 protein-containing complex -ComplexPortal CPX-102 dapk-calm_human part_of GO:0032991 PMID:10629061 IMP C GORULE_TEST:0000039-1 complex taxon:9606 20200218 GO_Central +ComplexPortal CPX-102 dapk-calm_human part_of GO:0032991 PMID:10629061 IMP C GORULE_TEST:0000039-1 protein_complex taxon:9606 20200218 GO_Central ! FAILS GORULE:0000039 - TEST 2 - Protein complex annotated to an is_a descendant of GO:0032991 protein-containing complex -ComplexPortal CPX-102 dapk-calm_human part_of GO:0043020 PMID:10629061 IMP C GORULE_TEST:0000039-2 complex taxon:9606 20200218 GO_Central +ComplexPortal CPX-102 dapk-calm_human part_of GO:0043020 PMID:10629061 IMP C GORULE_TEST:0000039-2 protein_complex taxon:9606 20200218 GO_Central ! FAILS GORULE:0000042 - TEST 1 - IKR evidence, no negation (NOT) in column 4 UniProtKB A0A0B4JCV5 CG9898 enables GO:0004252 PMID:30367934 IKR F GORULE_TEST:0000042-1 protein taxon:7227 20190311 GO_Central ! FAILS GORULE:0000046 - TEST 1 - self-binding’ term, no data in Column 8 From b06972e35588ef7689ce964fd0763d422b96cdf4 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:44:16 +0200 Subject: [PATCH 41/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index fc75465b..5a6bb1b5 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -64,9 +64,9 @@ UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TE ! FAILS GORULE:0000001 - TEST 26 - bad entity type UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-26 other taxon:318586 20230427 GO_Central ! FAILS GORULE:0000001 - TEST 27 - entity type missing -UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-27 taxon:318586 20230427 GO_Central +UniProtKB A1B2F4 aztD acts_upstream_of_positive_effect GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-27 taxon:318586 20230427 GO_Central ! FAILS GORULE:0000001 - TEST 28 - bad entity type -UniProtKB A1B2F4 aztD acts upstream of GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-28 misc_RNA taxon:318586 20230427 GO_Central +UniProtKB A1B2F4 aztD acts_upstream_of_positive_effect GO:0097696 PMID:26468286 IDA F GORULE_TEST:0000001-28 misc_RNA taxon:318586 20230427 GO_Central ! FAILS GORULE:0000001 - TEST 29 - Bad reference syntax (has namespace but not value) UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID: IDA P GORULE_TEST:0000001-29 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 GO_Central ! FAILS GORULE:0000002 - TEST 1 - has a 'NOT' annotations to 'protein binding ; GO:0005515 From 2cb5d1e3f4dce11d9587751de7ddf46c2262eade Mon Sep 17 00:00:00 2001 From: pgaudet Date: Fri, 26 Jul 2024 16:50:51 +0200 Subject: [PATCH 42/42] Update gorules_test_errors.gaf --- docs/gorules_test_errors.gaf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/gorules_test_errors.gaf b/docs/gorules_test_errors.gaf index 5a6bb1b5..230b3ab4 100644 --- a/docs/gorules_test_errors.gaf +++ b/docs/gorules_test_errors.gaf @@ -146,7 +146,7 @@ MGI:1100518 Smad7 bla involved_in GO:0017015 MGI:MGI:3836072|PMID:18952608 IC GO ! FAILS GORULE:0000020 - TEST 4 - obsolete term in 'extension' (column 16) with no replacement UniProtKB O76187 darA enables GO:0004672 PMID:9802899 IDA UniProtKB:P34149 F GORULE_TEST:0000020-4 Darlin darA protein taxon:44689 20100205 GO_Central involved_in(GO:0090503) ! FAILS GORULE:0000020 - TEST 5 - obsolete term in 'extension' (column 16) with a replacement -UniProtKB O76187 darA enables GO:0004672 PMID:9802899 IDA UniProtKB:P34149 F GORULE_TEST:0000020-5 Darlin darA protein taxon:44689 20100205 GO_Central involved_in(GO:0014067) +UniProtKB O76187 darA enables GO:0004672 PMID:9802899 IDA F GORULE_TEST:0000020-5 Darlin darA protein taxon:44689 20100205 GO_Central involved_in(GO:0014067) ! FAILS GORULE:0000022 - TEST 1 - retracted paper UniProtKB O76187 darA involved_in GO:0017015 PMID:37278189 IDA F GORULE_TEST:0000022-1 protein taxon:44689 20230513 GO_Central ! FAILS GORULE:0000027 - TEST 1 - Prefix not in /db-xrefs.yaml