Table of contents

Summary

GAF Parser Summary

There are 50 GAF parser warnings.

GAF summary

Found 26178 annotations in 26198 lines.

GAF Validation Summary Errors are reported first.

For rule GO_AR:0000008 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000008) No annotations should be made to uninformative high level terms, there are 91 violations with type Warning.

GAF Prediction Summary

Found 1030 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-07-12/extensions/go-gaf.owl

Report

Group: ecocyc - Dataset: ecocyc

SUMMARY

This report generated on 2019-07-16

Header From Original Association File

Contents

gorule-0000001

gorule-0000008

gorule-0000020

gorule-0000027

gorule-0000029

gorule-0000033

other

MESSAGES

gorule-0000001

GAF lines are parsed according to GAF 2.1 specifications

Messages

gorule-0000008

No annotations should be made to uninformative high level terms

Messages

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

Messages

gorule-0000027

Each identifier in GAF is valid

Messages

gorule-0000029

All IEAs over a year old are removed

Messages

gorule-0000033

Public Reference IDs (PMID, PMC, doi, or GO_REF) should be preferred over group specific Reference IDs

Messages

other

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
# GAF Parser ERROR count: 0
#------------
# GAF Parser WARNING count: 50
46 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0A6F1 carA Contributes_to GO:0004088 PMID:1827118 IMP F gene taxon:83333 20090223 EcoliWiki
51 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P00968 carB Contributes_to GO:0004088 PMID:14718657 IDA F gene taxon:83333 20120615 EcoliWiki
56 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P00968 carB Contributes_to GO:0004088 PMID:1737023 IGI EcoliWiki:carA F gene taxon:83333 20090122 EcoliWiki
183 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P06959 aceF Contributes_to GO:0004738 PMID:3903169 IDA F gene taxon:83333 20091016 EcoliWiki
351 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0ACF4 hupB Contributes_to GO:0003677 PMID:10551881 IDA F gene taxon:83333 20100507 EcoliWiki
637 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0A6Y1 ihfB Contributes_to GO:0043565 PMID:10551881 IDA F gene taxon:83333 20100507 EcoliWiki
765 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P76014 dhaL Contributes_to GO:0016740 PMID:11350937 IDA F gene taxon:83333 20110715 EcoliWiki
784 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0A877 trpA Contributes_to GO:0004834 PMID:8463331 IDA F gene taxon:83333 20090818 EcoliWiki
790 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0A879 trpB Contributes_to GO:0004834 PMID:8325869 IDA F gene taxon:83333 20090824 EcoliWiki
925 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AGD3 sodB Contributes_to GO:0004784 PMID:3022287 IMP F gene taxon:83333 20090316 EcoliWiki
945 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0A6X7 ihfA Contributes_to GO:0043565 PMID:10551881 IDA F gene taxon:83333 20100507 EcoliWiki
1124 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P00452 nrdA Contributes_to GO:0004748 PMID:13973714 IDA F gene taxon:83333 20120615 EcoliWiki
1127 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P69924 nrdB Contributes_to GO:0004748 PMID:13973714 IDA F gene taxon:83333 20080917 EcoliWiki
1128 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P69924 nrdB Contributes_to GO:0004748 PMID:13973714 IDA F gene taxon:83333 20120615 EcoliWiki
1148 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFF0 nuoN Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080419 EcoliWiki
1151 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFE8 nuoM Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080419 EcoliWiki
1154 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P33607 nuoL Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080419 EcoliWiki
1157 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFE4 nuoK Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080419 EcoliWiki
1160 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFE0 nuoJ Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080419 EcoliWiki
1164 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFD6 nuoI Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080722 EcoliWiki
1168 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFD4 nuoH Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080419 EcoliWiki
1173 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P33602 nuoG Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080722 EcoliWiki
1176 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P33602 nuoG Contributes_to GO:0010181 PMID:7607227 IDA F gene taxon:83333 20080722 EcoliWiki
1179 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P31979 nuoF Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080722 EcoliWiki
1181 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P31979 nuoF Contributes_to GO:0010181 PMID:7607227 IDA F gene taxon:83333 20080722 EcoliWiki
1185 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFD1 nuoE Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080419 EcoliWiki
1186 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFD1 nuoE Contributes_to GO:0010181 PMID:7607227 IDA F gene taxon:83333 20080419 EcoliWiki
1190 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P33599 nuoC Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080722 EcoliWiki
1195 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFC7 nuoB Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20080722 EcoliWiki
1198 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFC3 nuoA Contributes_to GO:0003954 PMID:3122832 IDA F gene taxon:83333 20100621 EcoliWiki
1360 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AGD7 ffh Contributes_to GO:0003924 PMID:7612669 IDA F gene taxon:83333 20080805 EcoliWiki
1378 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P39452 nrdE Contributes_to GO:0004748 PMID:7809142 IGI EcoliWiki:nrdA|EcoliWiki:nrdB F gene taxon:83333 20110815 EcoliWiki
1382 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P37146 nrdF Contributes_to GO:0004748 PMID:7809142 IGI EcoliWiki:nrdA|EcoliWiki:nrdB F gene taxon:83333 20110815 EcoliWiki
1416 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P23845 cysN Contributes_to GO:0004781 PMID:2828368 IDA F gene taxon:83333 20110815 EcoliWiki
1420 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P21156 cysD Contributes_to GO:0004781 PMID:2828368 IDA F gene taxon:83333 20100510 EcoliWiki
1444 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P04993 recD Contributes_to GO:0004386 PMID:1618858 IDA F gene taxon:83333 20090811 EcoliWiki
1448 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P04993 recD Contributes_to GO:0008854 PMID:1618858 IDA F gene taxon:83333 20090811 EcoliWiki
1543 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFI2 parC Contributes_to GO:0003916 PMID:1334483 IDA F gene taxon:83333 20081208 EcoliWiki
1546 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AFI2 parC Contributes_to GO:0003918 PMID:8227000 IDA F gene taxon:83333 20081208 EcoliWiki
1768 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P22731 livF Contributes_to GO:0015190 PMID:2195019 IDA F gene taxon:83333 20100507 EcoliWiki
1937 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0A6E6 atpC Contributes_to GO:0046933 PMID:2863270 IDA F gene taxon:83333 20080731 EcoliWiki
1940 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0ABB4 atpD Contributes_to GO:0046933 PMID:2863270 IDA F gene taxon:83333 20080731 EcoliWiki
1942 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0ABA6 atpG Contributes_to GO:0046933 PMID:2863270 IDA F gene taxon:83333 20080731 EcoliWiki
1945 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0ABB0 atpA Contributes_to GO:0046961 PMID:2863270 IDA F gene taxon:83333 20110815 EcoliWiki
1946 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0ABA4 atpH Contributes_to GO:0046933 PMID:2863270 IDA F gene taxon:83333 20080731 EcoliWiki
1949 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0ABA0 atpF Contributes_to GO:0046961 PMID:2863271 IMP F gene taxon:83333 20100621 EcoliWiki
1952 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P68699 atpE Contributes_to GO:0046961 PMID:2863271 IMP F gene taxon:83333 20100621 EcoliWiki
1955 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0AB98 atpB Contributes_to GO:0046961 PMID:2863271 IMP F gene taxon:83333 20110815 EcoliWiki
2228 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P0A9N8 nrdG Contributes_to GO:0004748 PMID:8954104 IMP F gene taxon:83333 20120615 EcoliWiki
2232 WARNING Repairing qualifier 'contributes_to' from: Contributes_to UniProtKB P28903 nrdD Contributes_to GO:0004748 PMID:8954104 IMP F gene taxon:83333 20120615 EcoliWiki
#------------
#------------
# Validation for #26178 annotations in 26198 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 91
409 GO_AR:0000008 Warning Do not annotate to: GO:0006810 'transport' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P23895 emrE GO:0006810 PMID:12356478 IDA P gene taxon:83333 20081201 EcoliWiki
669 GO_AR:0000008 Warning Do not annotate to: GO:0006810 'transport' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P0A910 ompA GO:0006810 PMID:10636850 IDA P gene taxon:83333 20090309 EcoliWiki
883 GO_AR:0000008 Warning Do not annotate to: GO:0042710 'biofilm formation' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P0AFS5 tqsA GO:0042710 PMID:16385049 IMP P gene taxon:83333 20110607 EcoliWiki
884 GO_AR:0000008 Warning Do not annotate to: GO:0006810 'transport' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB P0AFS5 tqsA GO:0006810 PMID:16385049 IMP P gene taxon:83333 20110607 EcoliWiki
929 GO_AR:0000008 Warning Do not annotate to: G