Table of contents

Summary

GAF summary

Found 418265 annotations in 418308 lines.

GAF Validation Summary Errors are reported first.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 74 violations with type Error.

For rule GO_AR:0000003 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000003) Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field, there are 30 violations with type Warning.

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 935 violations with type Warning.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 2 violations with type Warning.

For rule GO_AR:0000017 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000017) IDA annotations must not have a With/From entry, there are 4 violations with type Warning.

For rule GO_AR:0000018 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000018) IPI annotations require a With/From entry, there are 375 violations with type Warning.

GAF Prediction Summary

Found 2602 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-11-16/extensions/go-gaf.owl

Report

Group: mgi - Dataset: mgi

SUMMARY

This report generated on 2019-11-18

Header From Original Association File

!gaf-version: 2.1
!software version: $Revision$
!date: 11/15/2019 $
!
! from Mouse Genome Database (MGD) & Gene Expression Database (GXD)
!
! 1. DB MGI
! 2. DB Object ID MGI:xxxx
! 3. DB Object Symbol
! 4. Qualifier
! 5. GO ID GO:xxxx
! 6. DB:Reference(s) MGI:MGI:xxxx|PMID:xxxx
! 7. Evidence Code 3-digit (not ECO:xxxx)
! 8. With (or)From optional
! 9. Aspect (GO DAG Abbreviation (F, P, C))
! 10. DB Object Name optional
! 11. DB Object Synonym(s) optional
! 12. DB Object Type
! 13. Taxon taxon:10090
! 14. Date YYYYMMDD
! 15. Assigned By
! 16. Annotation Extension same as GPAD/col 11
! 17. Gene Product Form ID Isorform
!

Contents

gorule-0000002

gorule-0000006

gorule-0000007

gorule-0000008

gorule-0000011

gorule-0000013

gorule-0000015

gorule-0000016

gorule-0000017

gorule-0000018

gorule-0000027

gorule-0000028

gorule-0000029

gorule-0000030

gorule-0000033

gorule-0000037

gorule-0000039

gorule-0000042

gorule-0000043

gorule-0000046

gorule-0000050

other

MESSAGES

gorule-0000002

No 'NOT' annotations to 'protein binding ; GO:0005515'

gorule-0000006

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

Messages

gorule-0000007

IPI should not be used with catalytic activity molecular function terms

gorule-0000008

No annotations should be made to uninformative high level terms

Messages

gorule-0000011

ND annotations to root nodes only; and only root nodes can have the evidence code ND.

gorule-0000013

Taxon-appropriate annotation check

gorule-0000015

Dual species taxon check

gorule-0000016

With/From: IC annotations require a With/From GO ID

gorule-0000017

IDA annotations must not have a With/From entry

Messages

gorule-0000018

IPI annotations require a With/From entry

Messages

gorule-0000027

Each identifier in GAF is valid

Messages

gorule-0000028

Aspect can only be one of C, P, F and should be repaired using the GO term

gorule-0000029

All IEAs over a year old are removed

gorule-0000030

Deprecated GO_REFs are not allowed

gorule-0000033

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

Messages