Table of contents

Summary

GAF Parser Summary

There are 1 GAF parser errors.

GAF summary

Found 503960 annotations in 503987 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 182 violations with type Warning.

For rule GO_AR:0000011 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000011) ND annotations to root nodes only, there are 2 violations with type Warning.

GAF Prediction Summary

Found 2432 predictions, see prediction file for details.

Used Ontology Summary

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

Report

Group: rgd - Dataset: rgd

SUMMARY

This report generated on 2019-11-18

Header From Original Association File

!gaf-version: 2.1
!{ The gene_association.rgd file is available at the GO Consortium website (http://www.geneontology.org/page/download-go-annotations) and on RGD's FTP site (ftp://ftp.rgd.mcw.edu/pub/data_release/). The file and its contents follow the specifications laid out by the Consortium, currently GO Annotation File (GAF) Format 2.1 located at http://www.geneontology.org/page/go-annotation-file-gaf-format-21. This requires that some details available for certain annotations on the RGD website and/or in other annotations files found on the RGD FTP site must be excluded from this file in order to conform to the GOC guidelines and to correspond to GAF files from other groups. }
!{ As of December 2016, the gene_association.rgd file only contains 'RGD' in column 1 and RGD gene identifiers in column 2. }
!{ As of March 2018, the gene_association.rgd file no longer includes identifiers for the original references (see below) for ISO annotations in column 6. For ISO annotations, entries in column 6 will be limited to RGD:1624291, RGD's internal reference which explains the assignment of GO ISO annotations to rat genes. }
!{ The gene_protein_association.rgd file (available on the RGD ftp site at ftp://ftp.rgd.mcw.edu/pub/data_release/) contains both RGD gene and UniProt protein IDs in columns 1/2. The gene_protein_association.rgd file also includes original reference IDs for rat ISO annotations, as well as the ID for RGD's internal reference which explains the assignment of GO ISO annotations to rat genes. "Original reference" refers to the identifier(s), such as PMIDs and/or other database IDs for the references used to assign GO annotations to genes or proteins in other species which are then inferred to rat genes by orthology. }
!{ Additional annotation files can be found on RGD's ftp site in the ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/ directory and its "with_terms" subdirectory (ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/with_terms/). The annotated_rgd_objects_by_ontology directory contains GAF-formatted files for all of RGD's ontology annotations, that is, annotations for all of the ontologies that RGD uses for all annotated objects from all of the species in RGD. Files in the "with_terms" subdirectory contain the same data with the addition of ontology terms for human-readability as well as additional information in the form of curator notes. }
!{ For additional information about the file formats for files in the annotated_rgd_objects_by_ontology/ directory and it's "with_terms" subdirectory see the README files at ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/README and ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/with_terms/WITHTERMS_README. }
!{ This file has been generated on 2019/11/09 }

Contents

gorule-0000002

gorule-0000006

gorule-0000007

gorule-0000008

gorule-0000011

gorule-0000013

gorule-0000015

gorule-0000016

gorule-0000017

gorule-0000018

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

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

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

gorule-0000018

IPI annotations require a With/From entry

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