Table of contents

Summary

GAF summary

Found 449395 annotations in 449421 lines.

GAF Validation Summary Errors are reported first.

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 is one violation 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 27 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 2711 predictions, see prediction file for details.

Used Ontology Summary

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

Report

Group: rgd - Dataset: rgd

SUMMARY

This report generated on 2019-07-16

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. }

Contents

gorule-0000033

other

MESSAGES

gorule-0000033

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

Messages