Table of contents

Report

Group: rgd - Dataset: rgd

SUMMARY

This report generated on 2021-09-01

Header From Original Association File

!gaf-version: 2.2
!generated-by: RGD
!date-generated: 2021-08-28
!
!{ The gene_association.rgd file is available at the GO Consortium website (http://geneontology.org/docs/download-go-annotations/) and on RGD's FTP site (https://download.rgd.mcw.edu/data_release/). The file and its contents follow the specifications laid out by the Consortium, currently GO Annotation File (GAF) Format 2.2 located at http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/. 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 march 2021, the gene_association.rgd file is provided in gaf 2.2 format. }
!{ 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 https://download.rgd.mcw.edu/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 https://download.rgd.mcw.edu/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 https://download.rgd.mcw.edu/data_release/annotated_rgd_objects_by_ontology/README and https://download.rgd.mcw.edu/data_release/annotated_rgd_objects_by_ontology/with_terms/WITHTERMS_README. }

Contents

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other

MESSAGES

gorule-0000001

GAF lines are parsed according to GAF 2.1 specifications

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 GO:0003824 catalytic activity or descendents

gorule-0000008

No annotations should be made to uninformative high level terms

gorule-0000011

ND evidence code should be to root nodes only, and no terms other than root nodes can have the evidence code ND

gorule-0000013

Taxon-appropriate annotation check

Messages

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-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

IEAs should be less than one year old.

gorule-0000030

Deprecated GO_REFs are not allowed

gorule-0000037

IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 as a reference

gorule-0000039

Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants

gorule-0000042

Qualifier: IKR evidence code requires a NOT qualifier

gorule-0000043

Check for valid combination of evidence code and GO_REF

gorule-0000046

The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms.

Messages

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Annotations to ISS, ISA and ISO should not be self-referential

gorule-0000055

References should have only one ID per ID space

Messages

gorule-0000057

Group specific filter rules should be applied to annotations

gorule-0000058

Object extensions should conform to the extensions-patterns.yaml file in metadata

gorule-0000061

Allowed gene product to term relations (gp2term)

Messages