GO annotations into GFF3

Question

[Ric]

Hi, I would like to add GO term into the GFF3 and I found the following mapping file (goa_uniprot_all.gpa).

gpa-version: 1.1
!
!This file contains all GO annotations for proteins in the UniProt KnowledgeBase (UniProtKB).
!
!It also contains all annotations for protein complexes, identified by ComplexPortal identifiers,
!and for non-coding RNAs, identified by RNAcentral identifiers
!
!Columns:
!
!   name                  required? cardinality   GAF column #
!   DB                    required  1             1
!   DB_Object_ID          required  1             2 / 17
!   Qualifier             required  1 or greater  4
!   GO ID                 required  1             5
!   DB:Reference(s)       required  1 or greater  6
!   ECO evidence code     required  1             7 (GO evidence code)
!   With                  optional  0 or greater  8
!   Interacting taxon ID  optional  0 or 1        13
!   Date                  required  1             14
!   Assigned_by           required  1             15
!   Annotation Extension  optional  0 or greater  16
!   Annotation Properties optional  0 or 1        n/a
!
!Generated: 2020-08-13 08:18 
!GO-version: http://purl.obolibrary.org/obo/go/releases/2020-08-04/extensions/go-plus.owl
!
UniProtKB       A0A000  enables GO:0003824      GO_REF:0000002  ECO:0000256     InterPro:IPR015421|InterPro:IPR015422           20200808        InterPro

UniProtKB       A0A000  enables GO:0003870      GO_REF:0000002  ECO:0000256     InterPro:IPR010961              20200808        InterPro                
UniProtKB       A0A000  enables GO:0030170      GO_REF:0000002  ECO:0000256     InterPro:IPR004839|InterPro:IPR010961           20200808        InterPro

However, I do not understand the difference between GO:0003824 and GO_REF:0000002. Which one should I choose for our GFF3 file?

Thank you in advance

Answer 1

[JC]

GO_REF is another annotation https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md