I have a list of UniProt ids that I want to get Gene Ontology annotations for. I need this information because I want this high-level information as an input to a neural network. The model I wish to develop is inspired by this paper: https://www.ijcai.org/Proceedings/2018/0468.pdf
Can anyone advise how I can programmatically access this information in the Gene Ontology Annotation (GOA) Database? https://www.ebi.ac.uk/GOA/
The link to the FTP for the GOA database files is listed on the GOA Downloads page. The file containing the mapping info you seek, goa_uniprot.all, comes in two formats, .gaf and .gpa. The README in the FTP directory linked provides details on the structure of the files.
Below is the first 20 lines of the .gaf file after uncompressing. Column 2 contains the UniProtID and column 5 contains the associated GO term. (Note that column 4 is empty in the snippet below)
>$ head goa_uniprot_all.gaf -n 20
!gaf-version: 2.2
!
!The set of protein accessions included in this file is based on UniProt reference proteomes, which provide one protein per gene.
!They include the protein sequences annotated in Swiss-Prot or the longest TrEMBL transcript if there is no Swiss-Prot record.
!
!date-generated: 2021-02-12 21:14
!generated-by: UniProt
!go-version: http://purl.obolibrary.org/obo/go/releases/2021-02-08/extensions/go-plus.owl
!
UniProtKB A0A009GUA7 J508_4179 GO:0003677 GO_REF:0000002 IEA InterPro:IPR006119|InterPro:IPR036162 F Resolvase/invertase-type recombinase catalytic domain-containing protein J508_4179 protein taxon:1310609 20201128 InterPro
UniProtKB A0A009GUA7 J508_4179 GO:0006310 GO_REF:0000002 IEA InterPro:IPR006119|InterPro:IPR036162 P Resolvase/invertase-type recombinase catalytic domain-containing protein J508_4179 protein taxon:1310609 20201128 InterPro
UniProtKB A0A009GUA7 J508_4179 GO:0000150 GO_REF:0000002 IEA InterPro:IPR006119|InterPro:IPR036162 F Resolvase/invertase-type recombinase catalytic domain-containing protein J508_4179 protein taxon:1310609 20201128 InterPro
UniProtKB A0A009HCR2 J517_0313 GO:0005886 GO_REF:0000044 IEA UniProtKB-SubCell:SL-0039 C Biopolymer transport ExbD/TolR family protein J517_0313 protein taxon:1310618 20201128 UniProt
UniProtKB A0A009HCR2 J517_0313 GO:0016020 GO_REF:0000043 IEA UniProtKB-KW:KW-0472 C Biopolymer transport ExbD/TolR family protein J517_0313 protein taxon:1310618 20201128 UniProt
UniProtKB A0A009HCR2 J517_0313 GO:0016021 GO_REF:0000043 IEA UniProtKB-KW:KW-0812 C Biopolymer transport ExbD/TolR family protein J517_0313 protein taxon:1310618 20201128 UniProt
UniProtKB A0A009HCR2 J517_0313 GO:0015031 GO_REF:0000043 IEA UniProtKB-KW:KW-0653 P Biopolymer transport ExbD/TolR family protein J517_0313 protein taxon:1310618 20201128 UniProt
UniProtKB A0A009HCR2 J517_0313 GO:0005886 GO_REF:0000043 IEA UniProtKB-KW:KW-1003 C Biopolymer transport ExbD/TolR family protein J517_0313 protein taxon:1310618 20201128 UniProt
UniProtKB A0A009HCR2 J517_0313 GO:0055085 GO_REF:0000002 IEA InterPro:IPR003400 P Biopolymer transport ExbD/TolR family protein J517_0313 protein taxon:1310618 20201128 InterPro
UniProtKB A0A009HCR2 J517_0313 GO:0022857 GO_REF:0000002 IEA InterPro:IPR003400 F Biopolymer transport ExbD/TolR family protein J517_0313 protein taxon:1310618 20201128 InterPro
UniProtKB A0A009HLK9 J512_2607 GO:0006355 GO_REF:0000002 IEA InterPro:IPR000847|InterPro:IPR037402 P HTH lysR-type domain-containing protein J512_2607 protein taxon:1310613 20201128 InterPro
gzip. Open a terminal and run gunzip goa_uniprot.all.gz.
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