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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/

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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
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  • $\begingroup$ That is exactly the information that I need. I am using a Mac and I have used The Unarchiver and Archive Utility to try and unzip the file. I get a message saying that the file is incomplete. How did you unzip the goa_uniprot_all.gaf file? $\endgroup$
    – ChemBot
    Jun 29 at 11:02
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    $\begingroup$ @ChemBot that isn't a zip file, you can't unzip it. It is a gzipped file, so you need gzip. Open a terminal and run gunzip goa_uniprot.all.gz. $\endgroup$
    – terdon
    Jun 29 at 16:17

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