Answers.Body: <p>The link to the FTP for the <a href="ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/" rel="nofollow noreferrer">GOA database files</a> is listed on the <a href="https://www.ebi.ac.uk/GOA/downloads" rel="nofollow noreferrer">GOA Downloads page</a>. The file containing the mapping info you seek, <code>goa_uniprot.all</code>, comes in two formats, <code>.gaf</code> and <code>.gpa</code>. The README in the FTP directory linked provides details on the structure of the files.</p>
  <p>Below is the first 20 lines of the <code>.gaf</code> 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)</p>
  <pre><code>&gt;$ 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
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-29T11:02:16.627Z
Answers.Text: 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?
Answers.UserDisplayName: ChemBot
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-29T16:17:15.313Z
Answers.Text: @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`.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-27T23:53:33.193Z
Answers.LastActivityDate: 2021-06-29T16:19:26.737Z
Answers.LastEditDate: 2021-06-29T16:19:26.737Z
Answers.UserDisplayName: Throckmorton
Body: <p>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: <a href="https://www.ijcai.org/Proceedings/2018/0468.pdf" rel="nofollow noreferrer">https://www.ijcai.org/Proceedings/2018/0468.pdf</a></p>
  <p>Can anyone advise how I can programmatically access this information in the
  Gene Ontology Annotation (GOA) Database? <a href="https://www.ebi.ac.uk/GOA/" rel="nofollow noreferrer">https://www.ebi.ac.uk/GOA/</a></p>
  
Tags: <proteins><uniprot><gene-ontology>
Title: How do I get GO annotations for a list of UniProt IDs?
ThreadText: # How do I get GO annotations for a list of UniProt IDs?
  
  (Asked by: username_0 on 2021-06-27)
  
  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/>
  
  **Tags:** proteins, uniprot, gene-ontology
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-06-27. Score: 4 | Accepted answer
  
  The link to the FTP for the [GOA database files](ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/) is listed on the [GOA Downloads page](https://www.ebi.ac.uk/GOA/downloads). 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
  
  ```
  
  > **Comments:**
  > **username_0**: 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?  
  > **username_2**: @username_0 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`.  
  
  ---
  
  