Download data from QuickGO database with API

Question

[elisa.micarelli]

Hi, some years ago I was able to access automatically to QuickGO database with the following link: https://www.ebi.ac.uk/QuickGO/GAnnotation?org=9606&tax=9606&ids=POO533&format=tsv. Now, even if the link is still working the resulting page is not a text format and it can't be parsed. Looking at the API in https://www.ebi.ac.uk/QuickGO/api/index.html I didn't find a similar type of search.

How can I extract by command line the table resulting after to press the Export button in the following page: https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=P00533 ?

Anyone could help me?

Thanks in advance.

Elisa

Answer 1

[Pierre Lindenbaum]

from the API doc: https://www.ebi.ac.uk/QuickGO/api/index.html#!/annotations/downloadLookupUsingGET

$ curl -s -X GET --header 'Accept:text/tsv' 'https://www.ebi.ac.uk/QuickGO/services/annotation/downloadSearch?includeFields=goName&includeFields=taxonName&includeFields=name&geneProductId=P00533&taxonId=9606'  
GENE PRODUCT DB GENE PRODUCT ID SYMBOL  QUALIFIER   GO TERM GO ASPECT   ECO ID  GO EVIDENCE CODE    REFERENCE   WITH/FROM   TAXON ID    ASSIGNED BY ANNOTATION EXTENSION    DATE
UniProtKB   P00533  EGFR    colocalizes_with    GO:0005768  C   ECO:0000314 IDA PMID:16554368       9606    ParkinsonsUK-UCL        20160801
UniProtKB   P00533  EGFR    contributes_to  GO:0030235  F   ECO:0000314 IDA PMID:12828935       9606    UniProt     20050816
UniProtKB   P00533  EGFR    enables GO:0000166  F   ECO:0000322 IEA GO_REF:0000037  UniProtKB-KW:KW-0547    9606    UniProt     20181201
UniProtKB   P00533  EGFR    enables GO:0001618  F   ECO:0000322 IEA GO_REF:0000037  UniProtKB-KW:KW-1183    9606    UniProt     20181201
UniProtKB   P00533  EGFR    enables GO:0003682  F   ECO:0000314 IDA PMID:20551055       9606    UniProt     20130828
UniProtKB   P00533  EGFR    enables GO:0003690  F   ECO:0000303 NAS PMID:6325948        9606    UniProt     20050809
UniProtKB   P00533  EGFR    enables GO:0004672  F   ECO:0000256 IEA GO_REF:0000002  InterPro:IPR000719|InterPro:IPR001245|InterPro:IPR008266    9606    InterPro        20181201
UniProtKB   P00533  EGFR    enables GO:0004709  F   ECO:0000303 NAS PMID:15542601       9606    UniProt     20050812
UniProtKB   P00533  EGFR    enables GO:0004713  F   ECO:0000256 IEA GO_REF:0000002  InterPro:IPR016245|InterPro:IPR020635   9606    InterPro        20181201
(...)