Why is the UniProt REST API returning multiple results, when I am only providing one ID to be checked?

Bioinformatics Asked by Slowat_Kela on May 7, 2021

Can some explain why when I run a REST API query on UniProt for one ID (‘Q9UJL9’), the results for three IDs are returned?

The query I’m using is:,go(molecular%20function)&format=tab

(I didn’t hyperlink it since you need to see the query to see where I’m going wrong).

When I run the query above, the output is:

Entry   Gene ontology (molecular function)
Q9UJL9  DNA-binding transcription factor activity, RNA polymerase II-specific [GO:0000981]; DNA-binding transcription repressor activity, RNA polymerase II-specific [GO:0001227]; metal ion binding [GO:0046872]; RNA polymerase II transcription regulatory region sequence-specific DNA binding [GO:0000977]
Q8WWY3  identical protein binding [GO:0042802]; ribonucleoprotein complex binding [GO:0043021]; RNA binding [GO:0003723]; snRNP binding [GO:0070990]; U4atac snRNA binding [GO:0030622]; U4 snRNA binding [GO:0030621]
Q6A162  structural molecule activity [GO:0005198]

I checked the uniprot page of the query I want (Q9UJL9), the other items are interactors (along with many others) but not synonyms/linked (it seems, e.g my query is a zinc finger, one of the linked records, Q6A162, is a keratin protein).

One Answer

it is because you do a text search and the "word" Q9UJL9 appears in multiple entries. If you want an id search, specifically say so and for that the query syntax is id:Q9UJL9. You will want to follow a redirect, and there are some rare cases where that might still lead to more than one entry if the id was made secondary and attached to multiple entries. e.g. P00001.

Correct answer by Jerven on May 7, 2021

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