getByCrossReference (pdb:) returns unexpected entry

[Ian Sillitoe]

We (CATH) had a query about linking from PDB to UniProtKB. Rather than use our local mapping, I figured I would use the Proteins API.

I was looking at using the endpoint getByCrossReference (eg /proteins/pdb:id)

https://www.ebi.ac.uk/proteins/api/doc/#!/proteins/getByCrossReference

So, when looking for the primary UniProtKB associated with PDB 1oai, the query is:

https://www.ebi.ac.uk/proteins/api/proteins/pdb:1oai

I expected a single result (Q9UBU9), however the query returns an additional result (P01724) and I couldn't see an obvious reason for this (there doesn't seem to be a mention of this PDB code in the UniProtKB document)

I'll probably shift this query over to the SIFTS API as that mapping is more explicit - just thought I would let you guys know in case this affected anyone else.

Best,

Ian

[andrew nightingale]

Hi Ian

Nice to hear that you are using the Proteins API as we've discussed in
the past. What you've found is a bug in the data services. Thanks for
letting us know, we will look into it and once we've fixed it we'll let
you know.

Best
Andrew.

On 2019-03-13 12:14, 'Ian Sillitoe' via ebi-proteins-api wrote:
> We (CATH) had a query about linking from PDB to UniProtKB. Rather than
> use our local mapping, I figured I would use the Proteins API.
>
> I was looking at using the endpoint getByCrossReference (eg
> /proteins/pdb:id)
>
> https://www.ebi.ac.uk/proteins/api/doc/#!/proteins/getByCrossReference

> [1]

>
> So, when looking for the primary UniProtKB associated with PDB 1oai,
> the query is:
>

> https://www.ebi.ac.uk/proteins/api/proteins/pdb:1oai [2]
>
> I expected a single result (Q9UBU9 [3]), however the query returns an
> additional result (P01724 [4]) and I couldn't see an obvious reason

> for this (there doesn't seem to be a mention of this PDB code in the

> UniProtKB document [5])
>
> I'll probably shift this query over to the SIFTS API [6] as that

> mapping is more explicit - just thought I would let you guys know in
> case this affected anyone else.
>
> Best,
>
> Ian
>

> --
> You received this message because you are subscribed to the Google
> Groups "ebi-proteins-api" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to ebi-proteins-a...@googlegroups.com.
> To post to this group, send email to
> ebi-prot...@googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/ebi-proteins-api/907c4aa1-d01c-4d38-8946-fbd6734f75ee%40googlegroups.com
> [7].
> For more options, visit https://groups.google.com/d/optout.
>
>
> Links:
> ------
> [1]
> https://www.ebi.ac.uk/proteins/api/doc/#!/proteins/getByCrossReference
> [2] https://www.ebi.ac.uk/proteins/api/proteins/pdb:1oai
> [3] https://www.uniprot.org/uniprot/Q9UBU9
> [4] https://www.uniprot.org/uniprot/P01724
> [5] https://www.uniprot.org/uniprot/P01724.txt
> [6] http://www.ebi.ac.uk/pdbe/api/doc/sifts.html
> [7]
> https://groups.google.com/d/msgid/ebi-proteins-api/907c4aa1-d01c-4d38-8946-fbd6734f75ee%40googlegroups.com?utm_medium=email&utm_source=footer

[Shadab Ahmad]

Hi Ian,
The bug reported by you has been fixed now.

Thanks,
Shadab

To post to this group, send an email to ebi-prot...@googlegroups.com.
To view this discussion on the web, visit https://groups.google.com/d/msgid/ebi-proteins-api/08bb4b1eccea2fc8ff55fd22a8d2bdfc%40ebi.ac.uk.

[Ian Sillitoe]

Great - thanks for the fix and for letting me know.

Best,

Ian

--

Ian Sillitoe | Principal Research Associate (Bioinformatics)
CATH Manager | www.cathdb.info
University College London | 627 Darwin, Gower Street, WC1E 6BT