[Biojava-l] How to find Pubmed ID

[Jose Duarte]

Biojava doesn't parse pubmed ids by default. However you can do it with the
cif parser that Biojava uses underneath: ciftools-java . See the README
providing very clear examples on how to extract CIF fields:

https://github.com/rcsb/ciftools-java

Note that ciftools-java can also use the BinaryCIF format, which makes
parsing much faster.

Alternatively, you can avoid parsing CIF altogether and instead use the
RCSB PDB Data API for this (via the GraphQL interface). See this example in
the Data API tutorial: https://data.rcsb.org/#gql-example-2

Jose


On Mon, 27 May 2024 at 07:39, Enrico Morelli <morelli at cerm.unifi.it> wrote:

> Dear,
>
> is there a way to get PubMed ID from a CIF file downloaded from rscb.org
> site?
>
> In the CIF file is the line "citation.pdbx_database_id_PubMed   1910042".
>
> Thanks
>
> --
> -----------------------------------------------------------
>   Enrico Morelli
>   System Administrator | Programmer | Web Developer
>
>   CERM - Polo Scientifico
>   via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
> ------------------------------------------------------------
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
> https://mailman.open-bio.org/mailman/listinfo/biojava-l
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biojava-l/attachments/20240528/1784e17e/attachment.htm>