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 <more...@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@biojava.org > https://mailman.open-bio.org/mailman/listinfo/biojava-l >
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