Re: How to find Pubmed ID

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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 <[email protected]> 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  -  [email protected]
> https://mailman.open-bio.org/mailman/listinfo/biojava-l
>

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<div dir=3D"ltr">Biojava doesn&#39;t parse pubmed ids by default. However y=
ou can do it with the cif parser that Biojava uses underneath: ciftools-jav=
a . See the README providing very clear examples on how to extract CIF fiel=
ds:<div><br></div><div><a href=3D"https://github.com/rcsb/ciftools-java">ht=
tps://github.com/rcsb/ciftools-java</a><br></div><div><br></div><div>Note t=
hat ciftools-java can also use the BinaryCIF format, which makes parsing mu=
ch faster.</div><div><br></div><div>Alternatively, you can avoid parsing CI=
F altogether and instead use the RCSB PDB Data API for this (via the GraphQ=
L interface). See this example in the Data API tutorial:=C2=A0<a href=3D"ht=
tps://data.rcsb.org/#gql-example-2">https://data.rcsb.org/#gql-example-2</a=
></div><div><br></div><div>Jose</div><div><br></div></div><br><div class=3D=
"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Mon, 27 May 2024 at =
07:39, Enrico Morelli &lt;<a href=3D"mailto:[email protected]">morelli@=
cerm.unifi.it</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" sty=
le=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);paddi=
ng-left:1ex">Dear,<br>
<br>
is there a way to get PubMed ID from a CIF file downloaded from <a href=3D"=
http://rscb.org" rel=3D"noreferrer" target=3D"_blank">rscb.org</a> site?<br=
>
<br>
In the CIF file is the line &quot;citation.pdbx_database_id_PubMed=C2=A0 =
=C2=A01910042&quot;.<br>
<br>
Thanks<br>
<br>
-- <br>
-----------------------------------------------------------<br>
=C2=A0 Enrico Morelli<br>
=C2=A0 System Administrator | Programmer | Web Developer<br>
<br>
=C2=A0 CERM - Polo Scientifico<br>
=C2=A0 via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY<br>
------------------------------------------------------------<br>
_______________________________________________<br>
Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]=
g" target=3D"_blank">[email protected]</a><br>
<a href=3D"https://mailman.open-bio.org/mailman/listinfo/biojava-l" rel=3D"=
noreferrer" target=3D"_blank">https://mailman.open-bio.org/mailman/listinfo=
/biojava-l</a><br>
</blockquote></div>

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