[Bioperl-l] [Support #163271] dbfetch medlinedb errors when using pubmedxml or medlinexml

Carnë Draug carandraug+dev at gmail.com
Fri Sep 15 15:59:39 UTC 2017

On 15 September 2017 at 15:51, Rodrigo Lopez via RT <support at ebi.ac.uk> wrote:
> On Fri Sep 15 14:48:56 2017, carandraug+dev at gmail.com wrote:
>   > ---------- Forwarded message ----------
>   > From: Rodrigo Lopez via RT <support at ebi.ac.uk>
>   > Date: 5 December 2016 at 16:35
>   > Subject: [Support #163271] dbfetch medlinedb errors when using pubmedxml or medlinexml
>   > To: carandraug+dev at gmail.com
>   >
>   > Dear User,
>   >
>   > Thank you for your feedback. We are aware there is a problem with some formats
>   > for MEDLINE in dbfetch. An engineer is looking into this as we speak.
>   > Apologies for the inconvenience.
>   Hi
>   I was wondering if there's any plan on fixing this issue?  We have
>   been experiencing the issue since November last year and EBI as
>   confirmed the issue to be on dbfetch in December.
>   Could you shed me any light on the issue?
>   Thank you
>   Carnë
> Dear Carne,
> I'm sorry this fell through the cracks. the NIH changes the distribution of the
> Medline data every year and I forgot to assign work after the new distribution
> was completed in early January. I will get someone to look into this. In the
> meantime, EuropePMC has provided a comprehensive API that should provide access
> to these data in XML. Please see: http://europepmc.org/RestfulWebService
> Kind regards,
> Rodrigo.

Hi Rodrigo

Thank you for mentioning the alternative.  I was asking as a bioperl
developer, which provides and interface to dbfetch [1].  Since then,
we get reports of it no longer working.

I'm CC'ing the bioperl mailing list to have your answer with an
alternative available to those interested.

Thank you

[1] https://metacpan.org/pod/Bio::DB::Biblio::biofetch

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