[open-bibliography] PubMed

[Daniel Mietchen]

Agreed- contact PubMed right away. On
http://www.ncbi.nlm.nih.gov/pubmed
and all the PubMed pages, there is a link "Write to the Help Desk".
They have usually gotten back to me in time with useful replies.

Cheers,

Daniel

On Mon, Nov 9, 2015 at 5:11 PM, Thad Guidry <thadguidry at gmail.com> wrote:
> Thomas,
>
> Just reach out to Pubmed themselves and ask them those same questions.
>
>
> Thad
> +ThadGuidry
>
> On Mon, Nov 9, 2015 at 8:47 AM, Thomas Krichel <krichel at openlib.org> wrote:
>>
>>   Daniel Mietchen writes
>>
>> > Why not go ahead and post it here?
>>
>>   ok. But pubmed is not open data, as far as I know.
>>
>> > If it's indeed too technical to be discussed here, someone might
>> > forward it to a more appropriate venue.
>>
>>   The issue is in fact simple. How to get a complete copy of
>>   pubmed data? I still have to understand what the difference
>>   between entrez, medline and pubmed is is, but I refer to
>>   complete copy as all the records that one can find in the
>>   web site.
>>
>>   I am a pubmed vendor, so I have access to the ftp site and the
>>   data therein.  From
>>
>> https://www.nlm.nih.gov/databases/journal.html
>>
>>   I know that
>>
>> | The approximately 2% of the records not exported to MEDLINE/PubMed
>> | licensees are those tagged [PubMed - as supplied by publisher] in
>> | PubMed.
>>
>>   I suspect that a lot of the most recent additions are temporarily in
>>   this category. These are the ones that I am keen on getting. Waiting
>>   is not an option.
>>
>>   I assume they are included in the API described at
>>
>> http://www.ncbi.nlm.nih.gov/books/NBK25498/
>>
>>   How do I get access to all of those records, and only those? One
>>   way that I can come up with is to
>>
>>   1. generated a list of suspected pmids
>>   2. check I don't have data for them
>>   3. submit them to the API
>>   4. check response to see which one I did not get a response to,
>>      queue for resubmission.
>>
>>   It's an approach more in tune with the Vikings, the Huns etc than
>>   the supposedly civilized 21st century. Is there any smarter way?  I
>>   have written to the NLM last week, no response yet.
>>
>>   1 is particularly problematic. Last night's data shows I have
>>   24997267 records and the maximum number is 26544013. Presumably I
>>   could first try to harvest that interval, then, in later runs start
>>   a little lower and go a little higher. For 4) I could use a queue
>>   rule saying I will not query a record if the current waits would be
>>   smaller than the sum of previous waits.  But that would involve
>>   keeping historic harvesting data and peridically processing it.  It
>>   is probably best to work in ascending order even though this may
>>   introduce a periodicity in the harvested numbers.
>>
>>
>> --
>>
>>   Cheers,
>>
>>   Thomas Krichel                  http://openlib.org/home/krichel
>>                                               skype:thomaskrichel
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