Pubmed Database Fetching

Yuzuke
Hi there,

i asked something about Pubmed / Zotero in this forum a while ago, but i still have some problems related to it, so i will ask here again since this forum is somehow related to it.

I am currently trying to download huge batches from Pubmed into my local database. Thats all what i want right now. My current method is working - but working far to slow. I am currently fetching each article via the ID:

$XML = simplexml_load_file("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$ID&retmode=xml");

This works but is far to slow since for 500 Entries i have to make 500 http calls. Luckily there is a way to receive huge loads of those entries at once! http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3.Application_3_Retrieving_large

So i wrote something like this in PHP:

private function Search() {
$this->SParameters['term'] = $this->Query;
$Url = $this->SUrl . http_build_query($this->SParameters);
$this->SResults = simplexml_load_file($Url);
}

private function Fetch() {
$this->FParameters['query_key'] = (string) $this->SResults->QueryKey;
$this->FParameters['WebEnv'] = (string) $this->SResults->WebEnv;
$Url = $this->FUrl . http_build_query($this->FParameters);
$this->FResults = file_get_contents($Url);
}

My Problem is now, that i want to fetch ALL articles, not just specific ones defined via a search Query. So i tried something like $Query = ''; or $Query = ' '; But that gives me back:

Warning: file_get_contents(http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmax=500&query_key=&WebEnv=) [function.file-get-contents]: failed to open stream: HTTP request failed! HTTP/1.1 400 Bad Request

So what i am going to do now? How can i download huge batches of Pubmed articles without 10million http calls? Is there any way on how i can set the Query to $Query = ''; so i can download the articles from ID 0 to ID 10.000 not just the ones with $Query = 'test'; in one http call?

Thank you very much!
  • adamsmith
    sorry, this leads too far astray of what this forum is for - which is supporting the general use of Zotero.
    This sounds like a good question for stackoverflow or a php support forum.

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