Limited # of downloadable citations?

sgoodman · Post by **sgoodman** » Thu Jun 08, 2006 3:54 pm

Hi - I have Bookends 9, and tried to dowload approx. 14,000 citations from PubMed. The program stopped at about 6800. I then copied these into a database. How do I get the additional 7200? If I delete the citations in memory and run the search again, it will download the same 6800 and stop. If I retain the 6800 in memory, so it knows where it is, it won't download anymore. Is there any way to either download the whole shebang, or to resume the download at the point it stopped? Thanks.

Steve Goodman

Post by **Jon** » Thu Jun 08, 2006 3:56 pm

Hi,

There is no limit placed on download # by Bookends. I've never tried to download that many at once, though, and it's possible that there is some other limitation I'm not aware of. As a workaround, perhaps you could do the same search by limit by years. If you could do chunk of 5000 or so it would take you 3 searches/downloads.

Oh, and one thing -- increase your database cache (Preferences). For a db of 20K references, I'd probably try setting it to 20 MB (rough guess).

Jon
Sonny Software

sgoodman · Post by **sgoodman** » Thu Jun 08, 2006 4:57 pm

Hmmmm. I thought that would work, but it didn't. I increased the cache from 8 MB to 25 MB, but increased the # of dowloaded citations only from 6800 to 6900, roughly. Plenty of hard disk space (8 GB).

I can't split the search by year, because it is all from a single year.

Any other ideas?

SG

Post by **Jon** » Thu Jun 08, 2006 5:02 pm

Not off the top of my head (hm, if you specified English would that reduce the number a lot -- or some other criterion if you want foreign language journals too). It's conceivable that this is a PubMed limitation (don't know that, just guessing). I'll have to play with this myself and see what I find out.

Jon
Sonny Software

Post by **Jon** » Sat Jun 10, 2006 9:03 am

Hi,

I could reproduce this a few days ago, but now I'm getting all references downloaded from a search that yields > 7200. This makes me think it was indeed a problem with PubMed. Does it work for you now or not?

Jon
Sonny Software

tom · Post by **tom** » Mon Jun 12, 2006 5:46 am

my system (1 Ghz PowerBook G4, 768 MB RAM, BE set to 30 MB internal cache) is limited to receive 7194 references from PubMed...

Post by **Jon** » Wed Jun 14, 2006 6:22 pm

Hi Tom,

Search for

CD45

I get > 7200 refs, and can download them all. What happens when you try?

Jon
Sonny Software

tom · Post by **tom** » Thu Jun 15, 2006 3:56 am

Hi Jon,

I get "Done. Received 6941 of 7223 total." on the bottom of the search window. Another try gives: "Done. Received 6454 of 7223 total." A third one: "Done. Received 7052 of 7223 total."
It looks like a connection time out. The "Awaiting reply..." takes about 90 seconds

tom

Post by **Jon** » Thu Jun 15, 2006 7:26 am

Hi tom,

Yes, today I'm seeing that, too. This variability obviously is due to some issue with PubMed. Since it varies from search to search and even day to day, it may be the result of changes they are implementing on their server.

Jon
Sonny Software