papers to bookends via plugin or endnote xml

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Harry Lime
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Joined: Sun Sep 24, 2006 10:21 pm

papers to bookends via plugin or endnote xml

Post by Harry Lime »

I have been combining Papers and Bookends. The problem is the export to bookend via the direct route or via the endnote xml import gives long journal names and not the standard abbreviated names. Since the plugins come with Papers, this would seem to be their issue primarily, but looking through the endote xml file I could see the short journal names were included. So there does seem to be some issue with the xml import and I do not see anywhere to adjust that import filter.

Jon
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Re: papers to bookends via plugin or endnote xml

Post by Jon »

XML filtering isn't editable. If you are using a journal glossary it doesn't matter what the journal name is in the database -- Bookends will output the long or the short form as dictated in the format.

Jon
Sonny Software

Harry Lime
Posts: 11
Joined: Sun Sep 24, 2006 10:21 pm

Re: papers to bookends via plugin or endnote xml

Post by Harry Lime »

I would think so, but here is a ref in nature format that came from Papers:

Abal, M., Keryer, G. & Bornens, M. Centrioles resist forces applied on centrosomes during G2/M transition. Biology of the cell / under the auspices of the European Cell Biology Organization 97, 425-434 (2005).

and here is the same ref directly imported from PubMed:
Abal, M., Keryer, G. & Bornens, M. Centrioles resist forces applied on centrosomes during G2/M transition. Biol Cell 97, 425-434 (2005).

here is the some of xml from Papers:
<source-app name="Papers" version="1.8">Papers</source-app><rec-number>1824</rec-number><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Abal, M.</style></author><author><style face="normal" font="default" size="100%">Keryer, G.</style></author><author><style face="normal" font="default" size="100%">Bornens, M.</style></author></authors></contributors><periodical><full-title><style face="normal" font="default" size="100%">Biol Cell</style></full-title></periodical><titles><title><style face="normal" font="default" size="100%">Centrioles resist forces applied on centrosomes during G2/M transition</style></title><secondary-title><style face="normal" font="default" size="100%">Biology of the cell / under the auspices of the European Cell Biology Organization</style></secondary-title></titles></record></records></xml>


So it appears as though Bookends is importing the secondary title rather than the full one from the endnote xml. I get the same result with the direct path to BE.

Thanks for your unbelievably fast assistance!!

Jon
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Re: papers to bookends via plugin or endnote xml

Post by Jon »

Hi,

I see this, too. I've modified Bookends so that if the full-title is provided for a journal, it will supersede anything in the secondary-title node and be assigned as the journal name.

This fix will be in the next update, which is probably on track for early next week. If you still have problems with it, please contact me for tech support off-forum.

Jon
Sonny SOftware

Harry Lime
Posts: 11
Joined: Sun Sep 24, 2006 10:21 pm

Re: papers to bookends via plugin or endnote xml

Post by Harry Lime »

Awesome, thanks!

Harry Lime
Posts: 11
Joined: Sun Sep 24, 2006 10:21 pm

Re: papers to bookends via plugin or endnote xml

Post by Harry Lime »

When this fix is applied, will it correct both the direct Papers to BE export as well as BE's import of endnote xml? Thanks

Jon
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Re: papers to bookends via plugin or endnote xml

Post by Jon »

Sure. The data Papers sends directly to Bookends is in EN XML format.

Jon
Sonny Software

eric
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Re: papers to bookends via plugin or endnote xml

Post by eric »

Hi jon,

Did this update get added? Or is it the next update? It seems like i am still getting the full length journal name when papers sends it to bookends. BTW I have bookends 10.3.1 and papers 1.8.

thanks,
e

Jon
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Re: papers to bookends via plugin or endnote xml

Post by Jon »

Hi,

In that case I think it's working correctly. If two names are available, Bookends will take the long form. If you have an example that's not working, please send it to me and tell me what you think is incorrect (support@sonnysoftware.com).

Jon
Sonny Software

Harry Lime
Posts: 11
Joined: Sun Sep 24, 2006 10:21 pm

Re: papers to bookends via plugin or endnote xml

Post by Harry Lime »

IIRC, Jon released this fixed without a bump to the version number. If you download the version on the front page now it ought to work. The names get transferred rather than just initials, but that is not a big deal since they get stripped down when formatting.

eric
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Re: papers to bookends via plugin or endnote xml

Post by eric »

Hi Jon and harry,

Again thanks for the unbelievabley fast reply.

that said, I guess i am confused. I thought that harry wanted the short journal names? This is what i want, because otherwise i have to edit them all by hand. I see the short name in papers, but when it exports to bookends it becomes the long name. When i choose the nature format as you did above i get the full name, not the abbreviated form. Is there a formatting option that i do not have set correctly?

e.g.
Croft, M. T., Moulin, M., Webb, M. E. & Smith, A. G. Thiamine biosynthesis in algae is regulated by riboswitches. Proceedings of the National Academy of Sciences 104, 20770 (2007).

Want i want is:
Croft, M. T., Moulin, M., Webb, M. E. & Smith, A. G. Thiamine biosynthesis in algae is regulated by riboswitches. Proc. Natl. Acad. Sci. 104, 20770 (2007).

Jon
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Re: papers to bookends via plugin or endnote xml

Post by Jon »

Hi,

The Concise Medline glossary was created for exactly this situation. If you use it, and in the format you specify the "short" journal name (e.g. j rather than f), Bookends will substitute

Proc. Natl. Acad. Sci. U S A

(unless the format tells Bookends to omit periods).

So, select Concise Medline in the Extras -> Journal Glossary menu.

Jon
Sonny Software

eric
Posts: 4
Joined: Wed Dec 19, 2007 3:21 pm

Re: papers to bookends via plugin or endnote xml

Post by eric »

Ahhh that is exactly what i was missing.

thanks!
e

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