Bookends -> Refbase Problems

GertW · Post by **GertW** » Mon Sep 17, 2007 9:32 am

Hi there,
(this has been posted also to the Refbase forum)

I have a problem with exporting from Bookends into our lab's Refbase installation (which works fine otherwise) like in a thread in the Refbase forum. Qutoe: "Also, I haven't managed to import any references. The Upload to Refbase command in Bookends doesn't give any error messages, but after checking in Refbase I can't find any new references (of course I changed the server, username, and password from the default in Bookends preferences)."

has this been solved?

Also, an exported RIS-Format File from Bookends does not import into Refbase

"Unrecognized data format!"

while a RIS-Format file downloaded from ScienceDirect does import.

(The file also does not import into the refbase demo database)

Is this a bookends RIS export or a refbase import issue (I suspect the former, since the ScienceDirect RIS file imports)?

tnx.

Post by **Jon** » Mon Sep 17, 2007 9:54 am

Hi,

I can't comment on the refbase upload (it may or may not be a Bookends issue, but I think Matthias will have to see why refbase won't accept it), but as for RIS export/import, make sure you are using Bookends 10.0.3, and that the RIS filter is set to honor "consecutive spaces" (second tab of the format definitation). Older versions of Bookends would reduce two spaces to one, which in the case of RIS would result in an incorrect output...

Jon
Sonny Software

GertW · Post by **GertW** » Mon Sep 17, 2007 10:22 am

thanks for the quick reply.
Yes, using 10.0.3 and unticked "Don't clean up consequtive spaces" as you suggested, but still did not work (btw: output was with Mac line breaks; set those to UNIX for refbase import, still no luck).
I can send you the file by email if you like.

best

Gert

Jon wrote:Hi,

I can't comment on the refbase upload (it may or may not be a Bookends issue, but I think Matthias will have to see why refbase won't accept it), but as for RIS export/import, make sure you are using Bookends 10.0.3, and that the RIS filter is set to honor "consecutive spaces" (second tab of the format definitation). Older versions of Bookends would reduce two spaces to one, which in the case of RIS would result in an incorrect output...

Jon
Sonny Software

Post by **Jon** » Mon Sep 17, 2007 10:26 am

Hi,

No, don't untick it. Tick (check) it.

Does the RIS import into Bookends? Into EN? If so, the problem is at the refbase end -- it's seeing something it doesn't like, but I can't guess what it is. Have you been in contact with Matthias (of refbase)?

Jon
Sonny Software

GertW · Post by **GertW** » Mon Sep 17, 2007 10:44 am

OK, ticked it now (it was by default).
still no luck with Refbase, but imports fine into BE (not using EN anymore).
again, RIS files from the web (GoogleScholar, ScienceDirect) import fine into Refbase, just the ones from BE not

No, havven't been in touch with Matthias directly, just tried the Forum.

best

Gert

Jon wrote:Hi,

No, don't untick it. Tick (check) it.

Does the RIS import into Bookends? Into EN? If so, the problem is at the refbase end -- it's seeing something it doesn't like, but I can't guess what it is. Have you been in contact with Matthias (of refbase)?

Jon
Sonny Software

Post by **Jon** » Mon Sep 17, 2007 10:55 am

It seems that refbase is looking for something that Bookends isn't outputting. We'll need to hear from them (the refbase people) to find out what that is. Once we know, we can fix it by modifying what Bookends outputs or what refbase will expect.

Jon
Sonny Software

GertW · Post by **GertW** » Mon Sep 17, 2007 10:58 am

OK, just wrote Matthias and sent him the file.
tnx

Gert

Post by **Jon** » Mon Sep 17, 2007 11:53 am

BTW, you could examine the same reference downloaded from Google Scholar as RIS (which refbase accepts), imported to Bookends, and then exported as RIS (whidh refbase rejects). How do the two RIS files differ? My guess is that this would provide the necessary clues to the problem...

Jon
Sonny Software

GertW · Post by **GertW** » Mon Sep 17, 2007 12:05 pm

OK, from what I gather is that BE puts

JA - Mol. Phyl. Evol.
SP - 392-397

whereas Sciencedirect gives:

JO - Molecular Phylogenetics and Evolution
SP - 392
EP - 397

That's the only differences from what I figure.

So Journal abbreviation, and pages numbers are different, and the order of the fields.

Post by **Jon** » Mon Sep 17, 2007 12:16 pm

The difference between JO and JA is minor, and order of the fields shouldn't matter, as well. You can of course create a new RIS filter in Bookends (based on ours) and change JA to JO to see if that matters.

Here is the definition of those tags, btw, from

http://meerkat.adeptscience.co.uk/Knowl ... ations.pdf

JO - Periodical name: standard abbreviation. This is the 362 Appendix C
â€” RIS Format Specifications

JA - periodical in which the article was (or is to be, in the case of in-
press references) published. This is an alphanumeric field of up to 255
characters. If possible, periodical names should be abbreviated in the Index Medicus style, with periods after the abbreviations. If this is not possible (your large bibliography file in your wordprocessor has no periods after abbreviations), you can use the â€œ RIS Format (Addsperiods) â€

msteffens · Post by **msteffens** » Mon Sep 17, 2007 2:41 pm

Hi Gert and Jon,

I posted a response in the refbase forums.

IIRC, Bookends sends records in Endnote XML format to refbase, so the problem with import of RIS records is probably a separate issue.

If you're going to use the "Upload to refbase" feature of Bookends with your own refbase installation (as opposed to the one at refbase.org), then you'll need to use the most recent versions of Bibutils (currently v3.37) and refbase. Unfortunately, at the moment, the most recent refbase version (which supports the integration with Bookends) is only available in the refbase SVN repository, and not as a downloadable release package.

http://svn.refbase.net/
http://bibutils.refbase.net/

Sorry for the inconvenience! Things will get easier when we've released refbase 0.9.1. I also realize that error reporting (and messaging between refbase and Bookends) should be improved...

Hope this helps, Matthias

Post by **Jon** » Mon Sep 17, 2007 3:09 pm

Thanks, Matthias.

Please let us know how the RIS upload goes, too, Gert...

Jon
Sonny Software

GertW · Post by **GertW** » Tue Sep 25, 2007 6:11 am

OK, the problem with the RIS upload was solved, I think it was due to BE exporting the file with mac line breaks, but refbase wants UNIX line breaks (the old story). May be this could be changed?

However, I ran into other problems with the RIS export/import.
Series and other editors in book chapters: only the first editor is correctly mapped (ED), subsequent editors get mapped as authors (AU). From what I gather in the formats file everything is correct ($ED - $e). Editors are in my BE entries on seperate lines (like authors).

Further, I have includes the User1 field to be mapped to U1 ($U1 - $u1), and modified the import options in refbase import.inc.php to map this to call number ("U1" => "call_number", // User definable 1), which works great and is needed because some vital information about location of reprints is stored in this field.
But if I export directly from BE to refbase using refs -> upload to refbase, information in User1 does not get transferred. Can I modify a format (which one?) such that this happens?
best

Gert

msteffens · Post by **msteffens** » Tue Sep 25, 2007 7:31 am

Hi Gert, Bookends uploads records to refbase in Endnote XML format. refbase then uses Bibutils to transform this into RIS which it can import natively.

The contents of the 'label' tag in Endnote XML will be copied to the refbase 'call_number' field. OMM, Bookends exports contents of the 'User1' (Key) field to the 'label' tag in Endote XML which then gets imported into the 'call_number' field. I.e., by default, you should be able to transfer contents of the Bookends 'User1' field to the refbase 'call_number' field. Does this work for you?

Also note that in recent versions of Bibutils (v3.35 or greater) the RIS 'U1' tag is used to indicate the type of thesis (e.g. "Masters thesis" or "Ph.D. thesis"), i.e. future versions of refbase will associate the 'U1' tag with the 'thesis' field.

Post by **Jon** » Tue Sep 25, 2007 7:38 am

Hi,

The direct export can't be modified. User1 is mapped to the key field (for BibTeX users). It's possible we'll allow the use of different direct upload formats in the future.

Jon
Sonny Software