Old non-Bookends references (with wrong PMIDs): How to comply with the USA National Standard abbreviations for journals?

[Reinhard]

My references in Bookends come from Medline-imports up to 15 years ago. Many of them do not use the US National Standard abbreviations for journals. Do I have to change them manually (autofill from internet) or is there any other solution to this compatibility issue?

Thanks
Reinhard

[Reinhard]

If other users are interested too, it could be a nice new feature of Bookends:
To compare all journal names of references (type: journal) in the Bookend library with entries in the US abbreviation database. All differing names should be listed and a change to "XY" suggested.

[Jon]

Using Autofill From Internet is hardly "manual". Select all the references you want updated and then use AutoFill. Sit back for a few seconds (or minutes, if you have selected many hundreds) and Bookends will do it for you.

Jon
Sonny Software

[Reinhard]

Thanks Jon!
The problem is that I don't know which references contain a non-standard journal name. I only find them by accident, when I check the reference list of a newly written paper and realize that sometimes the same journals have different abbreviations in the same list.
But you are right, I could do it every time I find the bad guys

A database search for non-compliant journal names and a list of suggested changes (including the possibility of editing) would be great...but is not necessary of course...even without such a feature, Bookends is the best reference manager

[Jon]

Why not just do an Autofill for all references? Unless you've edited a field and don't want it updated (but I image that's rare). Do this on a COPY of your database (select all references and autofill -- they'll all be done at once).

Jon
Sonny Software

[Reinhard]

Thanks, but I am afraid to damage some of my 2700 references without even knowing.

In Endnote, for example, it occasionally happened that the automatic import of a pdf file resulted in a completely different reference entry in the Endnote library. I was very shocked, since I realized that I would never find this paper again...it would be lost in space and time.
So every time, when I imported dozens of pdfs into Endnote, I checked every single newly created reference.

Bookends' pdf import works much better though. Yet, it happened once that a pdf file import resulted in a wrong reference entry in Bookends...nothing matched, no author, no journal...

That's the reason, why I do not want to update all references automatically

[Reinhard]

Just to show you, what I mean.
I did an "autofill from internet" on Nature Reviews journals in my library, which did not have the correct abbreviation of the journals name.

In at least two occasions (different journal > easy to spot) it completely changed my reference to something it never was!

This is no bug of Bookends, it seems to be a bug of the online databases...I think.
Two screenshots are attached.

[Reinhard]

I think this happens, when there is no DOI in the Bookends reference and an old PMID number, which is not identical with the current one of the article.
Is it possible that 10 years ago the PMID numbers were different? They seem to have less digits in my older references?

[Jon]

PMIDs should never change. And they begin with 1. If there is no DOI and Bookends is using the PMID, it may be that the original PMID was input incorrectly or, conceivably (but unlikely) that there is a problem with the PubMed database.

Jon
Sonny Software

P.S. This is the article that was assigned the first PMID

Makar AB et al, 1975. Biochem Med. 13:117-26.

[Reinhard]

Well, I have been using the reference import feature (in Endnote) since 2000.
It is possible that I also imported references from ISIS (don't know anymore), but mostly from Pubmed, I am sure. It seems that I have many PMIDs, which do not start with "1".
See attached images.

Bookends does not understand PMIDs starting with "0"...and the autofill-option does not work.

[Jon]

You miss my point. The very first assigned PMID was #1.

This thread (which is the wrong forum to begin with -- this forum is for requesting formats) has gone off course. If you have other topics you want to discuss on the forums please start a new thread.

Jon
Sonny Software

[Reinhard]

Yes, you are right. You can delete it, if you want.

Anyway, it seems that even if someone downloaded references from Medline/Web of Sciences in the early days (around 2000) that PMIDs are not correct, which can result in wrong autofill results.
In both cases the PMIDs were wrong. Original references are attached.

And that's the reason, why I do not use the autofill option on all of my "historic" references simultaneously

[Reinhard]

I solved my problem with non-standard abbreviations of journal names.

Since I could not trust the autofill option due to old imported references with wrong PMIDs, I used the option in Bookends to list groups of journal names. In groups containing more than 5 references I did a find & replace (journal field).

The other solution would have been to delete the PMID in all references to prevent any false autofill events.
However, I preferred the find & replace by journal groups.

Since it is a problem related to old and migrated databases, it won't be necessary to implement a new feature in Bookends I suggested in a previous post.

Thanks
Reinhard

Just one last thing: I recently migrated from Endnote to Bookends and this seems to be the problem. Endnote stores the FULL journal names, but shows only the correct standard abbreviations. When someone imports an Endnote library into Bookends, most of the references will show full journal names!