Two bibliography formatting problems with Pubmed citations

deb

I am using Zotero version 1.5-sync3.5

1. There are no "." in the abbreviated journal name -- see this post http://forums.zotero.org/discussion/3139/pubmed-issues-with-journal-abbreviations/

2. I do not know if this is possible. I would like to format the pages as ###-### not as ###-#/###-## eg. 123-126 not as 123-6 as it comes from pubmed.

bdarcus

@deb: on 2, I think that's a data problem, and wouldn't necessarily expect Zotero to fix it. You might have to manually correct those items in your database.

Rintze

Also on 2: this has been discussed before, e.g. at http://forums.zotero.org/discussion/3603/citation-styles-problem-with-page-numbering-format/

I do think however that as Pubmed keeps popping up as the main culprit with regard to this page-numbering issue, that it might be useful to just change the Pubmed-translator to correct the numbering, at least in the short run. Trevor notes that "This would only be advisable if we were confident that the second number in a series of page numbers should be at least as many digits as the first number.". In my experience, that always has been the case though with the papers in Pubmed (i.e. I've never seen a journal paper that spanned multiple issues).

P.S. After some digging on the PubMed website I did find a list of examples of how the pages-XML-element can be filled:
http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#pagination

deb

anything about 1. ?

I really liked pulling the data from "<ISOAbbreviation> </ISOAbbreviation>" in pubmed XML as suggested by Rintze in the previous thread.

Rintze

I really liked pulling the data from "<ISOAbbreviation> </ISOAbbreviation>" in pubmed XML as suggested by Rintze in the previous thread.

To my surprise, while this exact behavior was introduced into the Pubmed Translator some time ago (https://www.zotero.org/trac/changeset/2847), the change has been reverted later (https://www.zotero.org/trac/changeset/3286). Maybe Sean can comment why the latter change was made?

Rintze

Maybe Sean can comment why the latter change was made?

Scrap that. I just found the related forum thread (to which I even commented myself):
http://forums.zotero.org/discussion/3513/bugs-with-pubmed-central-translator/?Focus=16752#Comment_16752
Apparently there are just some papers missing citation.Article.Journal.ISOAbbreviation , so the translator was changed to only look for citation.MedlineJournalInfo.MedlineTA.

As periods are easier to remove than to add, and as people seem to prefer the version with periods, could the NCBI Pubmed be changed to first select the abbreviated journal name (with periods) from citation.Article.Journal.ISOAbbreviation, and only when that fails, fall back to citation.MedlineJournalInfo.MedlineTA?

Rintze

I just added two patches to the zotero-dev Google group for the NCBI PubMed translator:

1)
http://groups.google.com/group/zotero-dev/web/NCBI PubMed abbreviations.patch
This patch preferentially takes the abbreviation title from citation.Article.Journal.ISOAbbreviation. Only when absent, the value from citation.MedlineJournalInfo.MedlineTA is taken.

2)
http://groups.google.com/group/zotero-dev/web/NCBI PubMed pagination.patch
This patch converts abbreviated page numbers (e.g. "112-9") to full page numbers ("112-119"). It can handle all the examples listed at http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#pagination

edit: see also the later patch here: http://forums.zotero.org/discussion/4833/problems-with-pubmed-site-translators/?Focus=29546#Comment_29546