Pubmed issues with journal abbreviations

Pierre

Hey,

Just a quick comment (and also request at the same time): when I save citations going through Pubmed, ALL the journal abbreviations are missing a dot at the end of each word (where there should be one). Example: I save an article from Journal of the American Chemical Society: I get "J Am Chem Soc" as an abbreviation when I use that citation (everything else is good). If I save the citation for the exact same article by accessing through the American Chemical Society website, then I get it abbreviated "J. Am. Chem. Soc." (as it should be). And it is the same for EVERY journal abbreviation saved via PubMed

I don't know if other people have had that problem, or even noticed it because it is quite subtle, but still makes citations incorrect... And it kinda sucks because getting references from PubMed is really practical...

Anyway, Thanks a lot to you guys who are putting so much effort to get things rolling smoothly, keep up the great work it's greatly appreciated!

Tjowens

An update to the pubmed translator was just pushed out which will add the period. Your copy of Zotero should auto-update within 24 hours, or you can update manually by clicking Update Now in the General pane of the Zotero prefs. To open the preferences pane click the gear icon, this will open the actions dropdown menu. Select preferences from that dropdown menu.

Pierre

Thanks a lot for the update! Now I have another problem... Zotero's now adding period at the end of every journal abbreviation, including the ones where the abbreviation is the same as the journal name and where there shouldn't be... Do you think it might be fixable?

Rintze

If I read the scrapers.sql file correctly the citation data is retrieved from pubmed's XML-output. In that case getting the journal abbreviation from the field "<ISOAbbreviation>Appl. Environ. Microbiol.</ISOAbbreviation>" instead of the field "<MedlineTA>Appl Environ Microbiol</MedlineTA>" would solve the problem. The only difference I ever observed between these fields is the punctuation.

JanK

Having the same problem here, I need the dots after the abbreviated journal titles. Did I get it right, this is not a problem that could be solved by editing the CSL file?
Maybe if the translator got both of the XML fields with different names (as some journals want abbreviation without dots) and then only the desired one would be formated in csl.

uqqkaas

As of April 2009, it seems that this issue is still not resolved. The abbreviations are not taken from the right field in the PubMed XML file : no dot in the abbreviations.

Rintze

The translator has been modified (the 1.0.x branch actually just received the update 2 days ago) to first try to read out the contents of the element, and only when that doesn't give results, to try to read the contents of the element. Title abbreviations found in the first element usually have periods, whereas those found in the latter haven't any. This choice has been made as it is easier to (automatically) remove periods than to add them.

It might be though that you haven't yet obtained the updated translator:
http://forums.zotero.org/discussion/4833/problems-with-pubmed-site-translators/?Focus=29612#Comment_29612

mdoube

It seems that PubMed citations are saved with full-stops (periods) after all abbreviated words in a publication except the last word.