PubMed lower case journal titles

aplested
Zotero is grabbing journal titles from Pubmed from the JT field. This is fine for single word journal titles, but where the journal title has more than one word, the 2nd,3rd etc words in this field are not capitalized. For example Journal of biological chemistry. The reason is that this is the medline rule for compound names. Of course this is not right for citations.

I think Zotero should capitalize thus : Journal of Biological Chemistry

Also, Zotero may have to make allowances for the somewhat eccentric contents of this field for some journals. One clear example is for Journal of Neuroscience, where the JT field is:

Journal of neuroscience: the official journal of the society for neuroscience.

Just the first bit please!

excerpt from http://www.nlm.nih.gov/bsd/mms/medlineelements.html
Journal Title (JT)
This field contains the full journal title, taken from NLM's cataloging data following NLM rules for how to compile a serial name. The NLM journal title abbreviation is in the (TA) element.
Examples are:
JT - Molecular microbiology
JT - American journal of physiology. Cell physiology
  • rs123
    Z should (please) retrieve both the JT and TA fields. If it only retrieves one, the TA is better for me because of the problems sited above. I need to use the TA field in my papers. thanks.
  • RintzeRintze
    edited January 23, 2009
    Zotero's PubMed translator should already retrieve both the full and abbreviated journal title.

    The fields it can retrieve are from a different list though (this one: http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html), as the translator relies on the XML-file accompanying each paper for the extraction of item info. The current translator saves the medlineta-field (http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#medlineta).

    On a more technical note: I did recently propose* to preferentially save the ISOAbbreviation field (http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#iso), but that hasn't been implemented yet.

    *http://forums.zotero.org/discussion/5078/two-bibliography-formatting-problems-with-pubmed-citations/?Focus=22195#Comment_22195
  • rs123
    ok, i see the problem now. I'm trying to move Zotero refs to Endnote so I can use the integrated citation features with Word or Pages.

    Zotero *was* grabbing the journal abbreviation too -- BUT i can't find a way to get Endnote to import the short journal name (JF in RIS) instead of the long one (JA in RIS).

    If I knew apple script, i'd just kill the RIS JF line in the RIS text export file and rename the JA field to JF. hmmm.
  • Matthias
    edited January 27, 2009
    @rs123:
    If I knew apple script, i'd just kill the RIS JF line in the RIS text export file and rename the JA field to JF. hmmm.
    AppleScript shouldn't be necessary, you'd just need to perform some regular expression search & replace actions using a regex-capable text editor (such as the free TextWrangler).

    Open your RIS file in a regex-capable text editor, then perform these search & replace actions (with Grep/Regex/Regular Expressions/etc enabled)

    Search for: ^JF - .+[\r\n]+
    Replace with: (nothing)

    Search for: ^JA -
    Replace with: JF -
    Note that, in the above search & replace patterns, there are two spaces in front of the dash, and one space after it.

    You could also try putting the abbreviated journal name into the RIS T2 field. OMM, this field seems to be imported by Endnote X.0.2.
  • rs123
    First, I tried to use Automator. I never succeed with that tool. Finally, i decided to (re)learn some unix commands. I came up with something similar to Matthias, but at the Terminal prompt:

    grep -v "JF - " "Desktop/Exported items.ris" | sed -e 's/JA - /JF - /' > "Desktop/zotero fixed for endnote.txt"

    the greg removes the JF lines. the sed changes the JA tag to JF. And Endnote imports the resulting file using the abbreviated journal names. whew. Now I just have to figure out how to fire it off without opening the terminal window, if such a thing is possible.
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