scientific names in article titles

shjenkins

I have just switched from ProCite to EndNote because Thomson Reuters no longer maintains or upgrades ProCite. I have experimented with Zotero and am sympathetic to the argument that it has some advantages over EndNote. I also greatly appreciate the fact that Zotero is open-source software, having become a fan of R for statistical analysis in recent years.

However, there appears to be one fundamental limitation of Zotero for my purposes as a mammalian biologist who has many references with scientific names in their titles. These names are typically italicized in bibliographies for journals in which I publish. It's important to keep in mind that the whole title is not italicized, just the scientific name. EndNote (and ProCite) make it easy to italicize items such as these in titles, or any other fields, but this seems impossible to do with Zotero.

I suppose one could use a code like {} to bracket scientific names, then do post-processing in Word after a bibliography was created to eliminate these codes and make the intervening text be italicized, but this seems like unnecessary effort. Andi, it would be painful to import the 1000s of EndNote references I have with titles containing scientific names into Zotero.

This is partly a suggestion for improving Zotero and partly a query to see if I'm missing something. If my understanding is correct, however, I can't make serious use of Zotero unless this issue is addressed, and I imagine there are many other biologists in the same boat.

S. Jenkins

dstillman

it would be painful to import the 1000s of EndNote references I have with titles containing scientific names into Zotero

Well, how do you plan to import them anyway? How does EndNote format your scientific names in RIS or BibTeX output?

fbennett

The citation formatter in Zotero 2.1 (development of which is in progress) implements CSL 1.0, which supports rich text in titles. Details are here.

ajlyon

This will be addressed, at least partly, in Zotero 2.1. That release is on its way (broadly speaking, probably at least a couple months away), and you can try out the development version here (http://www.zotero.org/support/dev/svn_and_trac_access). You will need to put <i></i> around such names, but it will work correctly, as far as I know. Frank, the developer of the new citation processor which supports this, can probably comment on this.

ajlyon

And of course Frank beats me to it. What he said :)

shjenkins

Thanks for your replies -- these planned improvements in Zotero sound promising.

In answer to Dan's question, I have used RIS to export selected references from EndNote to a file for importing to Zotero. Zotero instructions say that the RIS file should be saved as plain text, and in fact saving it in rtf format, which proeserves the italics, produces a file that can't be imported into Zotero. Perhaps one of the other export options in EndNote (html or xml) would work?

I realized after my initial posting that there are other special fonts besides italics that appear in titles of scientific papers, to wit, superscripts and subscripts. For example, papers about climate change with carbon dioxide in the title often use the chemical symbol for carbon dioxide -- C0 (subscript) 2.

Thanks again,

adamsmith

RIS is a plaintext format - unless Endnote can somehow export mark-up in RIS (such as <i> or something along the lines) you will have to fix this manually.
The other options Endnote export options are not supported by Zotero because they don't follow any known standard.

The planned mark-up features include subscripts and superscripts.

Rintze

I can't make serious use of Zotero unless this issue is addressed, and I imagine there are many other biologists in the same boat.

I'm also a mammalian biologist (I don't study mammals though), and have been using the following workflow successfully for several published papers:

http://forums.zotero.org/discussion/3875/rich-text-in-titles/?Focus=26555#Comment_26555
(along with the Word macro that I linked to in that thread)

It's not fully automatic, but for me it did (and does) the trick. The markup is the same as that which will be used with CSL 1.0, and includes support for bold, italics, superscript, subscript and small-caps.

Buz Wilson

I have an Endnote bibliography database with 1000's of taxonomic names. Unless Zotero, which seems really good so far, can import a Endnote database with all italics and other font effects preserved, I can't use it. I would have to correct every single reference, or try to remember to correct the italics in my papers. I haven't seen any work around for this problem yet. Instead of importing the ris database, I think Zotero will have to import the native Endnote database so everything can be gotten without loss.

adamsmith

you could see if the italics are exported in Endnote XML (just select XML as an export file format the style is actually irrelevant then) -- I think they should be and if they are, we import them. That option wasn't available for import to Zotero back in 2010.

We can't import native Endnote databases, even if it were technically possible (and it'd be hard) it's legally rather tricky.

Buz Wilson

Yes, that works - thanks much for the advice. The italics are preserved if Ednote XML export is used for import into Zotero. I recommend that Endnote XML should be suggested in the documentation instead of text. Now to try importing the whole database and indexing the pdf.

Buz Wilson

Whoa! I spoke too soon. Now the text in the Accession number is gone, which has my local reprint hardcopy index number. The Alt-Title is also not getting in the correct field. Both end up as a note "The following values have no corresponding Zotero field:"

adamsmith

what are those in Endnote XML? I'm surprised those worked via RIS\

edit: also, where do you think they should go in Zotero? We don't have an alt-title field.

Buz Wilson

I'm just comparing the txt vs the xml files.
for the txt RIS
AN - pdf
for the XML RIS
<accession-num>
<style face="normal" font="default" size="100%">pdf</style>
</accession-num>
This is a problem unless one can figure out a way to get the accession-num field put into the Zotero loc in archive field, which is where it showed up in the TXT RIS import.

In Endnote, the Alt-Title is usually where one puts the abbreviated version of the title. But I note that Endnote may be obfuscating things a bit because after the <title> which is the title of the paper, the XML file has this:
<secondary-title>
<style face="normal" font="default" size="100%">Zootaxa</style>
</secondary-title>
<alt-title>
<style face="normal" font="default" size="100%">Zootaxa</style>
</alt-title>
</titles>
<periodical>
<full-title>
<style face="normal" font="default" size="100%">Zootaxa</style>
</full-title>
</periodical>
<alt-periodical>
<full-title>
<style face="normal" font="default" size="100%">Zootaxa</style>
</full-title>
</alt-periodical>

Note that it puts the journal name where it should be putting the short title field.

adamsmith

OK, the accession-num thing we can probably do.

The alt-title I'm not sure I follow - what does Zotero import for those? Presumably you don't want Zootaxa in the short-title field? or is that for the journal abbreviation field?

Buz Wilson

I did not put all of <titles> heirarchy in, but in there should only be just things relating to the title of the document. So definitely Zootaxa, which should be in the <periodical> heirarchy, should not be in the <titles> heirarchy. This is a bug to be reported to Endnote developers. If Zotero picks up the <periodical><short-title>, this should not be a problem. Occasionly, a document will have an abbreviated version of an exceedingly long title or an additional title such as a part number (old papers often have a number from the authors series), which can be put in the <titles><secondary title>, which in the Endnote database field is called Short Title. In these rarer cases, having Zotero parse it correctly would be helpful.

aurimas

Can you post an Endnote XML record for a single item in EndNote that represents the issue above to https://gist.github.com/ and link to it here?

Buz Wilson

This link as requested:
https://gist.github.com/anonymous/50aa565a55ce69bc3214
It is the one that shows an anomalous place for the periodical term Zootaxa. The xml file was correct for the other records that I checked (not all).