Citation copy-editing is one of those deceptively small burdens that have a way of taking over the working day. If left untended, the task of tidying up casually scribbled references can snowball to crisis proportions as a submission deadline approaches. Similarly, when a submission to one publisher is unsuccessful, significant effort may be required to recast its citations in the format required by another. Collaboration outside of one’s own field can bring with it an unwelcome tangle of fresh style-guide quandaries to ponder and fight through. These are things that the machines, if they want to make themselves useful, should be doing for us.

There is plenty of collective experience in this line, and as fate would have it, there are also plenty of collective solutions. In the TeX/LaTeX world, authors and their editors can today choose between BibTeX and BibLaTeX — both of them excellent utilities — with the several variants of the former supported by no fewer than four separate versions of the BibTeX program. [1] Users of WYSIWYG word processors can look to the bibliographic support built into Word or Open Office, or they can turn to an external solution such as EndNote ™, ProCite ™, Reference Manager ™, or more recently Zotero or Mendeley. Migrating data between these environments is a process fraught with uncertainty, but it is sometimes unavoidable when you need this kind of output, and it can only be produced on that kind of system …

… with so many solutions to choose from, it’s hard to go right. [2]

The citeproc-js citation processor is a Javascript implementation of the Citation Style Language (CSL), an XML schema for describing citation styles that aspires to strike this problem at its root. CSL is a general, open standard that enables fully modular control over bibliographic formatting. This means that CSL is capable of accurately describing styles used in many disciplines, from the sciences, through the humanities to law. It also means that a CSL style description can be used with any other application that understands the CSL language. And it means that the style description is separated to the extent possible from the target document; you can switch styles at any time, even after the writing process is complete. Generality, a comprehensive pooling of community resources, user-centric ease of use: all areas where, collectively, our current menagerie of productivity tools could do better.

CSL first saw wide application in the Zotero project. [3] Citeproc-js has been developed in the first instance for use in Zotero, [4] but it runs as a separate module via a (relatively) simple API, and with appropriate wrappers, it can be deployed pretty much anywhere. Potentially, any application that generates dynamic content — text processors, word processors, weblog environments, and dynamic websites — can use CSL and citeproc-js to provide publisher-correct citation and bibliography facilities without exceptional programming effort. [5]

Development of the CSL language has been spearheaded by Bruce D’Arcus. The citeproc-js processor adheres to version 1.0 of the CSL specification, [6] which has been engineered and documented during the past year primarily by Bruce and Rintze Zelle, with incidental contributions by myself and others. It will debut, together with the new processor, in Zotero 2.1, which should begin to emerge, if all goes well, during this calendar year.

Meanwhile, the processor itself is complete, documented, and more or less ready to go. [7] Here is a short run-down of some of the highlights:

Disambiguation

In author-date citation styles, works by the same author must be distinguished from one another in some way. The current Zotero processor performs name and cite disambiguation as required by the Chicago Manual of Style. There are in fact at least six other disambiguation methods in general use. CSL 1.0 and the new processor will support all of them.

Sorting

The AGU journals, in particular, impose extremely demanding sorting rules in the bibliography. [8] CSL 1.0 and the new processor support multiple sort keys with arbitrary sort order for each key. A wide variety of sorting schemes can be implemented, including the AGU sort.

Parallel citation support

Many legal styles, including the Bluebook style common in American law journals, require that law cases appearing in multiple reporters be cited to each reporter, with the case name in front, and the court and year of decision at the end. [9] The new processor supports this behavior.

On-the-fly document updates

The API of the new processor supports targeted context-sensitive updates of citations in a document that are affected by an insertion, deletion or edit, for efficient transactions with a word-processor or weblog plugin.

Localization of dates

CSL version 0.8 currently supports the use of localized terms for style-supplied labels and the like. CSL 1.0 will add sophisticated localization of dates; both the language of month names and the ordering and formatting of elements will adjust appropriately when the language of a citation style is changed.

Sophisticated names handling

A great deal of work has gone into enhancing the handling of names in CSL 1.0. European conventions on the handling of particles such as “von”, “van”, “di” and the like can be accounted for appropriately both in the sorting and in the rendering of individual names.

In-field formatting

For scientific publishing, the new processor recognizes a limited subset of HTML as markup within titles, enabling superscript, subscript, small capitals, italics, boldface. The processor also implements the flip-flopping of italic and boldface, and of quotation marks, to avoid ambiguity in rendered citations. The HTML used in markup is transformed by the processor into the selected output format (HTML, RTF, LaTeX, or whatever) during rendering.

Multi-lingual citation support

The new processor implements experimental support for multi-lingual citations, providing a flexible mechanism for the transliteration of names and titles, for the supplementary translation of titles, and for the use of alternative sort strings needed for Asian languages.

As it leaves my laptop, citeproc-js is just a bare Javascript module with some test suite wrappers to check that it actually performs as advertised. But with the widening availability and increasing efficiency of Javascript runtime tools, I do hope that it has some prospect of escaping from its cage and wreaking order on the world of bibliography management. If you’re an integrator or site administrator, the fine citeproc-js manual is your first point of reference. If you’re an end user, keep an eye out for the CSL mark, coming soon (maybe) to an application near you!

Springer launched yesterday a new service allowing users to search, browse, annotate and reuse scientific images from their huge database of publications.

SpringerImages is a growing collection of scientific images that spans the scientific, technical and medical fields, including high-quality clinical images from images.MD. The continually updated collection – currently over 1.5 million images – gathers photos, graphs, histograms, figures, and tables, and is available to libraries and their patrons via a searchable online database. The SpringerImages interface enables users to search faster, more broadly and more accurately, through captions, keywords, context and more, even jumping from the image to the source article. Users can create personalized image “sets,” and can easily export images for use in their own presentations or lectures.

The service offers a range of potentially innovative features.

Being able to search, organise and download high quality images as PDF from a large corpus of books and journals might represent a breakthrough in the dissemination and reuse of non-textual content from the scientific literature. Usage factors related to images may provide additional metrics of scientific impact for authors and journal editors. From the end user’s point of view, the collaborative annotation functionality is an interesting addition, although it may not be obvious to convince users to massively start tagging and annotating images. Last but not least, a prominent button allows users to bookmark images via CiteULike (a Springer partner) in the same way as references (images available from SpringerImages will be the displayed as thumbnails from the correspondent article page). It is worth reporting details on the access conditions, as the full availability of the service (in particular access to full-resolution images) is tied to Springer’s institutional subscriptions. The set of freely accessible images is–helas–a tiny portion of the complete database.

Anyone can create an account and search the free and Open Access images indexed by SpringerImages. Access to the complete collection is available via subscription to libraries, research institutions and individuals. Images obtained from SpringerImages can be used for almost all noncommercial purposes, including integration into presentations and PDF documents.

Maybe I’m getting out of touch, but it’s only now that I found sciencewatch. It’s a service of Thomson Reuters (the makers of Web of Science) that collects and displays statistics on recent trends in science. Example:

Aug 2008 – SCHOLARLY USE OF THE WORLD WIDE WEB – Research Front Map – ScienceWatch.com

This is a citation network that shows highly cited papers on WWW. Diameter relates to citation: the two bigger circles are the paper that proposed the Hirsch index, and King’s paper on the scientific impact of nations. Clicking on the circles provides details on the papers.

There are many other fronts:

• Fast Breaking papers. These papers comprise the top 1% of papers in each field and each year
• Top Topics selects the Research Fronts with the largest absolute increase in size in each of the 22 major fields covered by Essential Science Indicators

Worth keeping an eye on.

Frankly, there are too many reference managers today. This  is counterproductive because we all need to spend time checking the newcomers, just in case there’s a new feature that we were missing.

Most reference managers graft themselves to word or to openOffice. For example, Mendeley, and zotero both use internal reference functionality in word. In doing so, they use features that are available only on those editors. I think this is a big error for at least 3 reasons:

1. I draft my papers on a text editor or oneNote. This has a lot of advantages for me. But I would not be able to use say Mendeley or Zotero on oneNote; and I do want to keep references on my notetaking tool. Using a text editor has a lot of nice advantages over a word processor too, if you know how to use it.
2. It’s a lot faster to massage your reference the way you like it. It takes several clicks on zotero to get an Author (year, p. XX) reference. In endNote, it’d be a few keystrokes.
3. There are bottlenecks in our digital lives that are plain text. For example, emails, forum posts, and google docs are cases of writing that may need reference management but are ill-served by most current offerings. I want to copy-paste chunks of scientific writing and still carry my references; there’s life outside word processors, and quite a lot of it!

So what reference managers work ok on plain text. Well, here is the surprise: as far as I know, only bibTeX and endnote. This is surprising because they are the oldest. One would have thought that newcomers would have taken advantage of what these older tools learned.

Lurking in the Zotero forums, I saw people asking for support of this exact feature. But it seems that it’s never going to happen. It would take a lot of reengineering, and all users that are happy with the current solution (and have amassed a large body of authored docs) would complain.

so, where does this leave me? I need to either comply and write everything in word to take advantage of Mendeley and Zotero, or stick to oneNote, but use endNote references. Of course I could also do everything on a text editor and use bibTeX, but right now, it’s more trouble than it’s worth.

Does anyone know a good solution for my setting?

Exciting that an anonymous donor jumped in:

Donate to CHNM in June and your contribution will be matched twice over. Thanks to a challenge grant from the National Endowment for the Humanities, the Center for History and New Media has the rare opportunity to build a $3 million endowment to support infrastructure expenses and ongoing development across its many projects. We’re delighted to announce that now your contribution to the Center for History and New Media will be matched for a limited time. If you give within the month of June your donation will be stretched even further since an anonymous donor has agreed to double the National Endowment for the Humanities matching funds.

If you or your institution used/still pays hundred of dollars per seat on other bibliography manager, consider donations of similar size. If you can raise awareness in your institution, please do so. Zotero is a project that benefits all (Open source) and has been legally attacked (in a childish way) by Thomson before.

Zotero Blog » Blog Archive » Help Zotero by Donating to the Center For History and New Media

It should be no surprise that many of us love Zotero, especially since they added support for reference sharing and synchronization.

I am probably the only exception in the AP team. As a longstanding MacTeX user, I keep my references organised with BibDesk, one of the sweetest pieces of (open source) software ever written for TeX users working on Mac OS. When hunting for references, I use CiteULike as a fast and effective solution to bookmark and tag papers. My workflow usually starts with an exploratory phase based on CiteULike. As soon as I have read a paper and need to cite it, I export its reference from CiteULike into BibDesk, filing the PDFs with the help of the autofile functionality in BibDesk. So far I have been quite happy with this workflow even if it involves a little bit of fiddling to correctly import references into my local library.

After some research and discussion in the support forums, I discovered that CiteULike and BibDesk can seamlessly integrate with each other. BibDesk has an external file group option that allows you to read structured references from any online source. CiteULike has a bibtex export feature that allows you to expose your references for consumption by software like BibDesk. This is all you need to get the two to work together. Here’s how my new workflow looks like:

1. Create a new external file group in BibDesk

Click on the cog icon on the bottom left of the BibDesk window and select “Add External File Group”. This will add a new folder in your library pointing to a remote source.

2. Point the new group folder to CiteULike

CiteULike can generate bibtex files on-the-fly from any reference list, e.g. your reference library, the list of papers for a specific author, papers tagged with a specific keyword etc. The bibtex export filter for any of these lists can be obtained by adding the /bibtex prefix to the corresponding URL. For instance, to export in bibtex format my full reference library:

http://citeulike.org/user/dartar/

I simply need to type the following URL:

http://citeulike.org/bibtex/user/dartar/

The following URL parameters are a useful addition:

• fieldmap=<oldval>:<newval> allows you to specify translation rules for custom fields, e.g. record creation date (what CiteULike calls Posted-At must be translated to BibDesk’s Date-Added)
• do_username_prefix=0&key_type=4 toggles an option to create bibtex keys using an AuthorYearTitle scheme when none is available (which I prefer to the default numeric key)

The final URL we will use is the following:

http://citeulike.org/bibtex/user/dartar?fieldmap=posted-at:date-added&do_username_prefix=0&key_type=4

3. Browse your CiteULike library from BibDesk

Once you have pointed BibDesk to the URL of the CiteULike bibtex filter, you can start directly browsing your CiteULike library from BibDesk. You will see an “Import” button on the left of each item, which is greyed out when the reference is already imported in your local BibDesk library.

4. Import selected items

Click on “Import” to download a reference and file it in your local BibDesk library: you are done!

There is definitely room for further improvement (in particular to allow bidirectional sync’ing of references and PDFs and custom bibtex keys in CiteULike), but this solution will save you a lot of time when working with references between a local and a remote library. Kudos to the BibDesk and CiteULike team for being so responsive to feature requests from their user community!

On a related note, if you are a Mendeley user, you will be happy to learn that today their integration with CiteULike is finally seeing the light.

The general agreement is that mail is broken. We all use it but kind of hate it too. Well, it seems that Google came up with a very good alternative (ambitious, and technically impressive): Google Wave.

A long video of Wave’s capabilities here.

It’s very long at 1:20hrs, but worth it. It’s peppered with random bouts of applause, something I’ve never seen in a scientific/technical presentation before. About minute 1:04, Lars Rasmussen presents real-time translation and he gets about a minute of standing ovation.

Why is this important for academics? Looks like sending a word document back and forth with version numbers in the file name is no fun. And setting a VCS with a bunch of .tex files plus figures is not much better (mainly because doing diffs on LaTeX files is pretty horrible). One could always convince a collaborator to use Google Docs, but then you have no way to use a proper reference manager, figures are a mess, etc. In short, scientific paper collaboration is not really pleasant right now.

In fact, it might be more appealing than desktop equivalents (say MS word) to write papers with collaborators, and better than a long thread of mails to simply organize a dinner out. So I won’t be surprised if many people jump on this as soon as it’s out. Wave is solving so many problems so well that it’ll be a rotund success. Here’s the interface:

The basically new thing is that you can see your collaborator typing away in real time, maybe in different parts of your manuscript. Although similar things have been around for a while (see for example etherpad), the way Wave integrates with other google offerings such as chat/email –may well be enough to gain adoption.

Wave supports images, and more editing features in general than etherpad.

One thing we get for free is version control: you can even move a slider to see how changes happened in your document. It’s pretty spectacular.

While Wave won’t be out for a while, there are developer accounts where one can sign up and get a preview.

Surprising: It’s open source, both client and server (!). I have no idea how they plan to disentangle the server side from the rest of Google’s infrastructure… Unless they ask you to reproduce all of part of it on your server – which is unlikely- I’m not sure how you could get this thing running.

According to Wikipedia, “the semantic web is expected to revolutionize scientific publishing, such as real-time publishing and sharing of experimental data on the Internet.” The W3C HCLS group’s Scientific Publishing Task Force is going to explore how this could happen.

Currently, one describes experiments in a more or less ad-hoc way. The mapping between experiments, papers, and titles is… well, not the most consistent ever.

Do you want to know if the experiment you have in mind is done already? Good luck mining the literature. Although mostly everyone is well-versed on building queries in scientific search engines, the task is far from accurate.

Maybe the problem is in the way we write the literature. If we could write a description of every experiment in some kind of agreed format that both humans and machines understand, searches would be trivial.

An alternative would be to use an ontology to describe experiments. The ontology should not be too complicated to use. If a user feels overwhelmed by the large number of parameters required to describe an experiment, this user may hesitate to do it. Of course, every field would need to built its own ontology. The effort to integrate ontologies across fields may be titanic.

There is some progress in the direction of using named entity extraction as metadata already. For example, the pubmed interface gopubmed is above and beyond anything I have seen. It uses facets (left sidebar) to show metadata. I do not know the details on how it works, but going back to say Web of Science after gopubmed feels like going 5 years back in time. Is there any hope to have a similar interface for all scientific databases? I sure hope so.

This is an exciting release.

In a single stroke, Zotero may have added the most important feature of online apps such as citeUlike (collaboration) and the best feature of Mendeley (metadata extraction). I have no idea how well these work, as I have just moved to zotero recently and don’t want to risk trying the beta this soon, but if they work well, this is a quantum leap.

Here’s a  list of the new features:

Automatic synchronization of collections across multiple computers. For example, sync your PC at work with your Mac laptop and your Linux desktop at home.

Free automatic backup of your library data at Zotero.org.

Automatic synchronization of your attachment files to a server of your choice (e.g. iDisk, Jungle Disk, or university-provided web storage).

Recover recently deleted items with Zotero’s trash can.

Rich-text notes

New style manager allowing you to add and delete CSLs and legacy style formats

Automatic detection of PDF metadata (author, title, etc.)

Automatic detection and support for proxy servers

New Website Features

Browse through your library online.

New user profiles tied to Zotero accounts.

Preliminary support for following other Zotero users: In the future this will generate a twitter-like feed of users public research activity.

WYSIWYG CV creator, with the ability to dynamically generate all or part of your CV from Zotero collections.

Search for friends, colleagues, and other users by institutional affiliation, username, email address, or field of interest.

I’ve been using endNote for about 6 years now, so I have experience a hard case of vendor lock-in (I have plenty of text with references in the endNote format. This is giving me a really bad feeling about endNote makers, and the money I have invested in a clearly inferior product doesn’t make me happy either. Suing Zotero was the last drop. I finally moved to Zotero out of principle. What I find funny is that zotero uses less memory with the same database size, even building on top of Firefox. And Word integration is as good, if not better, than endNote’s.

If you collaborate with people who use another reference management system or (to a lesser extent) word processor/typesetting program, you know that things can get messy.

I just found out Bibtex4Word, and this could be a good solution:

BibTex4Word is an add-in for Microsoft Word that allows the citation of references from a BibTex database. BibTex4Word will insert a bibliography into your document using your choice formatting style.

It is intended for three types of user:

1. LateX users who need to use Microsoft Word. BibTex4Word allows you to use your existing BibTex database and favourite bibliography style.
2. Word users who can’t afford a commercial bibliography package but need to insert citations and bibliographies into their documents. Everything you need to manage references is available free.
3. Word users who have a commercial bibliography package but who don’t like it. BibTex4Word is lightweight, transparent and doesn’t mess up your documents. It is also free.

Bibtex4Word is GPL’d. the only downside is that it depends on latex, so you might need to install MikTex (http://www.miktex.org/) and use the MikTex package manager to install any style files that you want to use.