The ScienceOnline2012 conference last week again was a wonderful experience. This was my third time in North Carolina, and I had many great conversations in the sessions, hallways – and bars. One of many highlights was a lunch meeting with fellow PLoS bloggers and staffers:
Flickr photo by briandcrawford.
The Sloan Foundation has awarded a $125,000 grant to Columbia University and Mendeley to fund the development of a Citation-Style Language (CSL) editor. CSL is a XML-based language to format citations and bibliographies, and is used by the reference managers Zotero, Mendeley and Papers, and in many other places. Even though more than 1000 citation styles are available at CitationStyles.org (and built into the tools using CSL), it has until now been fairly hard to create new citation styles – editing XML files is not everyones idea of having fun. The CSL editor will be made available as open source software.
Building a dedicated CSL editor will be a tremendous boost to the format. The press release is here.
In related news, Mekentosj is giving away a Papers 2 serial number for every citation style submitted to CitationStyles.org.
ScienceCard is a web service that collects all scientific articles published by an author and displays their aggregate article-level metrics. Yesterday I added a mobile version to ScienceCard, simply browse to ScienceCard with your mobile phone or go to http://mobile.sciencecard.org. This is a first version based on my work with jQuery Mobile on CrowdoMeter, but I think ScienceCard works really well on a small screen.
Continue reading
Two weeks ago Euan Adie from altmetric.com and myself launched the website CrowdoMeter, a crowdsourcing project that tries to classify tweets about scholarly articles using the Citation Typing Ontology (CiTO). Despite the holidays we have gotten off to a good start with currently 597 classifications by 56 different users, already covering 93% of the tweets we wanted to classify. We will discuss the results of this project at the ScienceOnline2012 conference in two weeks, but the most important findings can also be watched in real-time here.
Last Friday Gunther Eysenbach published a very interesting paper in the Journal of Medical Internet Research (JMIR):
Can Tweets Predict Citations? Metrics of Social Impact Based on Twitter and Correlation with Traditional Metrics of Scientific Impact
Version 1.0 of Annotum, the free WordPress theme for writing scholarly articles, was announced in late November. Back in June I wrote about the first public version of Annotum, but until now using Annotum was experimental. Annotum is available in the WordPress Themes Directory at WordPress.org (and has been downloaded more than 9,000 times in the past three weeks), and is also available for users of WordPress.com. I have installed Annotum 1.0 here, please drop me a note if you want an account.
But how is an Annotum blog different from a regular WordPress blog?
Annotum is a WordPress Theme
WordPress can be extended via Plugins and Themes. Whereas Plugins add functionality, themes usually change the look and feel of a WordPress site. Annotum is a theme that includes a lot of plugin functionality. This strategy makes it easier to get started with Annotum, as there is only one theme to install and not a set of plugins that has to work with a particular theme. Annotum can still be extended via child themes, e.g. if you want a different look for your blog. And of course you can still use other scholarly plugins.
Annotum uses articles and not posts
Annotum uses the custom post type article for scholarly content. This can be confusing in the beginning, but makes it easier to separate scholarly content from regular blog posts.
The Annotum editor knows about document structure
Scholarly articles have more structure than blog posts, and you can add this structure with the Annotum editor (see below). This structure is enforced, and the WordPress HTML editor is disabled. This makes it easier to create content that conforms to the NLM-DTD XML format.
Annotum can import and export in the NLM-DTD format
More specifically, Annotum supports the Kipling subset of the NLM Journal Publishing DTD. NLM-DTD is the standard XML format for scholarly articles, and you can for example import published articles (with a license that allows reuse) into Annotum to get started. Unfortunately there aren’t that many NLM-DTD tools for authors (I haven’t tested theMicrosoft Word Article Authoring Add-In with Annotum), but this is a great way to get content written somewhere else into Annotum.
Annotum knows that articles can have multiple authors
This is of course important for scholarly articles, and the Co-Authors Plus Plugin also adds this feature to any WordPress blog.
Annotum knows about tables, figures, equations and references
Scholarly articles have special formatting requirements for these content types, particularly references. Annotum adds visual editors for all of them. Annotum also has an editor for LaTeX equations.
Annotum currently does not integrate with reference managers (Endnote, Mendeley, Zotero, etc.) or other WordPress tools that insert citations into blog posts (e.g kcite or Link to Link), but you can look up references via DOI and PubMed ID.
Annotum knows about reviewers and editors
Annotum has a built-in review system that knows about authors, reviewers and editors. Annotum allows comments only visible to authors and reviewers, and sends out notification emails. The Edit Flow plugin provides similar functionality.
Annotum can export to PDF
Annotum automatically creates a PDF version of your article (using the dompdf HTML to PDF converter). Annotum also works with my ePub Export plugin, using this hack to display the ePub link next to the PDF link:
Summary
Annotum is a complete and free solution for starting a scholarly journal using WordPress. It has everything you need to write great scholarly content with WordPress and improves a regular WordPress blog in several important ways. Thanks to the support for the NLM-DTD format, Annotum can also be used as a writing tool for articles intended for submission somewhere else. One of the biggest strengths of WordPress is that it is really a writing platform that can be extended in many interesting ways. Maybe we will see WordPress plugins that enhance the equation editor or the reference management – or that connect Annotum to traditional journal submission systems.
Science bloggers will also be interested in many of the features of Annotum, but they don’t need the review workflow and might find that the support for NLM-DTD restricts them in how they can write content. Annotum is at version 1.0, and it is therefore not surprising that it still has a few rough edges. My biggest wish for a future version is better support for revisions and inline comments – Google Docs and other collaborative writing tools do a much better job highlighting the changes made in a text.
I’m very proud to report that ScienceCard last week has been named finalist in the Mendeley/PLoS API Binary Battle. Not bad for a project that started only two months ago in a hackathon following the Science Online London conference and is done in my spare time. The winners of the contest will be named on November 30, but I’m more than happy that the project has even gotten this far.
The idea of ScienceCard is threefold:
Registration with ScienceCard is easy. You create an account by logging in via Twitter (using the OAuth 2 protocol for the technically inclined), and then add your account name from one or more author identifier services. I added Google Scholar today, the other options are Microsoft Academic Search, AuthorClaim and Mendeley (I’m working on Scopus Author ID). If you add an Microsoft Academic Search or AuthorClaim identifier, ScienceCard will import all your publications from these services. ScienceCard currently only understands publications with a DOI, other scholarly items could be added in the future. With Mendeley and Google Scholar you only link to these services, I’m still having trouble with the Mendeley OAuth 1 authentication and Google Scholar doesn’t have an API.
ScienceCard is importing all the relevant bibliographic information using the CrossRef service. And ScienceCard is creating a shortDOI for all papers. But more interestingly, ScienceCard is calculating article-level metrics for all publications, and composite numbers for authors. For this ScienceCard is using the PLoS Article-Level Metrics API code, but I have added more sources, including Mendeley, Microsoft Academic Search and altmetric.com (but here only the number of blog posts citing a paper). ScienceCard links to most sources so that you can see the actual citations there, only CrossRef and altmetric.com don’t offer that. A future update will show all citations directly in ScienceCard.
ScienceCard tries to display a nice profile page for each researcher, but also makes it easy to reuse the information somewhere else. Each author page is available in six different formats, simply add the extension after the (Twitter) username, e.g. http://sciencecard.org/mfenner.json
JSON is the most interesting format, because it makes it very easy to connect two different services. If you for example want to use ScienceCard data on your personal WordPress blog you can simply download my Contact Info Options WordPress plugin, add your ScienceCard username in your WordPress settings and do some hacking of the author template. The process is unfortunately different for every WordPress theme, but you can see an example WordPress profile that uses the Annotum theme (and publishing platform) here:
This WordPress author profile is generated on the fly using ScienceCard data, and will therefore automatically update.
The ScienceCard project is still at the beginning, and there are enough ideas to move this project forward in interesting ways. I’m particularly interested in improving the user interface and display of information, in adding datasets and other scholarly content, and in integrating with the ORCID unique author identifier service once the service launches in spring 2012. If you are interested to learn more about ScienceCard, please contact me via email or Twitter, or attend the altmetrics session at ScienceOnline2012, which I will do together with Euan Adie from altmetric.com and PLoS Impact Explorer, and Jason Priem from Total Impact (two other Mendeley/PLoS API Binary Battle finalists).
BibTeX is one of the most popular file formats for bibliographies, and is therefore commonly used to transfer bibliographies from one reference manager to another, or to other applications that handle bibliographic references. RIS and Endnote XML are probably the other two bibliographic file formats most commonly used. Most reference managers support all three formats, making it easy to move references around.
All three formats have been around for a while, BibTeX for example since 1985. Reference management has of course gone through many changes during this time, and an important change will happen next year: unique identifiers for scholarly authors. In 2012 the Open Researcher & Contributor ID (ORCID) initiative will start issuing unique identifiers for researchers, and researchers, universities, funding organizations, publishers and hopefully everyone else will start using them. But ORCID will only be successful if as many bibliographic tools as possible can handle ORCID identifiers, and if these tools can exchange these author identifiers.
None of the three bibliographic file formats mentioned above can handle unique author identifiers. If we take for example this paper from ScienceCard, then the authors would look like this in BibTeX:
author = {Kirstein, Janine and Dougan, David and Gerth, Ulf and Hecker, Michael and Turgay, Kürşad}
And like this in RIS:
AU - Kirstein, Janine AU - Dougan, David AU - Gerth, Ulf AU - Hecker, Michael AU - Turgay, Kürşad
I suggest we extend the BibTeX format to understand author identifiers like this:
orcid = {1274643, 8474644, 847412, 9183414, 7461414}
And RIS:
AI - 1274643 AI - 8474644 AI - 847412 AI - 9183414 AI - 7461414
This would look similar in Endnote XML. Will we see these changes to BibTeX, RIS and Endnote XML in 2012? I don’t know, but I very much hope so. Imagine what your Zotero, Mendeley or Endnote could do if the application knew about unique author identifiers, e.g. find all papers by a particular author, alert me when a particular author publishes something new, or organize your reference library by author.
Last week I attended the Transforming Scholarly Communication workshop in Cambridge, Massachusetts. The main goal of the workshop was to come up with practical recommendations for the topics #resources #review #literature #media #recognition and #platforms:
This workshop strives to be different in one important way—rather than focusing on utopian visions for their own sake, we will focus on the existing and newly developed technologies designed to enhance scholarship and scholarly communication in order to determine factors for their success and their potential.
Reinventing Discovery, the book by Michael Nielsen we all have been waiting for, has finally been published on Friday. Today I flew to Boston for the Microsoft Research eScience Workshop: Transforming Scholarly Communication, and reading the book on the plane was the perfect preparation for the workshop.
Michael says in the book:
I wrote this book with the goal of lightning an almighty fire under the scientific community. … We have an opportunity to change the way knowledge is constructed.
You can download the chapter 1 as PDF, and you can also watch the videos of two of his recent presentations: TEDx Waterloo in March and Science Online London in September.
The book uses examples from science and related disciplines – e.g. programming or chess – to examine both the opportunities and challenges of doing Open Science. The book is good reading, because Michael is aware of the many challenges that we face before science can be done differently. One example for this is the peer-reviewed journal article as the main currency to evaluate researchers. Until scientists are also rewarded for producing or curating data, programming scientific software, etc., we will not be able to start a new era of networked science.
Highly recommended reading.
Timo Hannay has also written a review of the book for Nature Physics, and I’m sure we will soon see many more.
Reading List