The first visualization looks at the results of a search for the words tuberculosis and treatment in the abstract. The PLOS Search API found 266 articles, and the most common words in the abstracts can be nicely summarized in a word cloud.

To better understand how well the PLOS Article-Level Metrics cover usage data, citations and the social web, I looked at the numbers for all 47,430 PLOS articles in the latest data dump from April (available here, using the API would not work for this).

This dataset of course also includes recently published articles. About 90% of the articles older than two years have been cited at least once.

Among the social web tools, Mendeley clearly has the best coverage of PLOS articles. We are of course also interested to find out how many Mendeley readers our articles have (whether it is 1 or 100), and a density plot is good way to show this. For this plot I used all PLOS Biology research articles from 2009.

Article-Level Metrics produces a lot of data, and this can be overwhelming. We therefore try to find patterns in the data. One interesting question is how HTML pageviews correlate with PDF downloads. One would assume that HTML pageviews correlate with readers taking a quick look at the abstract or specific information in the paper, whereas the PDF downloads correlate better with readers of the whole paper. For this analysis I looked at a fairly homogenous set of articles, the 181 research articles published by PLOS Biology in 2009.

This is a very nice correlation, and the outliers also tell an interesting story – the paper with 5000 PDF downloads for example is also the most highly-cited in this set of articles.

Article-Level Metrics only make sense in context, and the most important ones are probably article age, subject area and journal. Article age (as days since publication) can be plotted on the x axis, and bubble charts allow visualization of two quantitative parameters (total views and CrossRef citations in this case). For this visualization we look at a set of articles funded by the European Union 7th Framework Programme. They were picked up by a search for fp7 in the financial disclosure section. This is of course only a first step to find every FP7-funded paper, and we are working with the EU OpenAIRE project on a more complete search strategy.

There are probably a bit too many bubbles on the chart, but you can clearly see how papers grow from tiny dots at the far lower left to nice big bubbles as they become older.

Although it is possible to add information about individual papers to bubble charts (e.g. using the Google Visualisation API), it sometimes is helpful to see all paper titles at once. Dot charts are one way to provide this information, and this of course only works for a smaller number of papers.

Not surpringly most people seem to be interested in how to publish and how to present your research. I wouldn’t have thought that the article about Wikipedia is so popular.

Dot charts are limited in the number of categories you can display at once. Heatmaps are better for a more complete analysis. They provide context by comparing the metrics for an article to other other articles in the same set. Darker colors mean higher numbers and the articles are sorted by age (oldest papers at the bottom). Twitter (the rightmost column) was only recently added as ALM source and we can’t retrieve older tweets in retrospect.

The heatmap shows that the different ALM not necessarily correlate with each other (with the exception of the different citation metrics).

A variation is the calendar heatmap which looks at ALM events on a calendar. We can do this only for sources that provide dates for every single event (currently only CiteULike and Twitter), and I want to focus on Twitter, looking at all PLOS papers published in 2012 (125 as of today) with an author from Stanford University.

Remember that PLOS started collecting tweets in May. You can clearly see that July 6 was a busy day, and this is because of all the tweets about a paper published the day before.

This work would not have been possible without the help from Najko Jahn, Jochen Schirrwagen and Harr Dimitropoulos from the OpenAIRE project, and Scott Chamberlain from the rOpenSci project. All calls to the PLOS APIs were made with the rOpenSci rplos library.

A lot of this is obviously work in progress. Feel free to make suggestions in the comments, in the PLOS API Developers Google Group, via the @PLOSALM Twitter account, or in the plosOpenR Github repository.

The release of ALM 2.0 also includes a few changes to the API, and starting July 31, requests to the PLoS ALM API at http://alm.plos.org have to use the new API format. We have documented the changes in PLoS ALM 2.0 API Changes and at https://github.com/articlemetrics/alm/wiki/API. Please ask any questions you might have in the PLoS API Developers Google Group at https://groups.google.com/forum/?fromgroups#!forum/plos-api-developers.

Grand prize

openSNP
Share your personal genome from 23andMe or deCODEme to find the latest relevant research and let scientists discover new genetic associations. “The APIs of Mendeley and PLoS and all submissions in the Binary Battle have shown how creative people can re-use the data APIs in many ways.” Bastian Greshake at openSNP.

Runner up

PaperCritic
Post-publication peer review in an open environment. Rate papers, write critical reviews or read those from others.

Extra prize
rOpenSci

R-based tools to facilitate Open Science; including R packages for both Mendeley and PLoS.

Finalists

Collabgraph

Visualize who is collaborating in your research field with data from your Mendeley library or BibTeX file.
Collabgraph

Droideley
Read your Mendeley library on the go with this client for Android mobiles.
Droideley

KLEENK

Make “smart” connections between articles, books and any other research object and learn from connections made by other researchers.
KLEENK

PLoS Impact Explorer
See which research is getting the most buzz online from news outlets, blogs, Twitter and elsewhere, all in one place.
PLoS Impact Explorer

ReaderMeter
Research impact is now crowd sourced. Future impact of research is estimated using real-time bookmarking aggregated from Mendeley.
ReaderMeter

ScienceCard
Discover all of the citations, bookmarks and other points of impact for all of your publications or personal library.
ScienceCard

TiNYARM
Share and keep track of what you read on your mobile device then watch the leader board to see who is on top.
TiNYARM

Total-Impact
Get a broad picture of the true impact of what you’re reading with data aggregated from many sources.
Total-Impact

Just eight days after announcing our call for App ideas, we received over 70 top-rate suggestions for scientific and medical apps from our community. Many addressed issues already important to PLoS—post-publication peer review and contextualizing and filtering research for a variety of disciplines. Others submitted ideas that were just plain cool but outside of the scope of the Binary Battle competition.

Now we are passing these ideas along to members of the developer community, who have the coding skills to bring them to life.

Below, we have broken these ideas into two groups:

• Ideas that can use the PLoS or Mendeley APIs and can be entered into the Binary Battle competition
• Cool ideas that don’t use the PLoS or Mendeley APIs (and are therefore outside of the scope of this competition) but you might want to tinker with anyway.

Selected Binary Battle-eligible ideas include:

• An app for displaying the impact of diverse research outputs on your CV or website. For example, how many blogs have written about your paper, how often have your datasets been mentioned in scientific lit, etc. An existing app that does just that, called Total Impact but it needs to be taken from prototype to full-fledged app. More info here and here. Suggested by Heather Piwowar: hpiwowar(at)gmail(dot)com or total-impact(at)googlegroups(dot)com
• Create an easily embeddable, dynamically-updating list of PLoS or Mendeley papers from a particular lab or institution that researchers can put on their websites. Suggested by Sébastien M. Crouze:  seb(dot)crouzet(at)gmail(dot)com
• From a bunch of papers, recursively extract all the references they contain and establish a ranking of the most cited papers. It will help to found “must read” papers from a certain website, subject area, author(s), or institutions. Suggested by anonymous.
• Search papers in Mendeley or PLoS based on geography or genes. Suggested by Sjurdur Hammer:  sjurdur(at)hotmail(dot)com and anonymous, respectively
• A tool that will automatically export illustrations and figures (as well as their attributions and CC licenses) from PLoS papers to the Wikimedia Commons. Suggested by anonymous.
• More ideas here

Other cool ideas

• A searchable directory that could collate grant/funding opportunities from across all Federal, State and Foundation entities that are currently silo-ed into individual, closed databases on individual websites. This master databank should then be sortable by field, interest area, investigators (e.g. young investigators, tenure-track faculty, postdoc, etc.), funding amount, etc. Suggested by Llewellyn Cox, PhD:  llewellc(at)usc(dot)edu
• A citizen science measurement app (like NYC Cricket Crawl) via GPS, photo, video, audio recording that sends data in standardized format. Suggested by mik3cap.
• An app for identifying bat species from the sounds they make. You would hold up the smartphone and it would record a sound and then give you a species identification on the phone. Suggested by Dr. Kate Jones: kate(dot)jones(at)ioz(dot)ac(dot)uk
• An educational App which finds the most recent common ancestor between any two species on the planet. Suggested by aulridgejr(at)gmail(dot)com
• More ideas here

To sign up to develop an idea or request an API key from PLoS, fill out this form. We encourage you to work with other devs who share an interest in the idea you choose, and also to contact the scientist who conceived of the idea, should you seek more input or wish to invite them to collaborate.

Finished apps for the Binary Battle competition must be received by September 30^th. Tim O’Reilly looks forward to seeing your creations – happy coding!

Data that can be retrieved from the PLoS Article-Level Metrics API for every PLoS article include:

• Usage statistics for HTML page views, PDF downloads and XML downloads for each article from the Public Library of Scienceand PubMed Central websites.
• Citation counts from PubMed Central, CrossRef, Scopus.
• Number of times an article has been bookmarked at CiteULike.
• Number of blog posts mentioning an article in Nature Blogs.

For more information, see the Article-Level Metrics API and Using the Article-Level Metrics API.

http://api.plos.org/search-examples/schema.xml

• How your app will make science more open
• Your project name
• Your operating system
• Your affiliation
• Why your entry deserves to be selected for a NephoScale Cloud Server.

Here’s what Bruce Templeton, CEO of NephoScale, said about why they are supporting this contest:

“we want to remove any barriers to entry in this API contest so that developers, some of who may be working in academia, can get creative and build apps that make science more open”.

The prizes include:

• Grand prize: $10001 + $1000 Amazon Web Services credits
• Second prize: $5000 + $500 Amazon Web Services credits
• $1000 plus a Parrott AR Drone Quadricopter to the best combined PLoS/Mendeley app.

Since Mendeley got this competition up and running before PLoS joined the party, you can see what some people have already made using the Mendeley API. Mendeley is also organizing two simultaneous Hackathons at their NY and London offices on Saturday June 11-Sunday June 12, 2011.

The last day to submit your app is September 30th, 2011 and the winner will be announced on November 30th, 2011.

For more information see:
http://dev.mendeley.com/api-binary-battle/