After a few months of private testing, Mendeley announced the public release of their open API. This will allow developers and researchers to build applications and data analysis on top of a massive database of human-annotated scientific references.

We are excited to see our friends at Mendeley push forward on the open science front by making their database accessible to third parties and I look forward to seeing what developers will build on top of this data goldmine. In the meantime, check out the Mendeley Developer Portal or follow the dedicated twitter account for updates.

Imagine a world where real-time search is the norm. You will get just the information you seek landing on your lap the exact minute it becomes available, without you having to explicitly search for it. Will this change the way you do science? SciSurfer thinks it will.

The release cycle of scientific knowledge is slow. It may take up to 2 years for a paper to get accepted in a journal. The publishing process in itself will add a buffer of a few months (arguably because of the time cost of having a paper edition, even though most people will never use it). So, for some of us, it doesn’t feel like we are missing much if we do not get the latest updates on our field the very same minute they are published. Just going to conferences yearly feels like more than enough. But there is a portion of the academia that needs constant updates on their field, as close to real-time as possible. If you are in the life sciences, getting the latest paper about a molecule or a gene you work on before your competitor does may make or break your career.

For those academics, sciSurfer may be a very valuable tool. The basic idea of sciSurfer is to integrate all journal feeds and search over them. Note that they do not archive RSS, so only the latest articles are available. This is a different way to think about search, closer to twitter’s than to Google’s.

In use

If you are used to RSS feed readers, the interface will look familiar. Left side there’s a list of journals and searches. Every time there’s a new unread item the containing ‘folder’ turns bold. On the right side there’s a list of articles (title, authors, and abstract). The journal it comes from is shown in green. The interface resembles Google reader (in fact, sciSurfer is built on app engine, so it may share code with reader).

What is the advantage of scisurfer over simply subscribing to the RSS feed of the journals? Search. Scisurfer does searches over all the journals they are indexing. This is pretty impressive, because I don’t know of any search engine that works on RSS feeds. Using an RSS reader, the equivalent to scisurfer would be to subscribe to the RSS of all journals, and apply searches over those. This is beyond the capabilities of most destop RSS readers. Implementing search by author, abstract, etc is also beyond the feature set of a normal RSS reader. In fact, it’s not that easy to deal with author names. We all have had the experience of getting papers by people with the same lastname and initials as our intended query term that are NOT the person we are looking for. Thomson Reuters has a solution: researcher ID. Researcher ID is based on the simple idea that each individual would get a unique identification (ID) number acting as a digital “calling card” that the researcher can place anywhere, such as a personal home page, a CV, or a university page. It has been out for more than two years now, so it’s still too early to say whether it has been adopted successfully.

Apart from the reader, there are two other tools, news and journals. Searching journals by name integrates the RSS feeds of otherwise disperse journals. Still, I haven’t found a good use for this tool.

Navigating trends

The main use I can think of for sciSurfer is monitoring Trending topics. We are getting used to explosions in popularity thanks to twitter and Facebook updates. Good twitter clients show you ‘what’s hot’ together with an explanation on why. Even Mendeley is getting status updates these days, making it look more and more like ‘facebook for scientists’.

There are several things to like about sciSurfer.  It integrates with your Google account, so it’s one less login to remember. The devs show that they are on top of things and the result is a fast turnaround when I requested changes. They are very open about feature requests. In my experience, when a journal was not in sciSurfer’s list, the devs added it within hours.

But by far the best result of using sciSurfer is that it makes you aware of what is going on in your field in a way that feels different and pleasant. The most similar feeling that I got online is when I found a neat Phd. student tagging articles in citeUlike that are relevant for me (it’s like finding a gold mine).

Mendeley uses a similar real-time approach in their statistics. For example, they show what are the most read papers per discipline at a given point in time.

I’m not sure one can do searches according to popularity just yet on any of these tools, implementing a real-time soft peer review.

How does sciSurfer plan to make money? The free tool is limited to ten saved searches. They will charge for extra functionality. There’s an iPhone version coming, which may well be another source of funds.

Conclusion

As the number of publications grows, it becomes more and more difficult to follow the latest scientific trends. The approach that sciSurfer takes is that if you know your keywords then it should be trivial to filter the fire hose of information, by doing a trivial keyword match. While keyword match could go a long way, I’m skeptical that the future of search lies in dumb matching. The way I currently filter information is very social, that is, I’m surrounded by people I respect and I ‘feel’ what they believe is good research. If I’m like most researchers, then social filtering would be a natural fit. However, I rarely get value from social networks online (science-wise; no matter how hard social networks try to capture my attention!). It may well be that to form a reputation, scientists need to do far more than posting interesting updates in their microblogging feeds. And for us to follow their recommendations…

I’m not sure how big of a problem selecting classes is for students, and how much it can be automated, but now there’s a tool specifically solving this problem. CourseRank tracks scheduling conflicts, together with some other Interesting features. For example, it gathers course/professor reviews, workload estimations and aggregates questions and answers.

Right now the selection of universities is not that great. It makes sense since the service is specifically tailored to each university, so I can imagine the implementation can take a while.

Springer announced last week the launch of LaTeXSearch.com, a free online service allowing users to search a huge database of LaTeX snippets from Springer journals and publications. This follows the launch of a similar service, a few months ago exposing Springer’s database of scientific images (which suggests a precise strategy on how to build Web services on top of content in their publication database).

LaTeXSearch does what it promises, using similarity algorithms “to normalize and compare LaTeX strings so that, if similar equations are written slightly differently, the outputs are normalized and matched, granting you the broadest possible results set”. The only glitch is that snippets are not cached but generated on the fly, with the annoying result that it can take quite some time to display the rendered version of LaTeX formulas in search results.

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.

Wolfram Alpha, the brainchild of Stephen Wolfram (who allegedly put its company to work on this project for several years before its official launch in May this year), has been out for a while now and is probably no more making the headlines. The long list of examples on the frontpage, organised visually or by topic, proudly shows off what Alpha is capable of. The natural language interface may still be a bit sloppy and some data may be flagrantly missing (how about a dump of the world’s scientific literature, Stephen?), but all in all it manages to live up to the promise of a universal tool to compute an impressive amount of factual knowledge. Alpha allows you, among other things, to:

• plot the sky above your head tonight at 3am
• look up your genome for occurrences of a specific sequence
• compare current unemployment rates for countries you would like to move to
• display the taxonomic tree of your favourite bug
• spell boredom in Morse
• disclose the Answer to Life, the Universe, and Everything
• you can even check your body mass! (am I really 3kg away from my ideal weight?)

Depending on your field of expertise, Alpha is likely to provide a powerful combination of computational tools and relevant data sources to calculate virtually anything you might want to know about the universe.

Apart from technical use, though, I am curious to understand whether and how people will start using Alpha as a productivity tool and integrate it in their daily workflow.

Granted, the title of this post may be overstated, as I am sure there are better ways to use Alpha to work less and live happy. Here’s my take of the 10 best productivity tips I was able to find out, please prove me wrong with better examples and I will add them to the list below.

1. Word count for humans

How often have you tried to figure out how many pages or words make 7,000 characters? Alpha can help you out, even if you speak German.

2. Convert any character

Type a character (e.g. ∞) and quickly look up its corresponding Unicode, HTML, TeX or Mathematica representation. You can obviously do a reverse lookup as well.

3. Look up URL information

You can display a nice summary of information on site ownership (from WHOIS), popularity (from Alexa) and HTML structure for any given URL.

4. Find English words matching a specific pattern

No more tip-of-the-tongue frustrations! OK, I have to think of an actual use for this one but I am sure that the poets among us will appreciate.

5. Calculate time differences

Ever wondered how much hours are left before light comes through your friend’s window in Tokyo?

6. What’s in a word

Definitions, synonyms, antonyms, word frequency, pronunciation (AmE only though…), hy–phen–a–tion patterns for any word in the English language. I even discovered that “hack” and “adulteress” are neighbours in a synonym network.

7. Where am I?

Check your current network name and IP address.

8. Tame nutritional values

If you desperately need to know how much iron is in your spinach salad or how many calories your breakfast is worth, Alpha has answers for you.

9. Convert currency

Enjoy watching how your purchasing power in Europe kept falling indefinitely over the last months, before showing some timid sign of recovery.

10. Estimate download times

Stay zen when you know that it will take slightly more than one day to download those 90GB with your 7.5Mb/s broadband connection.

Even more ideas

There are plenty of tools and Web services to do most of the above searches, but it’s nice to be able to query anything from a single search field. I obviously can’t wait for the day when the full power of Alpha will be unleashed via its API so as to be mashed with external data sources and applications, or integrated as a clever QuickSilver plugin to put the world’s knowledge at the tip of your fingers. Unfortunately it will take some time before this happens.

In the meantime, if you are looking for inspiration, you can browse the Wolfram Alpha community page: it’s a goldmine of ideas (and a good source of information on some ridiculous flaws and limitations in Alpha).

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

Sciplore has produced an interesting hybrid between a mind mapping and reference management tool. Freemind Scholar adds two basic features over the excellent Freemind: you can have references (at this time, only bibTeX) inserted, and you can drag and drop hig hlights on pdfs (the pdf is linked).

This looks like the perfect IDE for sketching notes while reading papers. I use oneNote for this, but I’ve tried mind maps before and could easily revert to it.

As soon as they implement zotero/endnote references, I can imagine many people finding this tool very useful.

Freemind Scholar is in alpha right now. Feel free to try it out and send them your comments, chances are they will implement your feature requests since they are just starting.

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.