Social filtering of scientific information – a view beyond Twitter

ResearchBlogging.org

It’s not information overload, it’s filter failure. (Clay Shirky)

Bonetta (2009) gave an excellent introduction to the micro-blogging service Twitter and its uses and limitations for scientific communication. We believe that other social networking tools merit a similar introduction, especially those that provide more effective filtering of scientifically relevant information than Twitter. We find that FriendFeed (already mentioned in the first online comment on the article, by Jo Badge) shares all of the features of Twitter but few of its limitations and provides many additional features valuable for scientists. Bonetta quotes Jonathan Weissman, a Howard Hughes Medical Institute investigator at the University of California, San Francisco: “I could see something similar to Twitter might be useful as a way for a group of scientists to share information. To ask questions like ‘Does anyone have a good antibody?’ ‘How much does everyone pay for oligos?’ ‘Does anyone have experience with this technique?'” It is precisely for such and many more purposes that scientists use FriendFeed, which allows the collection of many kinds of contributions, not just short text messages.

Also in contrast to Twitter, comments to each contribution are archived in that context (and without a time limit), providing a solid base for fruitful, threaded discussions. In your user profile, you can choose to aggregate any number of individual RSS or Atom feeds‘, including scientific publications you bookmark in your online reference manager (e.g. CiteULike or Connotea), your blog entries, social bookmarks (Google Reader, del.icio.us, etc.), and Tweets; and any other items you wish to post directly to your feed. You then look for other users whose profile is relevant to your work and subscribe to them. Every individual item posted in your subscriptions will then appear on your personalized FriendFeed homepage, plus optionally a configurable subset of the feeds you subscribed to. You can choose to bookmark (‘like‘) any of these items (Facebook copied this ‘like’ functionality just before it bought FriendFeed), comment on them, and share discussion threads in various ways.

At first, this aggregation of information and threaded discussions might seem daunting. However, the stream of information can be channeled by organizing it into separate sub-channels (‘lists’; similar to but more versatile than ‘folders’ in email), according to your personal preferences (e.g. one for search alerts). In addition to individual users, you can also subscribe to rooms that revolve around particular topics. For example, the “The Life Scientistsroom currently has 1,267 members and imports one feed.

The feature that makes FriendFeed truly useful is its social filtering system. Active discussions move to the top of your FriendFeed homepage with each new addition, which automatically brings them to the attention of you and everyone else who reads those feeds. In a sense, the most current and the most popular entries compete for attention at the top, making notifications unnecessary. This means that your choice of both rooms and subscriptions affects and filters the content you see. In that way, for instance, you could set your preferences such that you would only see papers with a certain minimum number of ‘likes’ among your colleagues. Alternatively, you can opt to hide items with zero likes or comments, ensuring that only those that someone found interesting will reach you. Thanks to a very fine-grained search functionality, threads also remain easily retrievable.

Some of the synergistic effects of the many scientists interacting on FriendFeed are already apparent at this early stage of adoption. FriendFeed provides a convenient way to microblog from conferences by means of dedicated threads or discussion rooms created for the event, thus allowing to share comments within and across sessions, or even with people not physically present at the meeting. Such conference coverage has even received direct (e.g. ISMB09 , BioSysBio09 ) or indirect (e.g. ISMB08 ) support from the conference organizers.

Above and beyond conference coverage, scientists use FriendFeed to share papers, experiences on laboratory equipment, resources for teaching, or anything else commonly asked at mailing lists. A number of real-world scientific collaborations have already been sparked from such interactions. Collaborative grant proposals have been initiated, submitted and some of them approved after the idea was passed around and discussed on FriendFeed. Several bioinformatics problems have been solved by code-sharing and advice. Articles in scientific journals have been published by FriendFeed users after meeting and discussing on the platform [1-5].

Of course, since FriendFeed was not designed for scientists, there is room for improvement in terms of usability for scientific purposes. For instance, files can only be uploaded upon starting a thread, not while commenting on it, and there is currently no functionality which infers a measure of reputation to a user from his/her contributions (though the wide-spread use of real names somewhat allows that to be imported). As with all online contributions, citability and long-term archiving are unresolved issues, as is the permanence of services whose source code is not public. Fortunately, the development of social networks tailored to the needs of scientists is actively being pursued from various angles. The Polymath projects , in which researchers collaborate online to solve mathematical problems, provide a number of examples. The recent award of two NIH grants of over $US10M each for exactly such purposes is another. Ultimately, the continued enthusiastic adoption of the sophisticated variants of social filtering tools by a broad community of researchers interested in sharing their science will only increase the usefulness for and thus the capabilities of the online scientific community.

References:

Bonetta, L. (2009). Should You Be Tweeting? Cell, 139 (3), 452-453 DOI: 10.1016/j.cell.2009.10.017


1 Lister, A., Charoensawan, V., De, S., James, K., Janga, S. C. C., Huppert, J.,   2009. Interfacing systems biology and synthetic biology. Genome biology. 10 (6), 309+. http://genomebiology.com/2009/10/6/309
2 Saunders N, Beltr‹o P, Jensen L, Jurczak D, Krause R, et al. (2009) Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Comput Biol 5(1): e1000263. http://dx.doi.org/10.1371/journal.pcbi.1000263
3 Neylon C, Wu S (2009) Article-Level Metrics and the Evolution of Scientific Impact. PLoS Biol 7(11): e1000242. http://dx.doi.org/10.1371/journal.pbio.1000242
4 Daub J, Gardner PP, Tate J, Ramskšld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A. (2008): The RNA WikiProject: community annotation of RNA families. RNA. 14(12):2462-4 http://dx.doi.org/10.1261/rna.1200508
5. Huss & al. The Gene Wiki: community intelligence applied to human gene annotation. http://dx.doi.org/10.1093/nar/gkp760

Acknowledgment: This comment has received input from a number of FriendFeed users, as detailed in this thread, and was jointly blogged today by Björn Brembs (FriendFeed; blog post), Allyson Lister (FriendFeed; this blog post) and Daniel Mietchen (FriendFeed; blog post).

Inspiring Science Autumn Newsletter

I’ve been meaning to link to this Autumn’s Inspiring Science newsletter, put out by Claire Willis and others at the Science Learning Centre North-East. Not only does it have interesting articles on the science outreach they’ve been involved with recently and what’s coming up in the near future, but it also has a short article on me and my partnered teacher, Louise, as part of the Teacher Scientist Network. Find more about the programme on the Inspiring Science website. Enjoy!

Science Commons provide a list of considerations for researchers looking to license their ontology

Back in March, I wrote a blog post about my experiences trying to find out a) if ontologies should be licensed, b) if ontologies could be licensed, and c) what sort of license would be appropriate. After all, it isn’t clear what sort of thing an ontology is: is it software, or is it a document, or is it something else completely? In this post, I included a response I had received from the nice folks over at Science Commons, giving their perspective on the situation.

Today, I came across a Science Commons blog post by Kaitlin Thaney announcing OWL 2. In it, she also mentions that Science Commons now have a Reading Room article on Ontology Copyright Licensing Considerations which is well worth a read. It updates the information contained in my March post, and provides some useful thoughts on how we should go about licensing ontologies. The section below was the part that particularly caught my eye:

For sharing ontologies in a community or publicly, it would be prudent to think about copyright and licensing. For example, the ontology creator could say that “to the extent I may have copyright in my ontology, I license it in the following way.” In that way, she can reassure the community that even in the event copyright is later found to exist, they may rely upon her offer of a license. This provides an important “safety net” for the community of users, given the uncertainty about whether a given ontology may be copyrightable.

The above section seems to be the biggest new point compared with their earlier statement. While they primarily recommend CC0, they do acknowledge that many researchers may wish to choose an attribution-based licences such as the CC Attribution license.

If you create ontologies, then you should read this article: it’s short, easy to understand, and gives you the information you need to make your own decisions.

Inspiring Science Autumn Newsletter

I recently attended an open day at the Science Learning Centre North-East (SLCNE) in my role as half of a Teacher Scientist Network (TSN) partnership. There Louise, my partnered teacher, and I gave a short presentation on how the TSN works, and more specifically about our efforts last year. I enjoyed talking about what a positive experience it was, and also enjoyed seeing the other initiatives (such as Science in the Spotlight and Scientists@Work) that the SLCNE manages.

As an extra bonus, the newsletter for this Centre for Autumn had an article on my TSN partnership with Louise (hence the categorization of this post into the “Self Reference” section). Not only can you read the interview with me and Louise, but you can also read about:

  • ‘Liquid Science’ in March 2010 at Newcastle’s Liquid and Diva Nightclub
  • How you can get funding from the Royal Society (up to £3000!) for “teachers and scientists or engineers to work together on creative investigations involving 5–16 year olds”. The funding goes straight to the school, and the closing date is November 6th. More information: www.royalsoc.ac.uk/education/partnership.htm.
  • Details on the 2009 SLCNE Christmas Lecture from Dr. Laura Grant. She’ll be giving a ‘Cool Science’ presentation “which looks at some of the strange things that happen at low temperatures. The lectures will be performed at four venues across the North East during the first week of December and are suitable for Year 6/7 pupils.” More information: www.slcne.org.uk/christmas.

I strongly encourage you all to join in with your local SLC or branch of TSN, and to have a look at this season’s newsletter!

Two Journal Special Issues: Big Data, and Semantic Mashups for Bioinformatics

Both of these special issues are worth a look, as some of the papers look pretty interesting. I'll spend a little time in a later post on any articles I find particularly relevant.

  • Semantic Mashup of Biomedical Data Special Issue of the Journal of Biomedical Informatics. This includes a review article by Carole Goble and Robert Stevens: State of the nation in data integration for bioinformatics
  • Nature's Big Data Sepcial Issue. The article entitled "How do your data grow?" was one of the many articles in this issue that I enjoyed. It's interesting to note that these problems in management and curation of big data are only now getting special attention in Nature. When I worked at the EBI, it was common knowledge among the database curators that 1) it would be very difficult for them to find other work as curators if they left the EBI, and 2) the time and high skill level it takes to annotate and curate biological database entries means that it is very difficult to get high coverage in such databases. It's nice to finally see some recognition of all the work the biocurators do by a journal such as Nature. Finally, there are high-profile articles stating that curation begins at home, with the researcher, and that curation needs much more support from researcher-level all the way up to the level of the database curators.

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Google Notebook and the Google Cloud in Bioinformatics

Ever since my friend Frank posted an article about how he has one foot in the internet "cloud", I have been a little worried about how much of my cloud is composed of Google apps. I currently have a Google cloud composed of Google Mail, Calendar, Reader, Docs, Groups, and most recently Notebook. It's convenient, the apps are useful, and it means I can access much of the information relevant to my work in bioinformatics wherever I am. I'm by no means a Google-only person (I use Vox rather than Blogger, for instance), and my set of a dozen or so "home" pages that I like to load whenever I open Firefox doesn't even have Google in a majority of tabs. But I can't help feeling slightly guilty and a little be worried about how dependent I've become on Google products. Then on top of that, I can't help feeling silly to be feeling guilty. It's my choice, after all!

So, moving past all that: today I've added Google Notebook to my cloud. I wanted to have somewhere where I could stash all those interesting papers that are sent to me each week via my personal tame searches on PubMed (aka MyNCBI: perform a regular search, click on "Save Search" and then ask email updates to be sent to you). I tried Connotea but never went and actually looked at it. I tried reading them when the emails arrived, but the time I have to read papers is never regular. So I deliberately had a look at the Google App list, and found Notebook. You can make notes on anything, but there is also a Firefox plugin that allows you to just highlight any portion of a web page you want and then place it directly in its own section of one of your notebooks. Further, Google Notebook is private unless you make it public. Here I can put all of my thoughts on these papers, whenever I have a minute to do it. Each clipping can be labelled, and comments can be added. The plugin is nice, but I've already made it break on one of the PubMed result pages. I suppose I'm talented?

Perhaps I'll finally get both the time to read all those interesting-sounding papers as well as have a single location that I'll actually visit. Only time will tell.

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More Neanderthal News: FOXP2 and language

I've got a lot of curiosity when it comes to history and the history of the human species, so stories that pop up about Neanderthals always arouse my interest. Previously I have posted about the great likelihood that humans and Neanderthals lived side by side for a couple thousand years in Europe, and just last week there was some new information about Neanderthals. As The Register reports, it turns out that their version of the FOXP2 (info, more info) gene matches the human version. The Reg had picked up on this information via an interview with Dr. Paabo in the New York Times on 18 October. Some take-home points:

  • This pushes the date back for the mutation of FOXP2 into its human form from up to 200,000 years ago (with 50,000 years ago being the best guess by many) to at least 350,000 years ago, or the time of the evolutionary split between humans and Neanderthals. This is Big News.
  • It could have been contamination with human DNA. Both articles go into this problem in some detail. There were a number of checks put into the work by Paabo et al, and hopefully these measures were enough to ensure that there was no contamination.

It could have also been – through some freak chance – convergent evolution, and the same mutation developed separately in the two species, however even though it is my own idea, I don't think there's much chance of this being right 🙂 Of course FOXP2 cannot be the only contributory factor to our facility for speech. However, it is interesting to see more information is coming out about it, and about our relationship to Neanderthals.

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