There’s an interesting piece in the most recent issue of Nature.  Corie Lok discusses how researchers are dealing with the information firehose that is scientific literature.  How big is that firehose?

The 19 million citations and abstracts covered by the US National Library of Medicine’s PubMed search engine include nearly 830,000 articles published in 2009, up from some 814,000 in 2008 and around 772,000 in 2007. That growth rate shows no signs of abating, especially as emerging countries such as China and Brazil continue to ratchet up their research.

With that amount of data overload, how is an established researcher going to keep up with relevant work in their field? Nevermind how a new investigator can get a handle on establishing a research focus, or a midcareer scientist switch tracks.  That’s where literature mining comes in.  There are several start-up services on the web to help scientists find relevant research, make connections, and generate hypotheses. A few of these are discussed in Lok’s article, but there are many others.

PubMed – My default search engine for research papers, this is the first stop for many scientists.  So let’s try a little experiment.  Searching “alcoholism” generates the following – Results: 1 to 20 of 66827. PubMed does have tools to help you narrow your search.  Say I’m interested in the genetics of alcoholism. Searching “alcoholism genetics” returns – Results: 1 to 20 of 5940. A lot of research to go through. Restricting that search to only publications in the last 5 years, in English, and about humans gives Results: 1 to 20 of 1283. Still a lot of literature, even if you’re only reading the abstracts.

That’s where literature mining can really make a difference.

Scientific Literature Mining Services

• pubget – One of the most time consuming tasks in research is going through the literature and trying to stay current. Add to that most institution’s clunky access to online resources, and the process can be painfully slow.  I can search for articles from my library homepage, but have to go through several extra steps to actually get my hands on the pdf. The “find full text” function in the newest version of EndNote has been a tremendous help in accessing content, but for those researchers at institutions that don’t provide that service (and even those that do but want an additional resource), pubget is a handy tool.  When you create an account, pubget signs in to your institution and allows you to search the subscribed resources. When you find a reference you want, just click the pdf icon and there it is. No clicking through to content provider websites. You can tag references as “keepers” to come back to them later, or search for the newest articles from a particular journal. Unfortunately, it doesn’t allow you to annotate the pdfs. Not yet anyway.

Click here to view the embedded video.

• GoPubMed – A search engine where “your keywords are submitted to PubMed and the resulting abstracts are classified using Gene Ontology and Medical Subject Headings (MeSH).” So using our example search “alcoholism genetics” pulls 5,940 abstracts from PubMed. What’s different about GoPubMed’s results is the navigation panel.

GoPubMed top terms

You can click the check boxes next to the relevant terms. Restricting the search to “genetic predisposition to disease” gives 720 references. Under the Knowledge Base > Named Groups category, you could restrict it further to only studies using adult subjects, or to exclude studies in children. GoPubMed provides additional information on your search topic as well, including top authors (who’s doing the research) and top journals (who’s publishing the research). There’s even a network of top authors, so you can see how they collaborate on your search topic.

Author network for genetic predisposition to alcoholism.

Philanthropologist might recognize a name toward the top of that network. A useful tool for finding potential collaborators.

• NextBio – A freemium service (basic is free, pro is subscription) that allows researchers to set up a profile, but also has a database for lit mining.  Searching for “alcoholism” in NextBio brings up several relevant sources, including associated genes, literature, researchers, news, even clinical trials.
  

  NextBio genes associated with alcoholism

• EbiMed – analyzes PubMed results “to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species.” Searching “alcoholism” here turns up a table of links to various sources, including proteins, genes, and biological processes related to the search term.
• PubGene – specifically for finding genes, PubGene draws a network of genes associated with a particular keyword.
  

  PubGene network for alcoholism

This network is searchable. Clicking on a gene allows you to browse the literature associated with that gene, in addition to highlighting associations with other genes.  As a geneticist, this tool has considerable utility.

• PubAnatomy – “integrates [the] Allen Brain Atlas gene expression data, relationships between brain regions and diseases for more efficient exploration of Medline database and gene expression data.” A keyword search for “alcoholism” lights up regions on the brain map associated with the disease.

PubAnatomy brain map

And clicking one of those highlighted regions displays the relevant references for that brain structure, as well as genes that are active in that region.

• Neuroscience Information Framework – “An initiative of the NIH Blueprint for Neuroscience Research, the Neuroscience Information Framework advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.” This tool can search the full text of articles (at least those that are open source), rather than just the abstract. But it does much more.

Second from the bottom, NIF diplays grants related to your search. You can read the abstract, see who is doing research on your topic, and which granting agencies are funding that research. Useful info when preparing your own proposals.

All of these tools help scientists sip from that firehose, giving different ways to access and interact with the data. What an exciting time to be starting a career in science.

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Lok, C. (2010). Literature mining: Speed reading Nature, 463 (7280), 416-418 DOI: 10.1038/463416a

I’ve had this post percolating in draft form for a while, as I come across more web-based resources for scientists.  Yesterday, I saw an article in Cell by Laura Bonetta titled “Should You be Tweeting?”  (OK, I downloaded the pdf of the article from my university library.  I haven’t touched a physical journal, except the ones I receive as part of my membership in professional societies, in years.)  Bonetta discusses how scientists are using the 140 character social networking site, and it’s limitations. Some tweet links to new research, while others feel it provides insufficient space for scientific conversation.

I’ve been torn about tweeting. My hubby, the computer geek, got an account a couple of years ago but rarely uses it.  He gets a real thrill out of trying new technologies, whereas I prefer to understand their utility before signing up.  Twitter, in particular, seemed like so much navel-gazing to me, especially with all the celebrity accounts.

There have been several web services launched in the last few years aimed specifically at the science community, however. I’ve experimented with some of them, and wanted to provide links to these resources for others.

Social Networking for Scientists:

• Graduate Junction – Billed as “The Academic Network for all early career researchers”, Graduate Junction is geared toward graduate level and postdoctoral academics.  Users create a profile, basically an online CV, covering all relevant academic experience. You can search for others with similar interests and create “research links,” your virtual research network, connecting you with potential collaborators around the world.  There are groups organized around various topics, like bioinformatics and evolutionary genetics. The site also has advice forums covering topics from writing your thesis and work/life balance to giving talks and postgraduate jobs.  They are also sponsoring an online poster competition, and are developing a searchable conference database.  Overall, a nice resource for those beginning a career in research. Registration required but free.
• ResearchGate – The “leading professional network for scientists.” Like Graduate Junction, users have a profile, there are groups, and the ability to network with other researchers.  But ResearchGate goes a step further, allowing self-archiving of your publications and providing abstract search functionality, so others can read about your research and you can search for connections via their published work. The abstract search could also be used to do a lit review, with a “literature pool [that provides] access to publication metadata of more than 35,000,000 documents of many different institutes and universities.” In addition, ResearchGate has a global job search.  There is lots of potential for connecting with relevant researchers in your field, with 200,000 members and growing. Registration required but free.
• Labmeeting – Allows users to organize, collect and share publications and also has a lab management feature. You can create a paper collection, upload EndNote libraries and pdfs, and set alerts to be notified about relevant papers.  The uploading pdfs feature is really nice, because labmeeting can match your pdfs to the correct reference in PubMed, eliminating the need for entering citations manually. In the lab management section, you can schedule events and share protocols in the group notebook. Users also have a profile and the ability to network with colleagues. When I signed up a couple of years ago, a .edu email address was required.  They’ve since restricted membership, so you have to request an invitation, be a member of one of their chosen institutions, or pay a yearly subscription fee ($99).
• MySciNet – Hosted by the AAAS as part of the Science Careers website, “MySciNet is a place for scientists and students from diverse backgrounds to network and build the personal and professional connections needed to succeed in the sciences.” Again, users can set up a profile and join groups (like Women in Science) that fit their interests. What distinguishes MySciNet from the other social networking sites is that it provides practical, relevant advice on how to succeed as a researcher. With articles on how to write a good personal statement, returning to science, and maximizing your mentoring, MySciNet is a valuable resource for navigating the science career path. Registration required but free.
• BioCrowd – BioCrowd is “social network designed exclusively for bioscience professionals.” Described as a cross between Facebook and LinkedIn, which may explain my aversion. It appears to be a pure social networking site/job search site, and may be geared more towards those in industry.  If it’s similar to LinkedIn, I’d be worried about being hounded by headhunters.  They do have a podcast detailing the development of BioCrowd, so I’ll reserve judgment until I give it a listen. Registration required but free.
• CiteULike – Sponsored by Springer, an academic journal publisher, CiteULike is a social reference management website. There’s a basic profile section, groups and connections (your network). You can upload your EndNote libraries and personal pdfs, create watchlists on various topics, and the coolest feature, get recommendations on new articles based on those already in your library. I’ve only been using CiteULike for a few months, but I like it for aggregating articles on my to-be-read list. I have several TOC subscriptions to various journals, and I can click on interesting articles in my email and post them to my CiteULike library for future reading. Registration required but free.
• Mendeley – Similar to CiteULike, Mendeley is a reference manager. It has a web-based interface, along with a desktop client (free download – available for all major platforms, including Linux), making it an EndNote competitor. Mendeley is compatible with both EndNote and CiteULike, so you can easily import your references from these sources.  You can also search journal publishers and other sites directly, and then import interesting articles using the Mendeley bookmarklet. In the desktop client, you can drag and drop your pdfs and Mendeley will automatically extract the citation information. You can read and annotate references in the included pdf viewer. Mendeley also has networking capability, so you can create a research profile, connect with colleagues, and share your annotated articles. There’s also a research trends section, where you can see the articles most viewed by Mendeley users, statistics for publications in your library, as well as your own articles. Registration required but free.
• Connotea – Another online reference manager, geared specifically for scientists and clinicians. The social networking aspects are primitive; the profile page is a text box. References are shared via email links to specific collections in your library. Not crazy about this one, because others are doing it better. Registration required but free.
• Academia.edu – Looks like a Facebook for academics, several members of my graduate department have a presence here. Registration required but free.
• Nature Network – Another Facebook clone, with blogging and discussion forums. Sponsored by Nature. Registration required but free.
• SciLink – I’d actually forgotten that I had an account here, which shows how much I use it.  What I like about it is it generates a network for you based on your publications. Registration required but free.
• ResearcherID – “A Global Community Where Researchers Connect” run by Thompson Reuters, ResearcherID provides scientists with a profile and list of their publications. “With a unique identifier assigned to each author in ResearcherID, you can eliminate author misidentification and view an author’s citation metrics instantly.” It was easier for me to track down all of my citations here, including conference abstracts, and they also provide metrics to measure your impact factor. Registration required but free.
• Epernicus – Another science networking site that I just learned about today, although Richard Dawkins is a member.  Adding publications was fiddly, but there appear to be lots of people from my graduate institution here. Registration required but free.
• ResearchBlogging – You might have noticed the little icon in the last post. As part of my goal to get back to blogging about interesting science, I registered Freethinker’s with ResearchBlogging. Sponsored by SEED, the site aggregates posts on peer-reviewed research which meet their criteria.  It’s a great way to see some of the best work in the science blogging community.

Quite a list, and by no means exhaustive (I left out Laboratree, as I haven’t used it, and it’s primarily a lab management tool). And yet none of these services do everything a researcher would want or find useful. I really don’t think Twitter fills a niche here, except for pointing out interesting articles. I think CiteULike’s recommendation algorithm may be better for that.  Just being a professional Facebook clone isn’t enough, as this wiki details.  The ability to track, import and share publications is critical to collaboration.  Lab management is a nice feature for bench scientists. The threaded conversations and collaboration potential of Google Wave also present network possibilities to researchers.

I’m curious what other scientists think of these online tools.  Do you use them?  Which ones?  Are there particular services you avoid? If so, why?  What would your ideal Science 2.0 experience be?

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Bonetta L (2009). Should you be tweeting? Cell, 139 (3), 452-3 PMID: 19879830