SciCurve: revealing life science’s curves

Screen Shot 2014-09-25 at 11.00.18 AMAfter the recent launch of Sciencescape, here is  another startup pledging to help us cope with the enormous amount of data and literature at our disposal. SciCurve uses PubMed‘s library of 23 million references to generate visually pleasing graphs and curves that helps you grasp trends in literature.  It comes with three main functionalities

Observing trends for your field of study.

For academic researchers, knowing about the publication trends in a field is fundamental when writing a review or a grant proposal. Is this field new? Has is been prolific in the 70s and is coming back? Or is it the latest hot field and is in exponential growth? SciCurve saves you the trouble of going through PubMed results and manually copy/pasting the number of search results. Simply enter one or more keyword and it will display a timeline of the number of publications and citation counts over the past 14 years.

Her's an exemple of teh trend function, showing an increasing number of publication since 2000, which is followed with an exponentially increasing number of citations.

The number of publications and citations for the keyword “biomaterials”. The raising  publication count since 2000 is followed by an increase in the number of citations.

 Exploring research networks.

One particularly challenging task when exploring the literature, is to quickly find the key papers, on which most of the field is based. Manually going through papers and tracing back the original work is time-consuming, and the large amount of information gathered could end up be confusing. SciCurve helps you analyse the literature automatically and helps you understand its findings by generating representations of how paper are interconnected.

The network tab displays a map of the network of publications based on citation relationships. Important papers tend to form nodes from which radiates the papers citing that work. Key papers, and the articles citing them can then easily be identified.

Example of a networks graph, with Biomaterials as a keyword.

Example of a network graph, with “biomaterials” as a keyword.

Second, the map function places on a map top papers of the field represented by circles of size proportional to their relevance. SciCurve clusters similar papers together, naturally point-out relevant sub-fields. This is particularly useful to understand what a field might entail.

Example of a map view with the keyword "Biomaterials" Clusters form show that sub-categories such as collagen, surface and engineering are prominent.

Example of a map view with the keyword “biomaterials”. Clusters reveals  sub-fields such as collagen, surface and engineering.

Finding who drives the scientific endeavour?

SciCurve also automatically generates author profile pages, including a map of their most frequent co-authors and a list of their publication. Wondering who are the most prolific authors in your field? SciCurve can identify the key authors in a particular field and map them out as a function of their publication record.

A map of the most published authors in the field of biomaterials

A map of the most published authors in the field of biomaterials

The graphs and maps, but not the raw data, can be downloaded in the free version of SciCurve. An enterprise version, with more advanced functionalities is offered for a fee. SciCurve also supports Zotero and Mendeley integration which allows you to easily export  references to your favorite citation management tools.

Beyond a rather obvious usefulness for academics and R&D scientists, this sort of tool could be interesting for general practitioners and other medical specialists that do not have the time to grasp the latest trends in medical research. Publishers and research databases could also use this approach to improve their search engines by providing a more data-rich and more visual experience to their users.

A look at Pubmed’s new commenting platform

Screen Shot 2013-11-04 at 10.00.50 AMPubmed is implementing a new function that enables researchers to share their thoughts about scientific publications. By allowing readers to comment and debate about specific papers publicly,  PubMed Commons is trying to extend the peer-review of manuscripts after their publication. If successful, PubMed Commons will become a platform for scientific discussions that could foster constructive criticism and eventually improve published papers and science. The service is currently in its pilot version which is restricted to recipients of NIH or Wellcome Trust funding. But I’ve put together a couple of screeenshots to give you a quick look at this interesting new feature.

Nothing much has changed from the familiar Pubmed abstract page. But notice that at the bottom of the page, a new “Reader Comments” section has appeared. Comments can be directly typed in the text box.

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Although comments of any length can be posted, it is recommended to keep it short and clear. Simple formatting options are offered, but need to be written as code in the text box.

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For example, links to other articles can be added by including the PMID number.  A direct link with author and year appears when published.

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All contributions are published under the Creative Commons Attribution 3.0 License and can be edited or deleted after publications. The comments are assigned a unique and permanent link so that they can be easily referred to. It is also not allowed to use anonymous pseudonyms to maximize accountability for comments. As of today about 200 articles have comments link to them, which is negligible compared to the 23 million referenced papers in Pubmed. But that will surely increase greatly with the service going live in the near future.

Similar initiatives such as Pubpeer and publishers such as Faculty of 1000, Frontiers and Plos already offer similar functionalities. However, the relatively small size of their user-communities and the lack of incentive for researchers to comment publicly on papers have limited their success up to now.  Pubmed Commons is starting off with a very large number of regular users, so perhaps this will be a different story. I believe that post-publication review will start being a serious alternative to the traditional post-publication peer review when at least two factors are combined:

  1. Commenting needs to happen on a centralized system, which is already familiar to researchers and that counts a certain critical mass of active users. Pubmed common has the potential to make that happen and Pubpeer’s talks about joining forces with Pubmed Commons could only help.
  2. Researchers need to accept that publications are not absolute truths, set in stone for eternity. Everyone should be allowed to make (honest) mistakes, if they are ready to accept constructive criticism. Publication should be dynamic documents, living with the evolution of knowledge. Papers are constantly being commented, criticized and applauded, but why keep these behind closed doors?