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Literature Mining I (working with papers) Public


Learn how to extract data, trends, and other information from the scientific literature. The first in a series of two badges.

Required Evidence

1) Confirmation of materials

Please Tweet notification to @balicea1 once you have successfully unzipped the tutorial materials. If you do not have a Twitter account, please send an e-mail to balicea Link: More Info

2) Dissecting methods section

Using Towlson (2013), please describe what parameters are calculated to define a "rich club of the connectome". More Info

3) Working with paper altmetrics

Using the neuronal network paper mentioned in Towlson (2013), find the following information on the journal's website for the paper: a) how many times the paper has been viewed, and b) what is the definition of a “view” according to PLoS. More Info

4) Working with forward citations

Using the five papers in the .zip file plus the "neuronal network paper", please find how many times each paper has been cited (forward citation) using Google Scholar. Provide the number of times each paper has been cited (e.g. "cited by x") with a link to the associated Google Scholar search. More Info

5) Organizing data on multiple papers

Using the five papers in the .zip file plus the "neuronal network paper", create a CiteULike ( bibliography. Please provide a link to these citations in your CiteULike library (HINT: classification tags make life easier). More Info

6) Assembling data from multiple papers

Using Spencer (2011) and Towlson (2013), please describe what kind of data are publically-available for each paper and how you might go about reusing these data. More Info

7) Further reading on topic

In the .zip file, you will find a paper on "Literature Mining for the Biologist". Please read this paper at you own convenience. To get credit for reading the paper, please submit a URL link to the PubMed abstract for this paper. More Info

Badge Experts


Bradly Alicea


Created badge on 9/24/16

Badge Learners


Mark Watts


Joined badge on 9/24/16



Joined badge on 10/21/16