Summarize Publications Automatically
Python
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soodoku Merge pull request #5 from maruscia/py3
Automatic citation styles matching added
Latest commit 99dd7dd Apr 27, 2016

Readme.md

AutoSum: Summarize Publications Automatically

The tool exploits the labor already expended by scholars in summarizing articles. It scrapes words next to citations across all openly available research citing a publication, and collates the output. The result is a very useful summary and data that are in a format that allows easy discovery of potential miscitations.

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Table of Contents

  • Get the Data
    Scrapes all openly accessible research citing a particular publication using links provided by Google Scholar. Note: Google monitors scraping on Google scholar.

  • Parse the Data
    Iterates through a directory with all the articles citing a particular research article, and using regular expressions, picks up sentences near a citation.

  • Example from Social Science


Get the Data

To search for openly accessible pdfs citing the original research article on Google Scholar, use Scholar.py.

  1. Input: URL to Google Scholar Page of an article.
  2. What the script does:
    • Goes to 'Cited By..'
    • Downloads a user specified number of publicly available papers (pdfs only for now) that cite the paper to a user specified directory.
    • Creates a csv that tracks basic characteristics of each of the downloaded paper -- title, url, author names, journal etc. It also dumps relative path to downloaded file.
  3. Sample output
Usage
usage: scholar.py [-h] [-u USER] [-p PASSWORD] [-a AUTHOR] [-d DIR]
                  [-o OUTPUT] [-n N_CITES] [-v] [--version]
                  keyword [keyword ...]

positional arguments:
  keyword               Keyword to be searched

optional arguments:
  -h, --help            show this help message and exit
  -u USER, --user USER  Google account e-mail
  -p PASSWORD, --password PASSWORD
                        Google account password
  -a AUTHOR, --author AUTHOR
                        Author to be filtered
  -d DIR, --dir DIR     Output directory for PDF files
  -o OUTPUT, --output OUTPUT
                        CSV output filename
  -n N_CITES, --n-cites N_CITES
                        Number of cites to be download
  -v, --verbose
  --version             show program's version number and exit

Example

python scholar.py -v -d pdfs -o output.csv -n 100 -a "A Einstein" \
"Can quantum-mechanical description of physical reality be considered complete?"

Parse the Data

To scrape the text next to the relevant citations within the pdfs, use autosumpdf.py:

  1. The script iterates through the pdfs using the csv generated above.
  2. Using citation information, or a custom regexp gets the text and puts it in the same csv. If multiple regex are matched, everything is concatenated with a line space.
  3. Sample output
usage: searchpdf.py [-h] [-i INPUT] [-o OUTPUT] [-v] [--version]
                    regex [regex ...]

optional arguments:
   -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        CSV input filename
  -o OUTPUT, --output OUTPUT
                        CSV output filename
  -t TXT_DIR, --text TXT_DIR
                        extract to specific directory
  -f, --force           force extract text file if exists
  -v, --verbose
  -a1 AUTHOR1, --author-1-lastname AUTHOR1
                        1st author of citation
  -a2 AUTHOR2, --author-2-lastname AUTHOR2
                        2nd author of citation
  -y YEAR, --year YEAR  Year of publication
  --version             show program's version number and exit
  -r REGEX, --regex REGEX
                        specify custom regex to filter citations.

Example

python searchpdf.py -v -i output.csv -o search-output.csv -r "\.\s(.{5,100}[\[\(]?Einstein.{2,30}\d+[\]\)])"

The custom regular expression (-r switch) matches a sentence (max 100 chars) following by author name "Einstein", any words (max 30 chars) and number with close bracket at the end.

Depending on the command line arguments (-a1, -a2, -y) the following citation patterns will be automatically used for finding matching sentences:

  • Author1_Last_Name Year
  • Author1_Last_Name et al.
  • Author1_Last_Name et al. Year
  • Author1_Last_Name et al., Year
  • Author1_Last_Name and Author2_Last_Name
  • Author1_Last_Name and Author2_Last_Name Year
  • Author1_Last_Name, and Author2_Last_Name Year
  • Author1_Last_Name and Author2_Last_Name, Year
  • Author1_Last_Name & Author2_Last_Name Year
  • Author1_Last_Name & Author2_Last_Name, Year

Example from Social Science

  • What to search for?

    • Example with Google Scholar
      Download 500 articles from Google Scholar:
      python scholar.py -v -d pdfs -o iyengar-output.csv -n 500 -a "S Iyengar" "Is anyone responsible?: How television frames political issues."
      
  • Searching in the Test Data

    • Sample input data
    • Use autosumpdf.py to filter citations to Iyengar et al. 2012:
      python autosumpdf.py -v -i testdata.csv -o search-testdata-new.csv -a1 "Iyengar" -y "2012"
      
  • Miscitations
    Social scientists hold that few truths are self-evident. But some truths become obvious to all social scientists after some years of experience, including: a) Peer review is a mess, b) Faculty hiring is idiosyncratic, and c) Research is often miscited. Here we quantify the last portion.

License

Released under the MIT License