papernetwork

Collect and analyze scientific literature from Semantic Scholar

Examples

Basic example of loading data from Semantic Scholar via the API, be sure to read the dataset license agreement:

from papernetwork import PaperNetwork, Paper, PaperList

# Define a list of DOI's you would like to download
list_of_dois = ['10.1093/nar/gkw1328', '10.1128/CMR.00016-17', '10.1038/s41564-019-0626-z']

# Pull the papers from semanticscholar.org via the API and parse them
my_network = PaperNetwork(doi_list=list_of_dois)

# Show the titles in the PaperNetwork object
print(my_network)  # Rapid resistome mapping using nanopore sequencing, Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis., Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

# The papers are internally stored in a OrderedSet-like object, accessible via the collection
my_collection = my_network.collection

# The papers themselves are individually stored in a Dict-like object
my_paper = my_collection[0]  # Take the first paper in the list


print(my_paper['title'])

# They keys of the object are defined by the Semantic Scholar API, see https://api.semanticscholar.org/
# To get an overview of the available keys
for key, value in my_collection[0].items():
    print(key)

# Currently the following keys are supplied by semanticscholar.org
# arxivId
# authors
# citationVelocity
# citations
# corpusId
# doi
# fieldsOfStudy
# influentialCitationCount
# is_open_access
# is_publisher_licensed
# paperId
# references
# title
# topics
# url
# venue
# year

A more elaborate example can be found in the examples directory to get started.

More detailed usage can be found in the test directory as well.

Run using:

python -m examples.simple_example

Installation

Use pip to install papernetwork from PyPI (recommend doing this inside a virtual environment):

pip install papernetwork

Or from source:

git clone --recursive https://github.com/evdh0/papernetwork.git
cd papernetwork
python setup.py install

Licence

The MIT License (MIT)

Authors

papernetwork was written by Eric van der Helm.