papernetwork 0.1.2

Collect and analyze scientific literature from Semantic Scholar

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.