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Web app to get the a list of authors that cite a given list of papers through the PubMed API
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README.md

get_citing_authors

Web app to get the a list of authors that cite a given list of papers through the PubMed API.

You can input papers either as a comma seperated list of PubMed IDs (PMIDs) or you can provide a PubMed search term and the app will get the authors that cite all of the search results.

Live example running on Heroku can be found here.

Using locally

Prerequisites

The app is written in Python 3.6, you may run into issues if you are running Python 2.7.

To install all the required packages, run the following in a terminal within the directory:

pip install -r requirements.txt

Usage

Once you have all the prerequisites installed, you can run main.py in the terminal from the directory it is located in to start a local webserver.

python main.py

You could access the functions of the app in the utils.py file individually if you prefer that too.

The two main functions are get_author_list_counts_search() and get_author_list_counts(). These take a search term and a list of PMIDs respectively.

get_author_list_counts_search() will get a list of PMIDs from the PubMed API by searching the database using the search term provided.

The output will be a Python dictionary where the keys are author names and the values are the number of times that author has cited any of the input articles.

API Key

Currently there is no API key used for all of the requests sent to the PubMed API. This limits the number of requests you can make.

To register your personal API key, you will need to register a free NCBI account and generate one. The functions get_cited_by_PMIDs(), get_PMIDs_metadata(), search_DB() in utils.py define an api_key value which is currently set to None. You will have to replace None with your API key given as a string.

Deploying

To deploy on Heroku, simply clone this repo to your Heroku repo.

Contributing

Happy to take feature requests and pull requests!

Authors

Project made possible by Labrigger

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