CORD 19 tools and utilities
COVID-19 Data Tools
Tools for making COVID 19 data slightly easier for everyone! If you A) think something would be useful in your research or B) have some helpful code to contribute, make an issue or PR ASAP so we can get your code shared!
pip install cord-19-tools
Downloading the data
To download and extract the data, use the
import cotools from pprint import pprint cotools.download(dir="data")
For now this just downloads the data from the CORD-19 dataset, metadata is not included (will be by end of day), extracts all the tarfiles, and places them in a directory
The Paperset class
This is a class for lazily loading papers from the CORD-19 dataset.
# no `/` at the end please! data = cotools.Paperset("data/comm_use_subset") # indexes with ints pprint(data) # returns a dict # and slices! pprint(data[:2]) # returns a list of dicts print(len(data)) # takes about 5gb in memory alldata = data[:]
Lets talk for a bit about how it works, and why it doesnt take a gigantic amount of memory. The files are not actually loaded into python until the data is indexed. Upon indexing, the files at those indexes are read into python, resulting in a list of dictionaries. This means you can still contribute while working on a low resource system.
Getting text and abstracts
For text, there is the
text function, which returns the text from a single document, the
texts function, which returns the text from multiple documents, and the
Paperset.texts() function, which gets the text from all documents:
print(cotools.text(data)) print(cotools.texts(data[12:18])) alltext = data.texts() # alltext = cotools.texts(alldata)
For abstracts, we have a similar API:
print(cotools.abstract(data)) print(cotools.abstracts(data[12:18])) allabs = data.abstracts() # allabs = cotools.abstracts(alldata)
You can also manipulate the documents with the
keys = comm_use.apply(lambda x: list(x.keys())) # then lets combine them into a set print(set(sum(keys, )))
The Hopkins data can be loaded with
load_hopkins. It loads three dicts, each containing data from the hopkins dataset:
confirmed, deaths = cotools.load_hopkins()
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