sciscore-tools

A set of tools to extract text from various file formats, run it through SciScore, and extract the results.

Setup

Should work on any Python 3 verison.

• Install the requires packages with pip install fasttext spacy numpy requests Unidecode
• pdftotext must also be installed from https://www.xpdfreader.com/download.html
• Obtain the methods-model.bin file and place it in the same directory as pdftools.py
• Obtain a auth.json file with your SciScore API credentials

Text extraction and API querying

First create a SciScore object with

import sciscore
api = sciscore.SciScore('report_folder')

where report_folder is the location to accumulate API responses. Then, call api.generate_report_from_file('example.pdf', 'example_doi') for each file you want the SciScore of, where example.pdf is a file of format .pdf, .doc, .docx, or .xml, and example_doi is the DOI or other identifier for the file, which will show up in a column of the final table.
When finished with running all your files, call api.make_csv('out.csv') to generate a csv with all the results together. Individual reports for each paper are also stored in report_folder.

sciscore-tools has utilities for retrieving .xml files given a PMID or PMCID from the PMC Open Access subset. First, download oa_file_list.txt from the PMC FTP. Then, you can call api.generate_report_from_pmid('34825147') for a PMID, or api.generate_report_from_pmcid('PMC8605177') for a PMCID. This will do all the processing internally, so you do not have to call generate_report_from_file again.