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NIH_IRP_PubDB

An application to catalog and measure NIH IRP publications.

Assuming that the user is interested in updating these measures in subsequent years, it is a two-stage process.

In the first stage, the scopus_search.py script takes as input a list of investigators, and returns all the papers listed in scopus since the specified date.

In the second stage, the update_citation_counts.py script takes as input the file produced in the previous year, and pulls all the unique EID (paper identifiers), updating the citation counts for those articles. We have experienced EIDs that change a bit year-to-year (on the order of one or two percent). Consequently, this script will print (and write to disk) EIDs that are missed. It is up to the user to go through an manually correct these by, for instance, creating a new csv file with a column labeled EID and using this as input for update_citation_counts.py.

scopus_search.py

Search SCOPUS for publications given a list of AU-IDs.

usage: scopus_search.py [-h] --ids idfile --out output --start startdate

Query Scopus Search API and output to csv file.

optional arguments:
  -h, --help         show this help message and exit
  --ids idfile       Scopus search file
  --out output       Output CSV filename
  --start startdate  Start date for query (YYYYMMDD).
  1. Export your SCOPUS_API_KEY environment variable:
export SCOPUS_API_KEY=1234567890abcdef1234567890abcdef
  1. Prepare a list of AU-IDs to query. These should go in a text file, one AU-ID per line. Comments are optional. Example au-ids.txt:
# Alice
0123456789
# Bob
1234567890
  1. Run scopus_search.py. First argument is the file containing the AU-IDs and the second argument is the output csv file:
python scopus_search.py --ids au-ids.txt --out output.csv --start 20160807

update_citation_counts.py

Given a CSV file with an EID for each publication, write to a CSV file with updated citation counts for each publication.

usage: update_citation_counts.py [-h] --input csvfile --output outfile

Take CSV file with EID column and output CSV file with updated citation
counts.

optional arguments:
  -h, --help        show this help message and exit
  --input csvfile   Citation count csv filename
  --output outfile  Output CSV filename
  1. Export your SCOPUS_API_KEY environment variable:
export SCOPUS_API_KEY=1234567890abcdef1234567890abcdef
  1. Run the update_citation_counts.py:
python update_citation_counts.py --input old_publist.csv --output updated_publist.csv