Publicly Accessible Research Compliance

Goals:

To determine the percentage of publicly accessible ARS publications

To automate the publication tracking process.

Scripts: The following scripts use information in VIVO from ARIS

Publication Info:

Uses Crossref to find the publisher and date of publication for a specific DOI.

PubAg:

The PubAg API allows users with an assigned API key to search through the metadata of articles to gain useful information. This API is used in this script because users can find either citations or full text of an article by inputting the AGID. Full text under a particular tell us that the article is publicly accessible on PubAg.

Searches through articles with AGIDs to see if there is full text in PubAg

Converts the AGID to a string 

Uses regex to find the phrase "Full Text"

PubMedCentral:

The DOI converter API for PubMedCentral converts DOIs to PMIDs or PMCIDs. This API was chosen for this script because an article having a PMCID tells us it is available on PubMedCentral where full text articles are shared with the public.

Converts article DOIs to PMCIDs 

Uses regex to find the phrases "true" and "false"

        False: not available

        True: available 

CHORUS:

CHORUS is a publisher-led dashboard that contains articles of federal-funded research. The CHORUS API holds metadata for available DOIs, and users can use this API to fiud if an article is publicly accessible on a given date.

Searches for the DOI on the CHORUS API page to see if the article is available in CHORUS

Converts DOI to a string to match the format on the CHORUS API page 

Public Access Journals:

This script checks to see if there are publicly accessible journals and articles. DOI number is based on the journal and articles. When the journal is open access, this script reads the DOI and returns it as 'YES' for publicly accessible. Public Access Journals script also looks at the SpringerNature and Elsevier APIs to check for accessibility from those organizations. The SpringerNature API requires an API key that allows users to read the metadata from a SpringerNature article. The API will tell a user if an article is open access. The Elsevier API uses a URL with the given DOI to return metadata that tells the user if an article is open access.

Reads the prefix of the DOI to determine if a publisher/organization is publicly accessible

Reads the suffix of the DOI to determine if a specific journal is publicly accessible

Uses the SpringerNature and Elsevier APIs to find publicly accessible articles from those publications

Accession Numbers:

This script calculates the percentage of all ARS 2017 accession numbers that have at least one associated dataset in Ag Data Commons.

  Iterates through the 'Accession' column to find any duplicate accession numbers
  
  Accession numbers are added to an empty list and the total count increases 
  
  Acession numbers with a dataset are added into a second empty and the counter for this list increases
  
  Divide the counter by the total to find the percentage.