NIH NCBI PubMed Central (PMC) Article Datasets - Full-Text Biomedical and Life Sciences Journal Articles on AWS

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/ncbi-pmc-dataset")

fs.listdir("s3://pmc-oa-opendata")

Description:

PubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal article at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). The PubMed Central (PMC) Article Datasets include full-text articles archived in PMC and made available under license terms that allow for text mining and other types of secondary analysis and reuse. The articles are organized on AWS based on general license type:

The PMC Open Access (OA) Subset, which includes all articles in PMC with a machine-readable Creative Commons license

The Author Manuscript Dataset, which includes all articles collected under a funder policy in PMC and made available in machine-readable formats for text mining

These datasets collectively span more than half of PMC’s total collection of full-text articles. PMC enables access to these datasets to expand the impact of open access and publicly-funded research; enable greater machine learning across the spectrum of scientific research; reach new audiences; and open new doors for discovery. The bucket in this registry contains individual articles in NISO Z39.96-2015 JATS XML format as well as in plain text as extracted from the XML. The bucket is updated daily with new and updated articles. Also included are file lists that include metadata for articles in each dataset.

Contact:

PubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal article at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). The PubMed Central (PMC) Article Datasets include full-text articles archived in PMC and made available under license terms that allow for text mining and other types of secondary analysis and reuse. The articles are organized on AWS based on general license type:

The PMC Open Access (OA) Subset, which includes all articles in PMC with a machine-readable Creative Commons license

The Author Manuscript Dataset, which includes all articles collected under a funder policy in PMC and made available in machine-readable formats for text mining

These datasets collectively span more than half of PMC’s total collection of full-text articles. PMC enables access to these datasets to expand the impact of open access and publicly-funded research; enable greater machine learning across the spectrum of scientific research; reach new audiences; and open new doors for discovery. The bucket in this registry contains individual articles in NISO Z39.96-2015 JATS XML format as well as in plain text as extracted from the XML. The bucket is updated daily with new and updated articles. Also included are file lists that include metadata for articles in each dataset.

Update Frequency:

Daily

Managed By:

NLM

Resources:

1. resource:
   • Description: .xml and .txt files with the full-text of articles; .txt and .csv file lists for metadata; all located in a public S3 bucket
   • ARN: arn:aws:s3:::pmc-oa-opendata
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, life sciences, STRIDES, txt, xml, csv

Tutorials:

1. tutorial:
   • Title: Accessing PMC Article Datasets Using Amazon Web Services
   • URL: https://www.ncbi.nlm.nih.gov/pmc/tools/pmcaws/
   • AuthorName: NCBI PMC
   • AuthorURL: https://www.ncbi.nlm.nih.gov/pmc/