Building a PubMed knowledge graph

Jian Xu, Sunkyu Kim, Min Song, Minbyul Jeong, Donghyeon Kim, Jaewoo Kang, Justin F. Rousseau, Xin Li, Weijia Xu, Vetle I. Torvik, Yi Bu, Chongyan Chen, Islam Akef Ebeid, Daifeng Li, Ying Ding

Research output: Contribution to journalArticlepeer-review

94 Citations (Scopus)


PubMed® is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguous, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National Institutes of Health (NIH) ExPORTER, collecting affiliation history and educational background of authors from ORCID®, and identifying fine-grained affiliation data from MapAffil. Through the integration of these credible multi-source data, we could create connections among the bio-entities, authors, articles, affiliations, and funding. Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation (AND) achieving an F1 score of 98.09%. PKG can trigger broader innovations, not only enabling us to measure scholarly impact, knowledge usage, and knowledge transfer, but also assisting us in profiling authors and organizations based on their connections with bio-entities.

Original languageEnglish
Article number205
JournalScientific data
Issue number1
Publication statusPublished - 2020 Jun 26

Bibliographical note

Funding Information:
This work was supported by National Social Science Fund of China [18BTQ076], Chinese National Youth Foundation Research [61702564], Natural Science Foundation of Guangdong Province [2018A030313981], Soft Science Foundation of Guangdong Province [2019A101002020], National Research Foundation of Korea [NRF-2019R1A2C2002577] and [NRF-2017R1A2A1A17069645], and US National Institutes of Health [P01AG039347]. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing storage resources that have contributed to the research results reported within this paper. URL: http://

Funding Information:
Project data from NIH ExPORTER. NIH ExPORTER provides data files that contain research projects funded by major funding agencies such as the Centers for Disease Control and Prevention (CDC), the NIH, the Agency for Healthcare Research and Quality (AHRQ), the Health Resources and Services Administration (HRSA), the Substance Abuse and Mental Health Services Administration (SAMHSA), and the U.S. Department of Veterans Affairs (VA). Furthermore, it provides publications and patents citing support from these projects. It consists of 49 data fields, including the amount of funding for each fiscal year, organization information of the PIs, and the details of the projects. According to our investigation, NIH-funded research accounts for 80.7% of all grants recorded in PubMed.

Publisher Copyright:
© 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences


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