An attempt to identify 199 PubMed items excluded from "Analyzing the consistency of retraction indexing"

McCumber, Corinne; Salami, Malik Oyewale

doi:10.13012/B2IDB-6684660_V1

Illinois Data Bank - Dataset

An attempt to identify 199 PubMed items excluded from "Analyzing the consistency of retraction indexing"

Cite this dataset:

McCumber, Corinne; Salami, Malik Oyewale (2025): An attempt to identify 199 PubMed items excluded from "Analyzing the consistency of retraction indexing". University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-6684660_V1

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Dataset Description	This project investigates retraction indexing agreement in PubMed between 2024-07-03 and 2025-05-09 in order to address an API limitation that resulted in 199 items being excluded from analysis in "Analyzing the consistency of retraction indexing". PubMed was queried on 2024-07-03 and on 2025-05-09 using the search “Retracted Publication[PT]”. PubMed is only able to return 10,000 items when queried via the E-Utilities API. When the pipeline was run 2024-07-03, the search between 2020 and 2024 returned 10,199 items, meaning that an expected 199 items indexed as retracted in PubMed were excluded. This dataset uses and compares information from PubMed as of 2025-05-09 to attempt to identify those 199 items.
Subject	Social Sciences
Keywords	retraction status; data quality; indexing; retraction indexing; metadata; meta-science; RISRS; PubMed
License	CC0
Funder	Alfred P. Sloan Foundation-Grant:G-2022-19409
Funder	U.S. National Science Foundation (NSF)-Grant:2046454
Funder	Harvard Radcliffe Institute for Advanced Study-Grant:2024-2025 Perrin Moorhead Grayson and Bruns Grayson Fellowship
Corresponding Creator	Corinne McCumber
Downloaded	61 times
Related Materials (10) Article Salami, M. O., McCumber, C., & Schneider, J. (2024). Analyzing the consistency of retraction indexing. MetaArXiv. https://doi.org/10.31222/osf.io/gvfk5 Dataset Salami, M. O. & McCumber, C. (2024). Redacted Dataset for Analyzing the Consistency of Retraction (Version 1) [Data set]. University of Illinois Urbana-Champaign Databank. https://doi.org/10.13012/B2IDB-8114408_V1 Code McCumber, C. & Salami, M.O. (2025). Analysis to identify 199 PubMed items excluded from "Analyzing the consistency of retraction indexing" (1.0.0) [Python]. GitHub. https://github.com/infoqualitylab/retraction_indexing_missing_pubmed_items Article Salami, M. O., McCumber, C., & Schneider, J. (2024, November 6-13). Reassessment of the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science. ASIS&T MET-STI 2024: Workshop on Informetric, Scientometric and Scientific and Technical Information Research. https://doi.org/10.5281/zenodo.14004526 Dataset Salami, M. O. & McCumber, C. (2024). Dataset for Reassessment of the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science (Version 1) [Data set]. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8457537_V1 Dataset Lee, J. & Schneider, J. (2023). Crossref data for Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science (Version 1) [Data set]. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9099305_V1 Dataset Salami, M. O., Lee, J., & Schneider, J. (2023). Stopwords and keywords for manual field assignment for the STI 2023 paper Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science (Version 2) [Data set]. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8847584_V2 Code Salami, M. O. & McCumber, C. (2024). Retraction indexing agreement: 2024 Preprint Final Code (2.0.0) [Python]. Zenodo. https://doi.org/10.5281/zenodo.14183542 Code Salami, M. O. & McCumber, C. (2024). Retraction indexing agreement: ASIS&T MET-STI2024 Paper Final Code (1.2.1) [Python]. Zenodo. https://doi.org/10.5281/zenodo.14052823 Code Salami, M. O., Schneider, J. & Lee, L. (2023). Retraction indexing agreement: STI2023 Paper Final Code (1.1.0) [Python]. Zenodo. https://doi.org/10.5281/zenodo.8336538

Versions

Version	DOI	Comment	Publication Date
1	10.13012/B2IDB-6684660_V1		2025-07-28

Change Log

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199_excluded_PubMed_items_README.txt 16.6 KB File
1_2025-05-09_merged_df.csv 44.2 MB View File
2024-07-03_pubmed.csv 19.4 MB View File
2025-05-09_pubmed.csv 23.7 MB View File
2_2025-05-09_pubmed_unionlist.csv 9.59 MB View File
3_2025-05-09_pubmed_unionlist_2025_only.csv 1.52 MB View File
4_2025-05-09_pubmed_unionlist_pub_date_cleaned.csv 1.57 MB View File
5_2025-05-09_pubmed_unionlist_pub_date_filtered.csv 953 KB View File
6_2025-05-09_pubmed_unionlist_retraction_notice_cleaned.csv 976 KB View File
7_2025-05-09_pubmed_unionlist_retraction_notice_filtered.csv 207 KB View File
missing_pubmed_items_sankey.png 262 KB File