Dataset for "Continued use of retracted papers: Temporal trends in citations and (lack of) awareness of retractions shown in citation contexts in biomedicine"

Dataset

Description

This dataset includes three files. Descriptions of the files are given as follows:

<b>FILENAME: PubMed_retracted_publication_full_v3.tsv</b>
- Bibliographic data of retracted papers indexed in PubMed (retrieved on August 20, 2020, searched with the query "retracted publication" [PT] ).
- Except for the information in the "cited_by" column, all the data is from PubMed.
ROW EXPLANATIONS
- Each row is a retracted paper. There are 7,813 retracted papers.
COLUMN HEADER EXPLANATIONS
1) PMID - PubMed ID
2) Title - Paper title
3) Authors - Author names
4) Citation - Bibliographic information of the paper
5) First Author - First author's name
6) Journal/Book - Publication name
7) Publication Year
8) Create Date - The date the record was added to the PubMed database
9) PMCID - PubMed Central ID (if applicable, otherwise blank)
10) NIHMS ID - NIH Manuscript Submission ID (if applicable, otherwise blank)
11) DOI - Digital object identifier (if applicable, otherwise blank)
12) retracted_in - Information of retraction notice (given by PubMed)
13) retracted_yr - Retraction year identified from "retracted_in" (if applicable, otherwise blank)
14) cited_by - PMIDs of the citing papers. (if applicable, otherwise blank) Data collected from iCite.
15) retraction_notice_pmid - PMID of the retraction notice (if applicable, otherwise blank)

<b>FILENAME: PubMed_retracted_publication_CitCntxt_withYR_v3.tsv</b>
- This file contains citation contexts (i.e., citing sentences) where the retracted papers were cited. The citation contexts were identified from the XML version of PubMed Central open access (PMCOA) articles.
- This is part of the data from: Hsiao, T.-K., & Torvik, V. I. (manuscript in preparation). Citation contexts identified from PubMed Central open access articles: A resource for text mining and citation analysis.
ROW EXPLANATIONS
- Each row is a citation context associated with one retracted paper that's cited.
- In the manuscript, we count each citation context once, even if it cites multiple retracted papers.
COLUMN HEADER EXPLANATIONS
1) pmcid - PubMed Central ID of the citing paper
2) pmid - PubMed ID of the citing paper
3) year - Publication year of the citing paper
4) location - Location of the citation context (abstract = abstract, body = main text, back = supporting material, tbl_fig_caption = table/figure captions)
5) IMRaD - IMRaD section of the citation context (I = Introduction, M = Methods, R = Results, D = Discussions/Conclusion, NoIMRaD = not identified)
6) sentence_id - The ID of the citation context in a given location. For location information, please see column 4. The first sentence in the location gets the ID 1, and subsequent sentences are numbered consecutively.
7) total_sentences - Total number of sentences in a given location
8) intxt_id - Identifier of a cited paper. Here, a cited paper is the retracted paper.
9) intxt_pmid - PubMed ID of a cited paper. Here, a cited paper is the retracted paper.
10) citation - The citation context
11) progression - Position of a citation context by centile within the citing paper.
12) retracted_yr - Retraction year of the retracted paper
13) post_retraction - 0 = not post-retraction citation; 1 = post-retraction citation. A post-retraction citation is a citation made after the calendar year of retraction.

<b>FILENAME: 613_knowingly_post_retraction_cit.tsv</b>
- The 613 post-retraction citation contexts that we determined knowingly cited the 7,813 retracted papers in "PubMed_retracted_publication_full_v3.tsv".
ROW EXPLANATIONS
- Each row is a citation context.
COLUMN HEADER EXPLANATIONS
1) pmcid - PubMed Central ID of the citing paper
2) pmid - PubMed ID of the citing paper
3) pub_type - Publication type collected from the metadata in the PMCOA XML files.
4) pub_type2 - Specific article types. Please see the manuscript for explanations.
5) year - Publication year of the citing paper
6) location - Location of the citation context (abstract = abstract, body = main text, back = supporting material, tbl_fig_caption = table/figure captions)
7) intxt_id - Identifier of a cited paper. Here, a cited paper is the retracted paper.
8) intxt_pmid - PubMed ID of a cited paper. Here, a cited paper is the retracted paper.
9) citation - The citation context
10) retracted_yr - Retraction year of the retracted paper
11) cit_purpose - Purpose of citing the retracted paper. This is from human annotations. Please see the manuscript for further information about annotation.
12) longer_context - A extended version of the citation context. (if applicable, otherwise blank) Manually pulled from the full-texts in the process of annotation.

<b>FILENAME: Annotation manual.pdf</b>
- The manual for annotating the citation purposes in column 11) of the 613_knowingly_post_retraction_cit.tsv.
Date made availableApr 6 2021
PublisherUniversity of Illinois at Urbana-Champaign

Keywords

  • citation context
  • citation to retracted papers
  • in-text citation
  • retraction

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