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

This dataset includes five 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.
- PMIDs in the "cited_by" column that meet either of the two conditions below have been excluded from analyses:
[1] PMIDs of the citing papers are from retraction notices (i.e., those in the “retraction_notice_PMID.csv” file).
[2] Citing paper and the cited retracted paper have the same PMID.
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.
- Citation contexts that meet either of the two conditions below have been excluded from analyses:
[1] PMIDs of the citing papers are from retraction notices (i.e., those in the “retraction_notice_PMID.csv” file).
[2] Citing paper and the cited retracted paper have the same PMID.
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 = tables and 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: 724_knowingly_post_retraction_cit.csv</b> (updated)
- The 724 post-retraction citation contexts that we determined knowingly cited the 7,813 retracted papers in "PubMed_retracted_publication_full_v3.tsv".
- Two citation contexts from retraction notices have been excluded from analyses.
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, table_or_figure_caption = tables and 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 724_knowingly_post_retraction_cit.tsv.

<b>FILENAME: retraction_notice_PMID.csv</b> (new file added for this version)
- A list of 8,346 PMIDs of retraction notices indexed in PubMed (retrieved on August 20, 2020, searched with the query "retraction of publication" [PT] ).