Dataset Search Results

To gather news articles from the web that discuss the Cochrane Review, we used Altmetric Explorer from Altmetric.com and retrieved articles on August 1, 2023. We selected all articles that were written in English, published in the United States, and had a publication date <b>prior to March 10, 2023</b> (according to the “Mention Date” on Altmetric.com). This date is significant as it is when Cochrane issued a statement about the "misleading interpretation" of the Cochrane Review. The collection of news articles is presented in the Altmetric_data.csv file. The dataset contains the following data that we exported from Altmetric Explorer: - Publication date of the news article - Title of the news article - Source/publication venue of the news article - URL - Country We manually checked and added the following information: - Whether the article still exists - Whether the article is accessible - Whether the article is from the original source We assigned MAXQDA IDs to the news articles. News articles were assigned the same ID when they were (a) identical or (b) in the case of Article 207, closely paraphrased, paragraph by paragraph. Inaccessible items were assigned a MAXQDA ID based on their "Mention Title". For each article from Altmetric.com, we first tried to use the Web Collector for MAXQDA to download the article from the website and imported it into MAXQDA (version 22.7.0). If an article could not be retrieved using the Web Collector, we either downloaded the .html file or in the case of Article 128, retrieved it from the NewsBank database through the University of Illinois Library. We then manually extracted direct quotations from the articles using MAXQDA. We included surrounding words and sentences, and in one case, a news agency’s commentary, around direct quotations for context where needed. The quotations (with context) are the positions in our analysis. We also identified who was quoted. We excluded quotations when we could not identify who or what was being quoted. We annotated quotations with codes representing groups (government agencies, other organizations, and research publications) and individuals (authors of the Cochrane Review, government agency representatives, journalists, and other experts such as epidemiologists). The MAXQDA_data.csv file contains excerpts from the news articles that contain the direct quotations we identified. For each excerpt, we included the following information: - MAXQDA ID of the document from which the excerpt originates; - The collection date and source of the document; - The code with which the excerpt is annotated; - The code category; - The excerpt itself.

Tab-separated value (TSV) file. 14745 data rows. Each data row represents publication metadata as retrieved from Crossref (http://crossref.org) 2023-04-05 when searching for retracted publications. Each row has the following columns: Index - Our index, starting with 0. DOI - Digital Object Identifier (DOI) for the publication Year - Publication year associated with the DOI. URL - Web location associated with the DOI. Title - Title associated with the DOI. May be blank. Author - Author(s) associated with the DOI. Journal - Publication venue (journal, conference, ...) associated with the DOI RetractionYear - Retraction Year associated with the DOI. May be blank. Category - One or more categories associated with the DOI. May be blank. Our search was via the Crossref REST API and searched for: Update_type=( 'retraction', 'Retraction', 'retracion', 'retration', 'partial_retraction', 'withdrawal','removal')

This project investigates retraction indexing agreement among data sources: Crossref, Retraction Watch, Scopus, and Web of Science. As of July 2024, this reassesses the April 2023 union list of Schneider et al. (2023): https://doi.org/10.55835/6441e5cae04dbe5586d06a5f. As of April 2023, over 1 in 5 DOIs had discrepancies in retraction indexing among the 49,924 DOIs indexed as retracted in at least one of Crossref, Retraction Watch, Scopus, and Web of Science (Schneider et al., 2023). Here, we determine what changed in 15 months. Pipeline code to get the results files can be found in the GitHub repository https://github.com/infoqualitylab/retraction-indexing-agreement in the iPython notebook 'MET-STI2024_Reassessment_of_retraction_indexing_agreement.ipynb' Some files have been redacted to remove proprietary data, as noted in README.txt. Among our sources, data is openly available only for Crossref and Retraction Watch. FILE FORMATS: 1) unionlist_completed_2023-09-03-crws-ressess.csv - UTF-8 CSV file 2) unionlist_completed-ria_2024-07-09-crws-ressess.csv - UTF-8 CSV file 3) unionlist-15months-period_sankey.png - Portable Network Graphics (PNG) file 4) unionlist_ria_proportion_comparison.png - Portable Network Graphics (PNG) file 5) README.txt - text file FILE DESCRIPTION: Description of the files can be found in README.txt

The PDF describes the process and data used for the heuristic user evaluation described in the related article “<i>Evaluating an automatic data extraction tool based on the theory of diffusion of innovation</i>” by Linh Hoang, Frank Scannapieco, Linh Cao, Yingjun Guan, Yi-Yun Cheng, and Jodi Schneider (under submission).<br /> Frank Scannapieco assessed RobotReviewer data extraction performance on ten articles in 2018-02. Articles are included papers from an update review: Sabharwal A., G.-F.I., Stellrecht E., Scannapeico F.A. <i>Periodontal therapy to prevent the initiation and/or progression of common complex systemic diseases and conditions</i>. An update. Periodontol 2000. In Press. <br/> The form was created in consultation with Linh Hoang and Jodi Schneider. To do the assessment, Frank Scannapieco entered PDFs for these ten articles into RobotReviewer and then filled in ten evaluation forms, based on the ten Robot Reviewer automatic data extraction reports. Linh Hoang analyzed these ten evaluation forms and synthesized Frank Scannapieco’s comments to arrive at the evaluation results for the heuristic user evaluation.

This dataset contains data from extreme-disagreement analysis described in paper “Aaron M. Cohen, Jodi Schneider, Yuanxi Fu, Marian S. McDonagh, Prerna Das, Arthur W. Holt, Neil R. Smalheiser, 2021, Fifty Ways to Tag your Pubtypes: Multi-Tagger, a Set of Probabilistic Publication Type and Study Design Taggers to Support Biomedical Indexing and Evidence-Based Medicine.” In this analysis, our team experts carried out an independent formal review and consensus process for extreme disagreements between MEDLINE indexing and model predictive scores. “Extreme disagreements” included two situations: (1) an abstract was MEDLINE indexed as a publication type but received low scores for this publication type, and (2) an abstract received high scores for a publication type but lacked the corresponding MEDLINE index term. “High predictive score” is defined as the top 100 high-scoring, and “low predictive score” is defined as the bottom 100 low-scoring. Three publication types were analyzed, which are CASE_CONTROL_STUDY, COHORT_STUDY, and CROSS_SECTIONAL_STUDY. Results were recorded in three Excel workbooks, named after the publication types: case_control_study.xlsx, cohort_study.xlsx, and cross_sectional_study.xlsx. The analysis shows that, when the tagger gave a high predictive score (>0.9) on articles that lacked a corresponding MEDLINE indexing term, independent review suggested that the model assignment was correct in almost all cases (CROSS_SECTIONAL_STUDY (99%), CASE_CONTROL_STUDY (94.9%), and COHORT STUDY (92.2%)). Conversely, when articles received MEDLINE indexing but model predictive scores were very low (<0.1), independent review suggested that the model assignment was correct in the majority of cases: CASE_CONTROL_STUDY (85.4%), COHORT STUDY (76.3%), and CROSS_SECTIONAL_STUDY (53.6%). Based on the extreme disagreement analysis, we identified a number of false-positives (FPs) and false-negatives (FNs). For case control study, there were 5 FPs and 14 FNs. For cohort study, there were 7 FPs and 22 FNs. For cross-sectional study, there were 1 FP and 45 FNs. We reviewed and grouped them based on patterns noticed, providing clues for further improving the models. This dataset reports the instances of FPs and FNs along with their categorizations.

This second version (V2) provides additional data cleaning compared to V1, additional data collection (mainly to include data from 2019), and more metadata for nodes. Please see NETWORKv2README.txt for more detail.

Citation context annotation for papers citing retracted paper Matsuyama 2005 (RETRACTED: Matsuyama W, Mitsuyama H, Watanabe M, Oonakahara KI, Higashimoto I, Osame M, Arimura K. Effects of omega-3 polyunsaturated fatty acids on inflammatory markers in COPD. Chest. 2005 Dec 1;128(6):3817-27.), retracted in 2008 (Retraction in: Chest (2008) 134:4 (893) <a href="https://doi.org/10.1016/S0012-3692(08)60339-6">https://doi.org/10.1016/S0012-3692(08)60339-6<a/> ). This is part of the supplemental data for Jodi Schneider, Di Ye, Alison Hill, and Ashley Whitehorn. "Continued Citation of a Fraudulent Clinical Trial Report, Eleven Years after it was retracted for Falsifying Data" [R&R under review with Scientometrics]. Overall we found 148 citations to the retracted paper from 2006 to 2019, However, this dataset does not include the annotations described in the 2015. in Ashley Fulton, Alison Coates, Marie Williams, Peter Howe, and Alison Hill. "Persistent citation of the only published randomized controlled trial of omega-3 supplementation in chronic obstructive pulmonary disease six years after its retraction." Publications 3, no. 1 (2015): 17-26. In this dataset 70 new and newly found citations are listed: 66 annotated citations and 4 pending citations (non-annotated since we don't have full-text). "New citations" refer to articles published from March 25, 2014 to 2019, found in Google Scholar and Web of Science. "Newly found citations" refer articles published 2006-2013, found in Google Scholar and Web of Science, but not previously covered in Ashley Fulton, Alison Coates, Marie Williams, Peter Howe, and Alison Hill. "Persistent citation of the only published randomised controlled trial of omega-3 supplementation in chronic obstructive pulmonary disease six years after its retraction." Publications 3, no. 1 (2015): 17-26. NOTES: This is Unicode data. Some publication titles & quotes are in non-Latin characters and they may contain commas, quotation marks, etc. FILES/FILE FORMATS Same data in two formats: 2006-2019-new-citation-contexts-to-Matsuyama.csv - Unicode CSV (preservation format only) 2006-2019-new-citation-contexts-to-Matsuyama.xlsx - Excel workbook (preferred format) ROW EXPLANATIONS 70 rows of data - one citing publication per row COLUMN HEADER EXPLANATIONS Note - processing notes Annotation pending - Y or blank Year Published - publication year ID - ID corresponding to the network analysis. See Ye, Di; Schneider, Jodi (2019): Network of First and Second-generation citations to Matsuyama 2005 from Google Scholar and Web of Science. University of Illinois at Urbana-Champaign. <a href="https://doi.org/10.13012/B2IDB-1403534_V2">https://doi.org/10.13012/B2IDB-1403534_V2</a> Title - item title (some have non-Latin characters, commas, etc.) Official Translated Title - item title in English, as listed in the publication Machine Translated Title - item title in English, translated by Google Scholar Language - publication language Type - publication type (e.g., bachelor's thesis, blog post, book chapter, clinical guidelines, Cochrane Review, consumer-oriented evidence summary, continuing education journal article, journal article, letter to the editor, magazine article, Master's thesis, patent, Ph.D. thesis, textbook chapter, training module) Book title for book chapters - Only for a book chapter - the book title University for theses - for bachelor's thesis, Master's thesis, Ph.D. thesis - the associated university Pre/Post Retraction - "Pre" for 2006-2008 (means published before the October 2008 retraction notice or in the 2 months afterwards); "Post" for 2009-2019 (considered post-retraction for our analysis) Identifier where relevant - ISBN, Patent ID, PMID (only for items we considered hard to find/identify, e.g. those without a DOI-based URL) URL where available - URL, ideally a DOI-based URL Reference number/style - reference Only in bibliography - Y or blank Acknowledged - If annotated, Y, Not relevant as retraction not published yet, or N (blank otherwise) Positive / "Poor Research" (Negative) - P for positive, N for negative if annotated; blank otherwise Human translated quotations - Y or blank; blank means Google scholar was used to translate quotations for Translated Quotation X Specific/in passing (overall) - Specific if any of the 5 quotations are specific [aggregates Specific / In Passing (Quotation X)] Quotation 1 - First quotation (or blank) (includes non-Latin characters in some cases) Translated Quotation 1 - English translation of "Quotation 1" (or blank) Specific / In Passing (Quotation 1) - Specific if "Quotation 1" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 1) - Methods; Results; or Methods and Results - blank if "Quotation 1" not specific, no associated quotation, or not yet annotated Quotation 2 - Second quotation (includes non-Latin characters in some cases) Translated Quotation 2 - English translation of "Quotation 2" Specific / In Passing (Quotation 2) - Specific if "Quotation 2" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 2) - Methods; Results; or Methods and Results - blank if "Quotation 2" not specific, no associated quotation, or not yet annotated Quotation 3 - Third quotation (includes non-Latin characters in some cases) Translated Quotation 3 - English translation of "Quotation 3" Specific / In Passing (Quotation 3) - Specific if "Quotation 3" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 3) - Methods; Results; or Methods and Results - blank if "Quotation 3" not specific, no associated quotation, or not yet annotated Quotation 4 - Fourth quotation (includes non-Latin characters in some cases) Translated Quotation 4 - English translation of "Quotation 4" Specific / In Passing (Quotation 4) - Specific if "Quotation 4" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 4) - Methods; Results; or Methods and Results - blank if "Quotation 4" not specific, no associated quotation, or not yet annotated Quotation 5 - Fifth quotation (includes non-Latin characters in some cases) Translated Quotation 5 - English translation of "Quotation 5" Specific / In Passing (Quotation 5) - Specific if "Quotation 5" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 5) - Methods; Results; or Methods and Results - blank if "Quotation 5" not specific, no associated quotation, or not yet annotated Further Notes - additional notes

This dataset presents a citation analysis and citation context analysis used in Linh Hoang, Frank Scannapieco, Linh Cao, Yingjun Guan, Yi-Yun Cheng, and Jodi Schneider. Evaluating an automatic data extraction tool based on the theory of diffusion of innovation. Under submission. We identified the papers that directly describe or evaluate RobotReviewer from the list of publications on the RobotReviewer website <http://www.robotreviewer.net/publications>, resulting in 6 papers grouped into 5 studies (we collapsed a conference and journal paper with the same title and authors into one study). We found 59 citing papers, combining results from Google Scholar on June 05, 2018 and from Scopus on June 23, 2018. We extracted the citation context around each citation to the RobotReviewer papers and categorized these quotes into emergent themes.

Citation context annotation. This dataset is a second version (V2) and part of the supplemental data for Jodi Schneider, Di Ye, Alison Hill, and Ashley Whitehorn. (2020) "Continued post-retraction citation of a fraudulent clinical trial report, eleven years after it was retracted for falsifying data". Scientometrics. In press, DOI: 10.1007/s11192-020-03631-1 Publications were selected by examining all citations to the retracted paper Matsuyama 2005, and selecting the 35 citing papers, published 2010 to 2019, which do not mention the retraction, but which mention the methods or results of the retracted paper (called "specific" in Ye, Di; Hill, Alison; Whitehorn (Fulton), Ashley; Schneider, Jodi (2020): Citation context annotation for new and newly found citations (2006-2019) to retracted paper Matsuyama 2005. University of Illinois at Urbana-Champaign. <a href="https://doi.org/10.13012/B2IDB-8150563_V1">https://doi.org/10.13012/B2IDB-8150563_V1</a> ). The annotated citations are second-generation citations to the retracted paper Matsuyama 2005 (RETRACTED: Matsuyama W, Mitsuyama H, Watanabe M, Oonakahara KI, Higashimoto I, Osame M, Arimura K. Effects of omega-3 polyunsaturated fatty acids on inflammatory markers in COPD. Chest. 2005 Dec 1;128(6):3817-27.), retracted in 2008 (Retraction in: Chest (2008) 134:4 (893) https://doi.org/10.1016/S0012-3692(08)60339-6). <b>OVERALL DATA for VERSION 2 (V2)</b> FILES/FILE FORMATS Same data in two formats: 2010-2019 SG to specific not mentioned FG.csv - Unicode CSV (preservation format only) - same as in V1 2010-2019 SG to specific not mentioned FG.xlsx - Excel workbook (preferred format) - same as in V1 Additional files in V2: 2G-possible-misinformation-analyzed.csv - Unicode CSV (preservation format only) 2G-possible-misinformation-analyzed.xlsx - Excel workbook (preferred format) <b>ABBREVIATIONS: </b> 2G - Refers to the second-generation of Matsuyama FG - Refers to the direct citation of Matsuyama (the one the second-generation item cites) <b>COLUMN HEADER EXPLANATIONS </b> File name: 2G-possible-misinformation-analyzed. Other column headers in this file have same meaning as explained in V1. The following are additional header explanations: Quote Number - The order of the quote (citation context citing the first generation article given in "FG in bibliography") in the second generation article (given in "2G article") Quote - The text of the quote (citation context citing the first generation article given in "FG in bibliography") in the second generation article (given in "2G article") Translated Quote - English translation of "Quote", automatically translation from Google Scholar Seriousness/Risk - Our assessment of the risk of misinformation and its seriousness 2G topic - Our assessment of the topic of the cited article (the second generation article given in "2G article") 2G section - The section of the citing article (the second generation article given in "2G article") in which the cited article(the first generation article given in "FG in bibliography") was found FG in bib type - The type of article (e.g., review article), referring to the cited article (the first generation article given in "FG in bibliography") FG in bib topic - Our assessment of the topic of the cited article (the first generation article given in "FG in bibliography") FG in bib section - The section of the cited article (the first generation article given in "FG in bibliography") in which the Matsuyama retracted paper was cited

The relationship between physical activity and mental health, especially depression, is one of the most studied topics in the field of exercise science and kinesiology. Although there is strong consensus that regular physical activity improves mental health and reduces depressive symptoms, some debate the mechanisms involved in this relationship as well as the limitations and definitions used in such studies. Meta-analyses and systematic reviews continue to examine the strength of the association between physical activity and depressive symptoms for the purpose of improving exercise prescription as treatment or combined treatment for depression. This dataset covers 27 review articles (either systematic review, meta-analysis, or both) and 365 primary study articles addressing the relationship between physical activity and depressive symptoms. Primary study articles are manually extracted from the review articles. We used a custom-made workflow (Fu, Yuanxi. (2022). Scopus author info tool (1.0.1) [Python]. <a href="https://github.com/infoqualitylab/Scopus_author_info_collection">https://github.com/infoqualitylab/Scopus_author_info_collection</a> that uses the Scopus API and manual work to extract and disambiguate authorship information for the 392 reports. The author information file (author_list.csv) is the product of this workflow and can be used to compute the co-author network of the 392 articles. This dataset can be used to construct the inclusion network and the co-author network of the 27 review articles and 365 primary study articles. A primary study article is "included" in a review article if it is considered in the review article's evidence synthesis. Each included primary study article is cited in the review article, but not all references cited in a review article are included in the evidence synthesis or primary study articles. The inclusion network is a bipartite network with two types of nodes: one type represents review articles, and the other represents primary study articles. In an inclusion network, if a review article includes a primary study article, there is a directed edge from the review article node to the primary study article node. The attribute file (article_list.csv) includes attributes of the 392 articles, and the edge list file (inclusion_net_edges.csv) contains the edge list of the inclusion network. Collectively, this dataset reflects the evidence production and use patterns within the exercise science and kinesiology scientific community, investigating the relationship between physical activity and depressive symptoms. FILE FORMATS 1. article_list.csv - Unicode CSV 2. author_list.csv - Unicode CSV 3. Chinese_author_name_reference.csv - Unicode CSV 4. inclusion_net_edges.csv - Unicode CSV 5. review_article_details.csv - Unicode CSV 6. supplementary_reference_list.pdf - PDF 7. README.txt - text file 8. systematic_review_inclusion_criteria.csv - Unicode CSV <b>UPDATES IN THIS VERSION COMPARED TO V3</b> (Clarke, Caitlin; Lischwe Mueller, Natalie; Joshi, Manasi Ballal; Fu, Yuanxi; Schneider, Jodi (2023): The Inclusion Network of 27 Review Articles Published between 2013-2018 Investigating the Relationship Between Physical Activity and Depressive Symptoms. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4614455_V3) - We added a new file systematic_review_inclusion_criteria.csv.

This dataset consists of the 286 publications retrieved from Web of Science and Scopus on July 6, 2023 as citations for Willoughby et al., 2014: Patrick H. Willoughby, Matthew J. Jansma, and Thomas R. Hoye (2014). A guide to small-molecule structure assignment through computation of (¹H and ¹³C) NMR chemical shifts. Nature Protocols, 9(3), Article 3. https://doi.org/10.1038/nprot.2014.042 We added the DOIs of the citing publications into a Zotero collection. Then we exported all 286 DOIs in two formats: a .csv file (data export) and an .rtf file (bibliography). <b>Willoughby2014_286citing_publications.csv</b> is a Zotero data export of the citing publications. <b>Willoughby2014_286citing_publications.rtf</b> is a bibliography of the citing publications, using a variation of the American Psychological Association style (7th edition) with full names instead of initials. To create <b>Willoughby2014_citation_contexts.csv</b>, HZ manually extracted the paragraphs that contain a citation marker of Willoughby et al., 2014. We refer to these paragraphs as the citation contexts of Willoughby et al., 2014. Manual extraction started with 286 citing publications but excluded 2 publications that are not in English, those with DOIs 10.13220/j.cnki.jipr.2015.06.004 and 10.19540/j.cnki.cjcmm.20200604.201 The silver standard aimed to triage the citing publications of Willoughby et al., 2014 that are at risk of propagating unreliability due to a code glitch in a computational chemistry protocol introduced in Willoughby et al., 2014. The silver standard was created stepwise: First one chemistry expert (YF) manually annotated the corpus of 284 citing publications in English, using their full text and citation contexts. She manually categorized publications as either at risk of propagating unreliability or not at risk of propagating unreliability, with a rationale justifying each category. Then we selected a representative sample of citation contexts to be double annotated. To do this, MJS turned the full dataset of citation contexts (Willoughby2014_citation_contexts.csv) into word embeddings, clustered them using similarity measures using BERTopic's HDBS, and selected representative citation contexts based on the centroids of the clusters. Next the second chemistry expert (EV) annotated the 77 publications associated with the citation contexts, considering the full text as well as the citation contexts. <b>double_annotated_subset_77_before_reconciliation.csv</b> provides EV and YF's annotation before reconciliation. To create the silver standard YF, EV, and JS discussed differences and reconciled most differences. YF and EV had principled reasons for disagreeing on 9 publications; to handle these, YF updated the annotations, to create the silver standard we use for evaluation in the remainder of our JCDL 2024 paper (<b>silver_standard.csv</b>) <b>Inter_Annotator_Agreement.xlsx</b> indicates publications where the two annotators made opposite decisions and calculates the inter-annotator agreement before and after reconciliation together. <b>double_annotated_subset_77_before_reconciliation.csv</b> provides EV and YF's annotation after reconciliation, including applying the reconciliation policy.

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] ).

File Name: Inclusion_Criteria_Annotation.csv Data Preparation: Xiaoru Dong Date of Preparation: 2018-12-14 Data Contributions: Jingyi Xie, Xiaoru Dong, Linh Hoang Data Source: Cochrane systematic reviews published up to January 3, 2018 by 52 different Cochrane groups in 8 Cochrane group networks. Associated Manuscript authors: Xiaoru Dong, Jingyi Xie, Linh Hoang, and Jodi Schneider. Associated Manuscript, Working title: Machine classification of inclusion criteria from Cochrane systematic reviews. Description: The file contains lists of inclusion criteria of Cochrane Systematic Reviews and the manual annotation results. 5420 inclusion criteria were annotated, out of 7158 inclusion criteria available. Annotations are either "Only RCTs" or "Others". There are 2 columns in the file: - "Inclusion Criteria": Content of inclusion criteria of Cochrane Systematic Reviews. - "Only RCTs": Manual Annotation results. In which, "x" means the inclusion criteria is classified as "Only RCTs". Blank means that the inclusion criteria is classified as "Others". Notes: 1. "RCT" stands for Randomized Controlled Trial, which, in definition, is "a work that reports on a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table." [Randomized Controlled Trial publication type definition from https://www.nlm.nih.gov/mesh/pubtypes.html]. 2. In order to reproduce the relevant data to this, please get the code of the project published on GitHub at: https://github.com/XiaoruDong/InclusionCriteria and run the code following the instruction provided.

Data for Post-retraction citation: A review of scholarly research on the spread of retracted science Schneider, Jodi; Das, Susmita; Léveillé, Jacqueline; Proescholdt, Randi Contact: Jodi Schneider jodi@illinois.edu & jschneider@pobox.com ********** OVERVIEW ********** This dataset provides further analysis for an ongoing literature review about post-retraction citation. This ongoing work extends a poster presented as: Jodi Schneider, Jacqueline Léveillé, Randi Proescholdt, Susmita Das, and The RISRS Team. Characterization of Publications on Post-Retraction Citation of Retracted Articles. Presented at the Ninth International Congress on Peer Review and Scientific Publication, September 8-10, 2022 hybrid in Chicago. https://hdl.handle.net/2142/114477 (now also in https://peerreviewcongress.org/abstract/characterization-of-publications-on-post-retraction-citation-of-retracted-articles/ ) Items as of the poster version are listed in the bibliography 92-PRC-items.pdf. Note that following the poster, we made several changes to the dataset (see changes-since-PRC-poster.txt). For both the poster dataset and the current dataset, 5 items have 2 categories (see 5-items-have-2-categories.txt). Articles were selected from the Empirical Retraction Lit bibliography (https://infoqualitylab.org/projects/risrs2020/bibliography/ and https://doi.org/10.5281/zenodo.5498474 ). The current dataset includes 92 items; 91 items were selected from the 386 total items in Empirical Retraction Lit bibliography version v.2.15.0 (July 2021); 1 item was added because it is the final form publication of a grouping of 2 items from the bibliography: Yang (2022) Do retraction practices work effectively? Evidence from citations of psychological retracted articles http://doi.org/10.1177/01655515221097623 Items were classified into 7 topics; 2 of the 7 topics have been analyzed to date. ********************** OVERVIEW OF ANALYSIS ********************** DATA ANALYZED: 2 of the 7 topics have been analyzed to date: field-based case studies (n = 20) author-focused case studies of 1 or several authors with many retracted publications (n = 15) FUTURE DATA TO BE ANALYZED, NOT YET COVERED: 5 of the 7 topics have not yet been analyzed as of this release: database-focused analyses (n = 33) paper-focused case studies of 1 to 125 selected papers (n = 15) studies of retracted publications cited in review literature (n = 8) geographic case studies (n = 4) studies selecting retracted publications by method (n = 2) ************** FILE LISTING ************** ------------------ BIBLIOGRAPHY ------------------ 92-PRC-items.pdf ------------------ TEXT FILES ------------------ README.txt 5-items-have-2-categories.txt changes-since-PRC-poster.txt ------------------ CODEBOOKS ------------------ Codebook for authors.docx Codebook for authors.pdf Codebook for field.docx Codebook for field.pdf Codebook for KEY.docx Codebook for KEY.pdf ------------------ SPREADSHEETS ------------------ field.csv field.xlsx multipleauthors.csv multipleauthors.xlsx multipleauthors-not-named.csv multipleauthors-not-named.xlsx singleauthors.csv singleauthors.xlsx *************************** DESCRIPTION OF FILE TYPES *************************** BIBLIOGRAPHY (92-PRC-items.pdf) presents the items, as of the poster version. This has minor differences from the current data set. Consult changes-since-PRC-poster.txt for details on the differences. TEXT FILES provide notes for additional context. These files end in .txt. CODEBOOKS describe the data we collected. The same data is provided in both Word (.docx) and PDF format. There is one general codebook that is referred to in the other codebooks: Codebook for KEY lists fields assigned (e.g., for a journal or conference). Note that this is distinct from the overall analysis in the Empirical Retraction Lit bibliography of fields analyzed; for that analysis see Proescholdt, Randi (2021): RISRS Retraction Review - Field Variation Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2070560_V1 Other codebooks document specific information we entered on each column of a spreadsheet. SPREADSHEETS present the data collected. The same data is provided in both Excel (.xlsx) and CSV format. Each data row describes a publication or item (e.g., thesis, poster, preprint). For column header explainations, see the associated codebook. ***************************** DETAILS ON THE SPREADSHEETS ***************************** field-based case studies CODEBOOK: Codebook for field --REFERS TO: Codebook for KEY DATA SHEET: field REFERS TO: Codebook for KEY --NUMBER OF DATA ROWS: 20 NOTE: Each data row describes a publication/item. --NUMBER OF PUBLICATION GROUPINGS: 17 --GROUPED PUBLICATIONS: Rubbo (2019) - 2 items, Yang (2022) - 3 items author-focused case studies of 1 or several authors with many retracted publications CODEBOOK: Codebook for authors --REFERS TO: Codebook for KEY DATA SHEET 1: singleauthors (n = 9) --NUMBER OF DATA ROWS: 9 --NUMBER OF PUBLICATION GROUPINGS: 9 DATA SHEET 2: multipleauthors (n = 5 --NUMBER OF DATA ROWS: 5 --NUMBER OF PUBLICATION GROUPINGS: 5 DATA SHEET 3: multipleauthors-not-named (n = 1) --NUMBER OF DATA ROWS: 1 --NUMBER OF PUBLICATION GROUPINGS: 1 ********************************* CRediT <http://credit.niso.org> ********************************* Susmita Das: Conceptualization, Data curation, Investigation, Methodology Jaqueline Léveillé: Data curation, Investigation Randi Proescholdt: Conceptualization, Data curation, Investigation, Methodology Jodi Schneider: Conceptualization, Data curation, Funding acquisition, Investigation, Methodology, Project administration, Supervision

This dataset contains the files used to perform the work savings and recall evaluation in the study titled "Data from Testing a filtering strategy for systematic reviews: Evaluating work savings and recall."

The data contains a list of articles given low score by the RCT Tagger and an error analysis of them, which were used in a project associated with the manuscript "Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews". Change made in this V3 is that the data is divided into two parts: - Error Analysis of 44 Low Scoring Articles with MEDLINE RCT Publication Type. - Error Analysis of 244 Low Scoring Articles without MEDLINE RCT Publication Type.

File Name: WordsSelectedByManualAnalysis.csv Data Preparation: Xiaoru Dong, Linh Hoang Date of Preparation: 2018-12-14 Data Contributions: Jingyi Xie, Xiaoru Dong, Linh Hoang Data Source: Cochrane systematic reviews published up to January 3, 2018 by 52 different Cochrane groups in 8 Cochrane group networks. Associated Manuscript authors: Xiaoru Dong, Jingyi Xie, Linh Hoang, and Jodi Schneider. Associated Manuscript, Working title: Machine classification of inclusion criteria from Cochrane systematic reviews. Description: this file contains the list of 407 informative words reselected from the 1655 words by manual analysis. In particular, from the 1655 words that we got from information gain feature selection, we then manually read and eliminated the domain specific words. The remaining words then were selected into the "Manual Analysis Words" as the results. Notes: Even though the list of words in this file was selected manually. However, in order to reproduce the relevant data to this, please get the code of the project published on GitHub at: https://github.com/XiaoruDong/InclusionCriteria and run the code following the instruction provided.

We used the following keywords files to identify categories for journals and conferences not in Scopus, for our STI 2023 paper "Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science". The first four text files each contains keywords/content words in the form: 'keyword1', 'keyword2', 'keyword3', .... The file title indicates the name of the category: file1: healthscience_words.txt file2: lifescience_words.txt file3: physicalscience_words.txt file4: socialscience_words.txt The first four files were generated from a combination of software and manual review in an iterative process in which we: - Manually reviewed venue titles were not able to automatically categorize using the Scopus categorization or extending it as a resource. - Iteratively reviewed uncategorized venue titles to manually curate additional keywords as content words indicating a venue title could be classified in the category healthscience, lifescience, physicalscience, or socialscience. We used English content words and added words we could automatically translate to identify content words. NOTE: Terminology with multiple potential meanings or contain non-English words that did not yield useful automatic translations e.g., (e.g., Al-Masāq) were not selected as content words. The fifth text file is a list of stopwords in the form: 'stopword1', 'stopword2, 'stopword3', ... file5: stopwords.txt This file contains manually curated stopwords from venue titles to handle non-content words like 'conference' and 'journal,' etc. This dataset is a revision of the following dataset: Version 1: Lee, Jou; Schneider, Jodi: Keywords for manual field assignment for Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science. University of Illinois at Urbana-Champaign Data Bank. Changes from Version 1 to Version 2: - Added one author - Added a stopwords file that was used in our data preprocessing. - Thoroughly reviewed each of the 4 keywords lists. In particular, we added UTF-8 terminology, removed some non-content words and misclassified content words, and extensively reviewed non-English keywords.

This annotation study compared RobotReviewer's data extraction to that of three novice data extractors, using six included articles synthesized in one Cochrane review: Bailey E, Worthington HV, van Wijk A, Yates JM, Coulthard P, Afzal Z. Ibuprofen and/or paracetamol (acetaminophen) for pain relief after surgical removal of lower wisdom teeth. Cochrane Database Syst Rev. 2013; CD004624; doi:10.1002/14651858.CD004624.pub2 The goal was to assess the relative advantage of RobotReviewer's data extraction with respect to quality.

Supporting information for "Urinary Phthalate Metabolite Concentrations and Hot Flashes in Pre- and Perimenopausal Women from the Midlife Women’s Health Study." This file contains tables of the results of stratified analyses of the associations of hot flash outcomes with urinary phthalates metabolites by menopause status, race/ethnicity, body mass index, and depressive status. This file also contains supplementary HPLC methods for the analysis of phthalate metabolites.

The data file contains detailed information of the Cochrane reviews that were used in a project associated with the manuscript (working title) "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".