DOI: 10.5281/zenodo.13166068
title: Methodology data of "A qualitative and quantitative citation analysis toward retracted articles: a case of study"

description: This document contains the datasets and visualizations generated after the application of the methodology defined in our work: "A qualitative and quantitative citation analysis toward retracted articles: a case of study". The methodology defines a citation analysis of the Wakefield et al. [1] retracted article from a quantitative and qualitative point of view. The data contained in this repository are based on the first two steps of the methodology. The first step of the methodology (i.e. “Data gathering”) builds an annotated dataset of the citing entities, this step is largely discussed also in [2]. The second step (i.e. "Topic Modelling") runs a topic modeling analysis on the textual features contained in the dataset generated by the first step. 


Note: the data are all contained inside the "method_data.zip" file. You need to unzip the file to get access to all the files and directories listed below.


 


Data gathering


The data generated by this step are stored in "data/":



	
"cits_features.csv": a dataset containing all the entities (rows in the CSV) which have cited the Wakefield et al. retracted article, and a set of features characterizing each citing entity (columns in the CSV). The features included are: DOI ("doi"), year of publication ("year"), the title ("title"), the venue identifier ("source_id"), the title of the venue ("source_title"), yes/no value in case the entity is retracted as well ("retracted"), the subject area ("area"), the subject category ("category"), the sections of the in-text citations ("intext_citation.section"), the value of the reference pointer ("intext_citation.pointer"), the in-text citation function ("intext_citation.intent"), the in-text citation perceived sentiment ("intext_citation.sentiment"), and a yes/no value to denote whether the in-text citation context mentions the retraction of the cited entity    ("intext_citation.section.ret_mention").
	Note: this dataset is licensed under a Creative Commons public domain dedication (CC0).
	 
	
"cits_text.csv": this dataset stores the abstract ("abstract") and the in-text citations context ("intext_citation.context") for each citing entity identified using the DOI value ("doi").
	Note: the data keep their original license (the one provided by their publisher). This dataset is provided in order to favor the reproducibility of the results obtained in our work.



 


Topic modeling
We run a topic modeling analysis on the textual features gathered (i.e. abstracts and citation contexts). The results are stored inside the "topic_modeling/" directory. The topic modeling has been done using MITAO, a tool for mashing up automatic text analysis tools, and creating a completely customizable visual workflow [3]. The topic modeling results for each textual feature are separated into two different folders, "abstracts/" for the abstracts, and "intext_cit/" for the in-text citation contexts. Both the directories contain the following directories/files:    



	

	
"mitao_workflows/": the workflows of MITAO. These are JSON files that could be reloaded in MITAO to reproduce the results following the same workflows.
	
	

	
"corpus_and_dictionary/": it contains the dictionary and the vectorized corpus given as inputs for the LDA topic modeling.
	
	

	
"coherence/coherence.csv": the coherence score of several topic models trained on a number of topics from 1 - 40.
	
	

	
"datasets_and_views/": the datasets and visualizations generated using MITAO.  
	



 


References



	
Wakefield, A., Murch, S., Anthony, A., Linnell, J., Casson, D., Malik, M., Berelowitz, M., Dhillon, A., Thomson, M., Harvey, P., Valentine, A., Davies, S., & Walker-Smith, J. (1998). RETRACTED: Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. The Lancet, 351(9103), 637–641. https://doi.org/10.1016/S0140-6736(97)11096-0
	

	
Heibi, I., & Peroni, S. (2020). A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article v1 (protocols.io.bdc4i2yw) [Data set]. In protocols.io. ZappyLab, Inc. https://doi.org/10.17504/protocols.io.bdc4i2yw
	
	

	
 
	Ferri, P., Heibi, I., Pareschi, L., & Peroni, S. (2020). MITAO: A User Friendly and Modular Software for Topic Modelling [JD]. PuntOorg International Journal, 5(2), 135–149. https://doi.org/10.19245/25.05.pij.5.2.3