retraction-indexing-agreement

This is a longitudinal project that assesses the retraction indexing of publications across bibliographic databases.

Tag v2.0.0 [Latest Release]

Description

This Jupyter notebook is used for the assessment of retraction indexing agreement among data sources: BCI, BIOABS, CCC, Compendex, Crossref, GEOBASE, MEDLINE, PubMed, Retraction Watch, Scopus, and Web of Science Core.

Setup 1. Follow these steps to set up the code: 2. Install the proper version of Jupyter notebook (our version: 6.4.11). 3. Install the standard Python libraries: ast, collections, datetime, json, os, re, time, and unicodedata. 4. Install third-party packages: tqdm, pandas, requests, seaborn, matplotlib, numpy, and yake. 5. Create configuration file (config.json). Insert your email and API keys for Elsevier databases (Compendex, GEOBASE, and Scopus) and Web of Science Core. Institutional token (insttoken) will be required for Elsevier if you are running the code.

Run the Code 1. Download the "retraction-indexing-agreement" folder or clone the web URL: https://github.com/infoqualitylab/retraction-indexing-agreement.git 2. Set your working directory to retraction-indexing-agreement and create data, result, src subfolders. Create subfolders for data as shown below. 3. Run the code in the src subfolder.

retraction-indexing-agreement/ | config.json data/ coverednotindexed/ crossref/ engineeringvillage/ journal/ pubmed/ retractionwatch/ scopus/ unionlist/ webofscience/ result src/ Step1_DataCollectionFromSources_and_UnionList.ipynb Step2_HandlingItemsWithoutDOI_ButWithPubMedID.ipynb Step3_DataCollection_of_Indexedasretracted_and_Coveredin.ipynb Step4_DataCollection_of_RetractionYear.ipynb Step5_JournalFieldClassification.ipynb Step6_ DataAnalysis Step7_ OtherInPaperAnalysis.ipynb

1. Enter your email, API Keys and insttoken into the config.json file
2. Run the files in the src files
3. Install the libraries as mentioned above
4. Run the cells accordingly

Cite code v2.0.0 as: - 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 - (part of https://doi.org/10.5281/zenodo.7851297)

Code contributors: - Jou Lee (ORCID: 0000-0001-8927-0370) prototyped an earlier version v1.1.0 pipeline for the STI2023 Paper.

Preprint: - 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 Indexing (Version 1) [Data set]. University of Illinois at Urbana-Champaign Databank. https://doi.org/10.13012/B2IDB-8114408_V1

Tag v1.2.1

Cite code v1.2.1 as: - 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 contributors: - Jou Lee (ORCID: 0000-0001-8927-0370) prototyped an earlier version v1.1.0 pipeline for the STI2023 Paper.

Paper: - 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

Slides: - Salami, M. O., McCumber, C., & Schneider, J. (2024, November 13). Reassessment of the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science [Conference presentation]. ASIS&T MET-STI 2024: Workshop on Informetric, Scientometric and Scientific and Technical Information Research, virtual. https://hdl.handle.net/2142/124990

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 Databank. https://doi.org/10.13012/B2IDB-8457537_V1

Tag v1.1.0

Cite code v1.1.0 as:
- Jou (Laura) Lee (2023). Code for Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science

Code authors: - Jou Lee (0000-0001-8927-0370) with contributions from Malik Salami (0000-0002-2329-5660) and Tzu-Kun Hsiao (0000-0002-2314-5777).

Paper: - Schneider, J., Lee, J., Zheng, H., & Salami, M. O. (2023, September). Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science [Conference paper]. In 27th International Conference on Science, Technology and Innovation Indicators (STI 2023). International Conference on Science, Technology and Innovation Indicators. http://doi.org/10.55835/6441e5cae04dbe5586d06a5f