DOI: 10.5281/zenodo.17183276
title: PreprintToPaper dataset
title: Connecting bioRxiv preprints with journal publications

description: PreprintToPaper dataset: connecting bioRxiv preprints with journal publications

Some preprints get published, while others remain preprints without ever being formally published in a journal. The PreprintToPaper dataset is the first of its kind, as it attempts to automatically collect publication information from bioRxiv preprints and track whether submitted preprints have resulted in a publication.

The dataset generated in this study was retrieved from the bioRxiv preprint server and the Crossref metadata API in July 2024. The dataset covers two time periods: the pre-pandemic period (2016–2018) and the COVID-19 pandemic period (2020–2022). The dataset contains detailed metadata about preprints and their published versions, including titles, authors, abstracts, institutions, submission and publication dates, licenses, and subject categories. The metadata was processed to facilitate analysis, for example, by standardizing date formats, normalizing author names, and selecting the first and last version of each preprint.

The PreprintToPaper dataset offers diverse opportunities to study changes in titles, abstracts, and author composition over different stages of a preprint, starting from the initial submission through revision stages to the final published version.

Main file provided:



PreprintToPaper.csv — This is the main dataset containing all processed preprints from both time periods.


Keywords

BioRxiv, Crossref, preprints, publications

Paper

A paper describing this dataset is currently under preparation.

Usage

Data Collection



Preprint metadata were retrieved via the bioRxiv API - api.biorxiv.org/details/[server]/[interval]/[cursor]/[format]

Published paper metadata were retrieved via the Crossref API based on published DOI. api.crossref.org/works/[doi]


As a result, 48,300 preprint records were obtained for the 2016–2018 period and 152,869 for the 2020–2022 period.

Data Processing



If both the initial and last versions of the preprint were available during the relevant period, both versions were retained. If only one version was available and it was the initial version, that version was retained. If only non-initial versions were available during the relevant period, the records were deleted.

Unlinked publications in bioRxiv were identified by checking preprints. The preprints were identified by checking preprints against two criteria: title similarity and author similarity. Title similarity was measured using a matching score, and only cases with a score between 0.75 and 1 were considered. For the 19,090 rows that met this threshold, an additional author match score was calculated to more accurately identify unlinked publications.

The dataset was categorized into 3 groups: published, preprint only and gray zone. See explanations below:



Published:  Preprints that were already linked on bioRxiv to a published article.

Preprint only:  Preprints that did not have any corresponding published version and could not be linked in bioRxiv.

Gray zone: Preprints with potential matches based on title and author similarity, but without a confirmed publication DOI link.




 

After data processing, in total, 33,687 preprints remained for the period 2016–2018, and 111,830 preprints for the period 2020–2022.

Final Dataset

The dataset includes 145,517 preprints, of which:



90,614 were linked to journal publications “Published”,

35,813 remain "Preprint Only",

19,090 are "Gray Zone".


Summary Statistics






Period



Gray Zone



Preprint Only



Published



Total Preprints







2016



359



1,019



3,343



4,721





2017



841



2,314



8,191



11,346





2018



1,121



4,115



12,943



18,179





2020



3,746



8,884



26,081



38,711





2021



5,292



8,987



22,539



36,818





2022



7,731



10,494



17,517



35,742





Total



19,090



35,813



90,614



145,517





 

 

Main Dataset Column Descriptions

 






Column Name



Description







biorxiv_doi



DOI for the bioRxiv preprint





biorxiv_title_1st



Preprint title - initial version





biorxiv_title_last



Preprint title – last version





biorxiv_authors_1st



Preprint authors – initial version





biorxiv_authors_last



Preprint authors – last version





biorxiv_author_corresponding_1st



Corresponding author – initial version





biorxiv_author_corresponding_last



Corresponding author - last version.





biorxiv_author_corresponding_institution



Affiliation of corresponding author





biorxiv_submission_date_1st



Submission date – initial version





biorxiv_submission_date_last



Submission date – last version





custom_biorxivVersion_dateDifference



Number of days between initial and last submission





biorxiv_version_last



Last preprint version number (e.g., 5 if 5 versions have been submitted)





biorxiv_type



Preprint type on bioRxiv (e.g., confirmatory, contradictory, new result)





biorxiv_license



Preprint license





biorxiv_category



Subject category assigned by bioRxiv (e.g., bioinformatics, genetics)





biorxiv_jatsxml



JATS XML structure (if available). This provides a link to the JATS XML file of the preprint. The file contains both metadata and full text of preprint.





biorxiv_abstract_1st



Abstract – initial version





biorxiv_abstract_last



Abstract – last version





biorxiv_published_doi



DOIs of published versions of preprints. The values come from two sources: (1) DOIs directly provided by bioRxiv for preprints with an official published link, and (2) DOIs additionally identified for preprints in the gray zone, where a publication was found but not directly linked in bioRxiv.





custom_status



Custom classification of the preprint status: Published, Preprint Only, or Gray Zone





crossref_journal_name



Journal name where the preprint was published (retrieved from Crossref)





crossref_title



Published paper title (listed in Crossref)





crossref_authors



Publish paper author list from Crossref





crossref_publication_date



Publication date (either online publication or issue date)





crossref_publication_date_type



Indicates whether the final date was from online publication or issue





custom_submission&publication_dateDiff



Days from preprint submission to publication





author_count_diff



Difference in the number of authors between the bioRxiv preprint and its published version. Positive = Positive values indicate more authors, negative = negative values indicate fewer.





title_match_score



Text similarity score (e.g., from SequenceMatcher) between the bioRxiv preprint title and the published article title. Only pairs with a score between 0.75 and 1.0 were considered potential matches.





author_match_score



Similarity score between preprint and published author lists, used to assess how closely the authors of a preprint match those of the corresponding published paper, particularly in gray zone cases. This score helps validate whether a gray zone publication link is correct.





 

Additional Human-Annotated Subset

In addition to the main dataset, a human-annotated subset is provided to support the evaluation of the automatic matching procedure. This subset includes preprints with custom_status = "gray zone" and a title match score of 0.75. The score is based on the similarity between titles and ranges from 0.75 to 1. The threshold of 0.75 was chosen based on checks performed on preprints with an official publication link in bioRxiv. In these checks, the similarity between preprint titles and the titles of their published versions was calculated, and in 91% of cases the score was ≥ 0.75. The results are presented in the file PreprintToPaper_GrayZone.csv. Matches in this subset were reviewed by two annotators using abstracts and, in some cases, full texts. This subset serves as an additional dataset for assessing the accuracy of the automatic matching procedure.

·       File name: PreprintToPaper_GrayZone.csv

 

Column Descriptions






Column Name



Description







year



Preprint submission year





biorxiv_doi



bioRxiv preprint DOI





suspected_published_doi



Suspected DOI of the published article. Contains DOIs identified for gray zone preprints, where a potential published version was found but cannot be fully confirmed.





author_match_score



This score was used in the gray zone subset with 0.75 title match score to validate potential matches. Cases with a high author match score (close to 1) were in the majority confirmed as true matches by both annotators, while cases with a score of 0 were evaluated as non-matched.





annotator1 / annotator2



Labels from two annotators (True, False, NA)





 

Version-History Subset

A separate version-history subset is provided to enable detailed analyses of how preprints evolve across multiple versions. This file contains all available in-period versions for preprints that have version 1 and at least one additional version within the study periods (2016–2018 and 2020–2022). Preprints with only a single version, or multi-version preprints for which version 1 is not present in our data, are not included in this subset. Each row corresponds to a single bioRxiv version.



File name: PreprintToPaper_MultipleVersions.csv


Column Descriptions




Column Name
Description




biorxiv_doi
DOI of the preprint.


biorxiv_title
Title of this version.


biorxiv_authors
Author list for this version.


biorxiv_author_corresponding
Corresponding author for this version.


biorxiv_author_corresponding_institution
Affiliation of the corresponding author for this version.


biorxiv_submission_date
Submission date of this version.


biorxiv_version
Version number on bioRxiv.


biorxiv_type
Preprint type on bioRxiv for this version.


biorxiv_license
License for this version.


biorxiv_category
Subject category assigned by bioRxiv.


biorxiv_jatsxml
JATS XML structure (if available) for this version.


biorxiv_published_doi
DOIs of published versions of preprints.




This version-level subset complements the main dataset (which stores only the first and last version per preprint) and allows users to study, for example, incremental title changes or author-list updates across multiple bioRxiv versions.