COVID-19 Preprints

This repository contains code used to extract details of preprints related to COVID-19 and visualize their distribution over time. Work by Nicholas Fraser and Bianca Kramer.

Preprint data is updated monthly by collecting preprints added or updated since the previous sample date. Details of the current release can be found in data/metadata.json, where release_date refers to the date on which the dataset was released, sample_date the date on which data was collected, and posted_date the cut-off point for preprints to be included in the accompanying visualizations based on their posting date.

From March 2023 onwards, the dataset is archived separately on figshare: https://doi.org/10.6084/m9.figshare.22707346.

A citable version of this repository is also available on figshare, here: https://doi.org/10.6084/m9.figshare.12033672.

Note that this dataset is not exhaustive, but aims to collate information from some of the main sources of preprint metadata.

The process for collecting preprint metadata is documented fully here. In general terms, preprint metadata are harvested from four main sources:

• Crossref (using the rcrossref package). All records with the type field defined as posted-content and subtype field defined as preprintare harvested, as well as records from SSRN (where the type field is instead defined as journal-article). Preprint records are then matched to known preprint repositories based on institution, publisher and group-title metadata fields.

• DataCite (using the rdatacite package). All records with the resourceType or resourceTypeGeneral field defined as Preprint are harvested. Preprint records are matched to known preprint repositories based on client fields.
  Note: as of 2022, arXiv also uses DataCite DOIs, with all backfiles receiving DataCite DOIs over the course of 2022. To prevent including this arXiv backlog, DataCite harvesting is currently limited to ResearchGate, Zenodo and Figshare.

• arXiv (using the aRxiv package). Records are harvested by searching directly for COVID-19 related keywords in titles or abstracts using the built-in search functionality of the arXiv API.

• RePEc (using the oai package)). All record types are initally harvested, and subsequently filtered for those with the Type field defined as preprint. NB RePEc is not a preprint server in itself but an indexing server for multiple individual archives.
  Note: For certain time periods (e.g. between 2021-07-15 and 2021-09-08 and after 2021-12-30) no new preprints got retrieved from RePEc.

For all sources, preprints are classified as being related to COVID-19 on the basis of keyword matches in their titles or abstracts (where available). The search string is defined as: coronavirus OR covid-19 OR sars-cov OR ncov-2019 OR 2019-ncov OR hcov-19 OR sars-2.

In some cases, multiple preprint metadata records are registered for a single preprint (e.g. ChemRxiv registers a new Crossref record for each new version of a preprint). In these cases, only the earliest posted version is included in this dataset. Depuplication is done based on versioning information in dois as well as on case-insensitive title-matching. Additionally, some preprints are deposited to multiple preprint repositories - in these cases all preprint records are included.