Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

OpenPaleo

Resources to investigate the 'openness' of Paleontological research.

Project concept

The idea of this project is to perform a range of meta-analyses into the published Palaeontology literature. This will include looking at factors such as:

  • Quantitative analysis of the 'openness' of Palaeontology research.
  • Citation frequences for different journals, compared to their impact factors.
  • How aware researchers are that they may have signed away copyright.

We strongly encourage others to participate in the project, propose their own ideas, and to contribute or re-use any of the data or other information available here.

Ultimately, this information might prove useful in developing standards, protocols, and best practices for palaeontological research and publishing.

Data sources

Google Scholar

Journal selection was for the top-20 cited Paleontology journals according to Google Scholar.

Scopus

Metadata were extracted from Scopus journal-by-journal (as csv files), with the only filter being on the dates, constrained to published articles between 2015-2016. This includes information such as:

  • Authors, titles, and year of publication.
  • Number of citations (according to Scopus).
  • Article Digital Object Identifier (DOI).

Scopus screenshot

It is worth noting here that due to the time scale of this study, virtually every paper analysed here could be legally self-archived in accordance with the journal policy (i.e., green Open Access), for free, and keeping with any published-enforced embargo period (at most 12 months here). It is further worth noting that this is clearly not the case.

A little hiccup

Note that there was an issue here with encoding of the csv exports from Scopus. This displaced some of the cells when viewed in Excel, so the delimiting was fixed for each file were needed to realign the cells properly. This was done simply be converting them to text, opening back up in Excel, specfying explicitly that commas were the delimiter and using UTF-8 encoding. After this, the files could be re-saved in csv format as needed.

For Acta Palaeontological Polonica, this was not entirely resolved, and two lines of fragmented entries were removed prior to subsequent analysis.

Clean data

Using Visdat R package to visually inspect the data, we were able to spot the misaligned rows and block shifted columns. These formatting errors were then fixed in MS-Excel and saved again in CSV format with UTF-8 encoding. Following this, the headers were formatted for user friendliness during analysis and the empty rows and columns were scrubbed off the data using Janitor R package.

PLOS ONE

Data for PLOS ONE were obtained using the Rplos package in R. The code, resulting data, and Unpaywall query results can all be found here. Note that some of the data here are different to that obtained to Scopus queries.

Unpaywall

The next phase is to use the Unpaywall DOI checker on the DOI list for each journal. This provides information such as:

  • The Open Access state (true or false)
  • Publication date
  • Source of evidence for Open Access status

All of the results of these steps are available within this repository.

Google Scholar

While Unpaywall checks to see if legitimate versions of articles have been made OA (i.e., via green self-archiving routes), researchers often also often tend to share their articles in non-copyright compliant ways. This includes on platforms such as ResearchGate or Academia.edu.

Therefore, data will be cross-checked with Google Scholar, which has this information at an article-level, to see:

  • Whether articles are freely available;
  • Which versions are available;
  • Which services or platforms are most used.

For this, Acta Palaeontological Polonica, Bulletin of Geosciences, PLOS ONE, and Palaeontologica Electronica were all removed prior to analysis, as they are all fully Open Access journals. All others are considered as 'hybrid' journals, and therefore contain a mixture of paywalled and non-paywalled content.

Author survey

These data will be supplemented by conducting an author survey, built in Google Forms. Suggestions for this survey will be supplemented using an open system through GitHub here.

Corresponding author addresses were obtained from Scopus correspondence address metadata. Here, they were extracted simply by setting : as the delimiter to separate the emails from the rest of the address, and added as a new column. Much of the email data were incomplete, and therefore required manual checks of the relevant literature to acquire.

The following aspects will be looked at, where applicable.

  • Open Access status
  • Article Processing Charge
  • If a self-archived version is available
  • Article license
  • Code availabaility and license
  • Data availabilty and license
  • Whether a new taxon was named
  • Whether new taxa have relevant PIDs (e.g., via ZooBank)
  • Whether specimens analysed are archived in a public reposiitory/museum
  • What the copyright status of articles is

Results will be reported anonymously, and available for inspection and reuse.

Wikidata / WikiCite

WikiCite provides a lot of integrated data around scholarly literature, linking research papers with authors, topics, species, and much, much more. All data is CCZero and integrates many online resources. Scholia gives an idea what it can do for paleontology.

Communications

The intention is to port this project into the Open Science Framework, and then to paleorXiv as a preprint submission. Whether or not it will be submitted to a peer reviewed journal is unknown for now.

Limitations

The journal selection choice explicitly excludes some multi-disciplinary Open Access journals such as PeerJ and Scientific Reports, which palaeontologists also frequently publish in.

Palaeontologica Electronica does not provide DOIs for published articles. However, it is a fully Open Access journal, and therefore cross-checking the data with Unpaywall would be redundant in this case.

About

Resources to investigate the 'openness' of Paleontological research

Resources

License

Code of conduct

Packages

No packages published