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13 open publishing tools

This is the second of three newsletters about open science tools. Please click here for Part 1 on 10 free tools that help you with your literature search. Part 3 will showcase tools for identifying research databases specific to your particular enquiry. This time we are looking at 13 open publishing tools. Beyond publishing papers without a fee, open science is about trying to make the whole research process transparent, for example by publishing data sets and protocols. By revealing this, true replication can be attempted. Some open access journals require a publishing fee (which they often refer to as an article processing charge) while others do not. This may reflect the journal’s quality, but then again, it may not. How can you find a quality open access journals? What criteria could you use and how easily can you filter through what is available? How do you find the right repository for your data or preprint? Do your funding sources have any specifications about open science?  Again, I extend thanks to Anna Clemens for the information below, which is substantially in her words.

DIRECTORY OF OPEN ACCESS JOURNALS (DOAJ)

This database can help to find the right destination for your publication. First launched in 2013 at Lund University in Sweden, the DOAJ is an independent database of peer-reviewed open access journals across disciplines. It is curated by its community. You can enter keywords or browse subjects to find a suitable journal. Article processing charges are stated and there is editorial information on peer review, aims and scope and the average time between submission and publication.

Publishing a preprint

Preprint repositories store are openly accessible manuscripts that have not been peer-reviewed or edited but have been checked in some way before being stored. There are multidisciplinary preprint servers and discipline specific ones.   For a curated database of Open Access Repositories, you can check OPenDOAR which is operated by the UK based not for profit organisation, JISC.

ARXIV 
Launched in 1991, arXiv is the oldest preprint repository and is operated by Cornell University. It stores manuscripts in mathematics, physics, computer science, economics, electrical engineering, quantitative biology and related subjects.   SSRN SSRN is a collection of more than 50 preprint repositories (called research networks– RN) across disciplines. For example, you’ll find repositories for architecture (ArchRN), biochemistry (BiochemRN), cognitive science (CSN), ecology (EcoRN), financial planning (FinPlanRN) and nursing (NursingRN). SSRN is run by the publisher Elsevier.

CHEMRXIV
The preprint server ChemRxiv accepts papers in specific to chemistry: catalysis, agricultural chemistry, nanoscience, chemical education and other fields. It was only launched in 2017 and is jointly owned and operated by various international chemical societies: the US, German, Chinese, and Japanese Chemical Societies and the Royal Society of Chemistry in the UK. You can forward your preprint for submission to certain journals with just a few clicks, which should save time compared to some journals’ submission portals.

BIORXIV AND MEDRXIV
As the titles indicate, BioRxiv and MedRxiv are preprint servers for life science and health science manuscripts, respectively. Both are operated by Cold Spring Harbor Laboratory, which is a not for profit organisation, and both allow for direct transfer to a large number of journals.   AUTHOREA
Authorea is a collaborative writing tool. Here you can publicly post your manuscript, and this can be displayed with interactive figures and hosted data. Authorea is owned by the academic publishing house, Wiley.

Publishing protocols, data sets and other research material

Some funders and publications also require researchers to store data sets and codes. For this, open access repositories for various research outputs are useful. Here are some, but an extensive database of data repositories in all fields is available at re3data.org which is funded by the German Research Foundation (DFG).

PROTOCOLS.IO
How often do you find all the protocols and details of a scientific paper’s methods? Protocols.io allows you to publish and even update any methodological information. Once published, you receive a DOI that you can link to the corresponding paper. You can also use this site as a reminder, running your protocols as checklists while conducting the research. Creating and publishing protocols as an individual researcher is free (and apparently will remain so), although this is a company-owned service and it charges companies and institutions for licenses.

FIGSHARE
On figshare, researchers can share posters, presentations, datasets, videos, code and other research outputs in various file formats. Users have 20 GB of free private space, which is great for collaborating on a project. The space for public files is unlimited. Similarly to protocols.io, figshare provides a DOI for all published files. The platform is owned by Digital Science, a company which also offers several open science tools.

ZENODO
A non-commercial alternative to figshare is Zenodo, which was developed within the EU-funded OpenAire program, mentioned in the first part of this 3 part series. Zenodo is an open-access repository for all types of research material: data, software, reports and papers. Each piece of uploaded material is allocated a citeable DOI. It is hosted and operated by the particle physics research facility, CERN, but includes a large array of research fields.

DRYAD
Dryad is a not for profit repository for research datasets that correspond to findings published in a paper. Before publication, a team of curators makes sure the uploaded data is useable. Similarly to Zenodo, you can upload your data in any file format and receive a DOI. Originally funded by the US National Science Foundation, now users are charged when their submissions are accepted.

GITHUB
If coding is part of your work, you’ll know about GitHub, a platform for hosting and collaboratively developing software–both privately and publicly. Founded in 2008, GitHub was acquired by Microsoft in 2018. As of November 2020, the free plan includes 500MB of private and unlimited public storage.

Comparing open science policies

Journals and funding agencies usually have specific policies about open science which are often time-consuming to locate. Here are two services just for this.

TRANSPOSE
The Transpose database compares the policies of different journals. You can explore stated policies on open peer review, co-reviewing and preprinting. This tool draws attention to how much journal policies vary and how vague some of these policies are.  

SHERPA SERVICES
The not for profit membership based organisation JISC offers three services that help authors and institutions to check open access compliance.

The tool Sherpa Romeo aggregates and analyses the open access policies of journals, similarly to Transpose (mentioned above). Sherpa Juliet lets you search the current policies of some funding bodies on open access publishing and data archiving. Sherpa Fact combines the functionality of both so you can check whether a certain journal complies with the open access policies of your funder.

So here you have 10 tools to explore. If you are using any of them already, please let me know what you think of them. If there are others you would like to share, I would love to receive an email. News about one data tool in the next blog is coming to you courtesy of a client.

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