So, I learn a couple of new things, and I liked a lot the preprint. As somebody that came from a wet lab, I can not stress enough the importance of the "experimental setup" that was already mentioned in a previous comment. This part is also relevant, as there are a lot of tricks that nobody writes (I think is called "Dark data") and equivalent to make the code open. After all, this experimental setup is necessary as for peer review pre- and post- publication.
To another point, when you talk about the preprints itself in the open access section there a contrast that maybe you can consider. I would like to read something as the opposition to them, but in the perspective that it can become a source of noise due to a large number of preprints published making harder to find the important data/code/tool. This point was raised by one of my colleagues when I make a case to preprint our work; he spent too munch time looking to preprints in arXiv to find the one that was relevant to the code. But that's up to you.
So, during the reading you mention these badges, in table three you mention Publons, as these guys give the award of "sentinel of science" just last year maybe it be worth mention. At least it was a splendid idea to recognize the peer review effort (even my advisor liked, and he is ancient school and he's not that old). Also, you could expand a couple of lines to the bad side, I don't remember which journal was ready to put like ranking to the reviewers for how fast they review and how many.
Keep the good work
Barcelona Supercomputing Center
While I like this preprint, I have some suggestions to expand its reach and make it more applicable:
1 - Open Science isn't just for reproducibility; it's also for credit. I think you should include some discussion of citation, at least where it's not common today (data citation: https://www.force11.org/group/joint-declaration-data-citation-principles-final; and software citation: https://doi.org/10.7717/peerj-cs.86.
2 - Open Science isn't just four pillars; there are a lot of other things that should be identified and made open/reproducible/credited, such as protocols, workflows, reagents, cell lines, etc.
3 - Open science isn't just science; it also applies to engineering, humanities, etc. I understand that open science is the buzzword you have to use, but the intro should at least say that this is really open research, not just open science.
I think it is a very timely article that should be distributed widely and discussed to a great extend! I understand it is impossible to cover the whole Open science controversy and reach in the introduction, but I would modestly suggest (on top of what Daniel has said before) that you comment on a few things:
- You mostly consider the part of Open science that is by and for researchers only. I agree Open research is a more appropriate term in this context, but still, Open science is useful as it covers more than Open research. The other aspects of Open science should be discussed very quickly in the introduction to give the reader an overview of the potential. You cite the book chapter by Benedikt Fecher & Sascha Friesike on the five schools, but bury this important aspect in the "four pillars" chapter. Maybe adding a section "Open science: more than Open research" or something similar would allow to explain this quickly.
- The paragraph on the "history of Open science" is a bit naive (no offense). Some historians of science are uneasy with this simplistic view (Science was closed, then open, then closed again). Maybe it is not so important to discuss this, as it is to point to the reasons for the current crisis (paywalls, pre-digital formats still in use, slow process of knowledge dissemination).
- Having 4 pillars is convenient, but I would no underestimate the importance of tools, both software (not to confuse with code) and hardware. Could these fall under a fifth pillar ("experimental setup") with software, reagent, workflows, material, methods, etc.
- "Papers" is a popular term that refers to the actual 20th century paper support. Wouldn't it be interesting to look for an alternative? I do not have a suggestion here, but is something published on a platform such as PeerJ still a "paper"?
- Maybe you should reuse the terms you used to describe the 4 pillars in the titles of the next chapters, not to confuse the reader (when you go from "paper" -> "open access", etc.)
- When you write "One of the basic premises of science is that it should be based on a global, collaborative effort, building on open communication of published methods, data, and results" you only account for an idealistic view of science. In reality, Open science has an enormous opportunity cost for 1. researchers themselves (hence the importance of credit and citation) 2. institutions 3. countries (somehow secrecy is believed to be a competitive advantage). In the past (and still today to a large extend), science was done for the benefit (prestige, economic or power advantage) of researchers, but also benefactors, universities, nations, etc. not the whole community. I love the idea that we need to insist on the "communism" dimension of research, but we should not ignore the obstacles to Open science and the fact that funders are mostly national agencies supporting national interests. One paragraph about the opportunity costs should not justify inaction, but show the complexity of the topic.
Box 1 is great! And could be expended a very little, with a minimal addition of details.
Also a lexicon would be very useful.
And of course, feel free to ignore my comments if not relevant.
Looking forward to see how this manuscript evolve! I'll certainly use it in my own work.
This is a nice overview of resources for open science, and I learned a few things as well. Here are my comments/suggestions:
1- I agree with the previous comment that "open research" or "open scholarship" might work better, although "open science" has more demonstrated usage.
2- I also agree that "paper" is a bit outdated. Other possibilities might be "report" or "peer-reviewed article."
3- The usage of the "goo.gl" shortlinks reminded me of research showing that many of these links used in legal decisions no longer work. There are so many links here that it is perhaps inevitable that some will not work in the future. However, journals might consider a best practice of using more persistent links in papers that refer to web pages. This preprint could serve as an exemplar by utilizing perma.cc or one of the other persistent link services (at least for the shortlinks).
4- In the open access section, you state that preprints have DOIs assigned, but I think this is not always true. You could say "some preprints." In any case, I think there would be a timestamp in the repository regardless of whether there was a DOI.
5- It is probably impossible to have a comprehensive list of preprint servers, but you could include OSF and the services built on it like SocArXiv, as well as preprints.org from MDPI. Also in this table, you use the Australian mirror URL for arXiv, when it should just be arxiv.org.
6- The list of resources for open access seems very wide-ranging, and I am not sure if the listing is in any order. To place more emphasis on useful tools, you could move DOAJ and Sherpa/Romeo to the beginning.
7- The section on open peer review is far more susceptible to misunderstandings than the other sections, since it is defined so many ways. Your table helps clarify this somewhat, but you could also refer to/borrow from the schema at the end of this OpenAIRE blog post: https://blogs.openaire.eu/?p=1371.
Thanks for this useful work- hope these comments help.
As studies into researchers’ attitudes regarding open science/research data management often point to a need for practical tips, this is a welcome guide containing a wealth of useful resources and advice from a researcher’s perspective, especially for those working in the life sciences.
Below are some comments/suggestions:
- Open Research could indeed be a more inclusive term than Open Science (although in some cultural contexts “science” is actually understood in a much broader sense than in the Anglosphere – see for example ‘Literaturwissenschaft’ in German: literally ‘literarature science’).
- While the authors rightly focus on the important pillars of open data, open code, open papers and open peer review, I was wondering what their thoughts are on the perhaps more recent calls for open lab notebooks (https://en.wikipedia.org/wiki/Opennotebookscience)? I guess this also touches on previous comments regarding openness of the experimental setup as an important dimension of open science.
- It is suggested that “privacy sensitive data” do not belong in the category of public assets available to the public. Although personal data can indeed not be made openly available for legal and ethical reasons, sometimes it can nevertheless be possible to legally and ethically share research data containing personally identifiable information, albeit usually under more restricted conditions (e.g. some trustworthy data repositories are equipped and have the right procedures in place to offer researchers restricted access to personal or otherwise sensitive data). While such data would of course not constitute fully open data in the sense of the Open Definition, maybe the data sharing story should be presented as somewhat more nuanced than a binary choice between either fully open or fully closed data?
- Technically speaking, there is a third type of data repository, namely the institutional data repository (although this kind is usually less relevant for research domains characterized by greater data volumes and larger degrees of standardization and international collaboration – as these domains often build their own international infrastructures).
- Some (well-known) data repositories focus more on publicly disseminating data than on their preservation, so when selecting a repository it’s usually a good idea to also check whether it has an explicit commitment to/policy regarding long-term preservation (of course, certification will provide a strong indication of this, but not all repositories in re3data.org are certified). Other sensible criteria to take into account can be found here: https://www.openaire.eu/opendatapilot-repository. One that is worth emphasizing is whether the repository assigns persistent and unique identifiers, because this is vital to enabling a culture of data citation (which in turn gives researchers credit for making data available).
- For publicly shared data, standard licenses are in principle more interesting than bespoke licenses, because they allow for legal interoperability. An interesting tool to help you select an appropriate standard license for data (or software) is the EUDAT License Selector (http://ufal.github.io/public-license-selector/), although it also includes licenses that are not conformant with the Open Definition.
- The FAIR data concept is indeed gaining prominence among data sharing advocates, and it may be useful to point out one of its distinctive features, namely its emphasis on making data findable, accessible, interoperable and reusable to humans as well as machines. Although discussions about the FAIR data concept’s implementation and operationalization are still very much ongoing and although appropriate metadata are definitely a crucial element, it also involves other things such as persistent identifiers, user licenses, non-proprietary formats and standard vocabularies. So maybe the FAIR data concept shouldn’t just be mentioned as part of the section on metadata?
- As regards open access to publications: besides posting preprints, another option for authors to make their work open while still publishing in subscription-based journals is to deposit post-prints in their institutional repositories, although some publishers require an embargo period before the post-print can be made open access. As enablers of the self-archiving, “green” route to open access, institutional repositories are nevertheless a vital part of the open access ecosystem.
- The Open Access Directory (http://oad.simmons.edu/oadwiki/Main_Page) and OpenAIRE (https://www.openaire.eu/) might be other useful resources.
- In the context of the general lack of credit for non-traditional research outputs (such as peer reviews), it might also be worthwile pointing to new initiatives attempting to address this issue such as the RIO Open Science Journal (http://riojournal.com/), which publishes a wide variety of research outputs (including e.g. grant proposals and data management plans).
Overall, a great guide for those who want to start practicing open science but don't know where to start!
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