chem-bla-ics: What about postprint servers?

“Now that preprint servers are picking up speed, let’s talk about postprint servers. Sure, we have plenty of places to place and find discussions about the content of articles (e.g. PubPeer, PubMed Commons, …), and sure we have retractions and corrections.

But what if we could just make revisions of articles?

And I’m not only talking about typo-fixes, but also clarifications that show up during post-publication peer-review. Not about full revisions; if a paper is wrong, then this is not the method of choice. They should happen frequently either, but sometimes it is just convenient. Maybe to fix broken website URLs?

One point is, ResearchGate, Academia, Mendeley, and the likes allow you to host versions, but we need to track the fixes and versioned DOIs. That metadata is essential: it is the FAIRness of the post-publication life time of a publication….”

Manifold v0.2.0 Released | Building Manifold

“On behalf of the entire Manifold team, I’m super excited to announce the release of Manifold v0.2.0! The release is up on Github now, and we’ll be rolling it out to our staging site later today. This release contains a number of new features and bugfixes, listed below. For the full list of revisions and pull requests, please consult the changelog.

Remember, Manifold is open source and freely available to all who are interested. While we have plans to build docker containers and OS packages, we’ve also written up installation instructions for all you early adopters out there. Take it for a spin and let us know how it goes.”

We need a GitHub for academic research.

“[T]he academic paper has some inherent limitations—chief among them that it can provide only a summary of a given research project. Even an outstanding paper cannot provide direct access to all of the research data collected or to the record of discussions among scientists that is reflected in lab notes. These windows into the messy and halting process of science, which can be extremely valuable learning objects, are not yet part of the official record of a research study.

But it doesn’t have to be this way. If we take advantage of the unique capabilities of the web to tell the full story of a research project—rather than merely using it as a faster printing press as we do today—we can build greater transparency into our approach to reporting science. Besides improving information-sharing among scientists, a push toward transparency could improve public trust in science and scientists. Now, when the very concepts of fact and truth under assault and many scientists feel compelled to march in response, is the perfect time to rethink our approach to scientific communication altogether….”

Scientists are getting proactive about self-corrections

“Journals pin corrections on scientific articles for all sorts of reasons — from the mundane, like minor typos and wording changes, to the significant, such as errors that warrant a detailed explanation.

But the process for correcting a published article can be needlessly burdensome and time-consuming, and stories abound of scientists trying to do the right thing, noting a minor error or update to their own work, but facing hurdles — from delays to flat out denials from journals.

Now, some researchers have decided to take matters into their own hands, using a comment feature on the widely used PubMed site. …”

Authors alerting readers via PubMed Commons | PubMed Commons Blog

“Journals can issue correction and errata notices to notify readers of errors and, as necessary, revise text and data in publications. Yet these processes can take time. Authors sometimes encounter obstacles to publishing corrections. Some authors use PubMed Commons to alert readers to issues or to refine language and interpretations. Correcting the record via journal notices is important, and it’s great to see authors add speed and transparency with post-publication updates….Journal corrections revise the version of record for a publication, and PubMed Commons does not replace that. But it does offer another way for authors to provide clarifications, point to interim and published corrections, and alert readers to errors quickly. And it’s good to see authors taking advantage of PubMed Commons to pass that information along to the community….”

Building Manifold | Building Manifold

“Welcome to Building Manifold, a blog that will document the process of creating Manifold Scholarship, a project at the University of Minnesota Press in partnership with the GC Digital Scholarship Lab at the Graduate Center, CUNY and Cast Iron Coding. Manifold Scholarship is funded through a generous grant from the Andrew W. Mellon Foundation as part of a series of 2015 grants made to university presses.

Manifold Scholarship is composed of two parts:

1) The creation of Manifold, an intuitive, collaborative, open-source platform for scholarly works. With iterative texts, powerful annotation tools, rich media support, and robust community dialogue, Manifold will transform scholarly publications into living digital works.

2) Rethinking the print-focused mode of scholarly authorship and university press editorial procedures and production workflows to accommodate the differences in creating content for iterative, networked publication….”

Amending Published Articles: Time To Rethink Retractions And Corrections? | bioRxiv

Abstract:  Academic publishing is evolving and our current system of correcting research post-publication is failing, both ideologically and practically. It does not encourage researchers to engage in consistent post-publication changes. Worse yet, post-publication “updates” are misconstrued as punishments or admissions of guilt. We propose a different model that publishers of research can apply to the content they publish, ensuring that any post-publication amendments are seamless, transparent and propagated to all the countless places online where descriptions of research appear. At the center, the neutral term “amendment” describes all forms of post-publication change to an article. We lay out a straightforward and consistent process that applies to each of the three types of amendments: insubstantial, substantial, and complete. This proposed system supports the dynamic nature of the research process itself as researchers continue to refine or extend the work, removing the emotive climate particularly associated with retractions and corrections to published work. It allows researchers to cite and share the correct versions of articles with certainty, and for decision makers to have access to the most up to date information.