Peter Suber, Half a dozen reasons why I support the Jussieu Call for Open Science and Bibl…

“1. I support its call to move beyond PDFs. This is necessary to bypass publisher locks and facilitate reuse, text mining, access by the visually impaired, and access in bandwidth-poor parts of the world. 

2. I applaud its recognition of no-fee or no-APC open-access journals, their existence, their value, and the fact that a significant number of authors will always depend on them. 

3. I join its call for redirecting funds now spent on subscription journals to support OA alternatives. 

4. I endorse its call to reform methods of research evaluation. If we want to assess quality, we must stop assuming that impact and prestige are good proxies for quality. If we want to assess impact, we must stop using metrics that measure it badly and create perverse incentives to put prestige ahead of both quality and access.

5. I support its call for infrastructures that are proof against privatization. No matter how good proprietary and closed-source platforms may initially be, they are subject to acquisition and harmful mutation beyond the control of the non-profit academic world. Even without acquisition, their commitment to OA is contingent on the market, and they carry a permanent risk of trapping rather than liberating knowledge. The research community cannot afford to entrust its research to platforms carrying that risk. 

6. Finally I support what it terms bibliodiversity. While we must steer clear of closed-source infrastructure, subject to privatization and enclosure, we must also steer clear of platform monocultures, subject to rigidity, stagnation, and breakage. Again, no matter how good a monoculture platform may initially be, in the long run it cannot be better than an ecosystem of free and open-source, interoperable components, compliant with open standards, offering robustness, modularity, flexibility, freedom to create better modules without rewriting the whole system, freedom to pick modules that best meet local needs, and freedom to scale up to meet global needs without first overcoming centralized constraints or unresponsive decision-makers. …”

Kopernio | One-click access to PDF articles

“Fast, one-click access to millions of research papers….One-click access to PDFs. No more VPNs, login forms, redirects, frantic Googling and chasing broken links….Jump over paywalls. Automatically search university library subscriptions, pre-print servers, institutional repositories and private blogs for free PDFs….Take your university library with you wherever you go; at home, at conferences, on the beach….Kopernio automagically files away the PDFs you read in your own private Kopernio locker. Come back and read them again later, anywhere, anytime….”

Science Beam – using computer vision to extract PDF data | Labs | eLife

“There’s a vast trove of science out there locked inside the PDF format. From preprints to peer-reviewed literature and historical research, millions of scientific manuscripts today can only be found in a print-era format that is effectively inaccessible to the web of interconnected online services and APIs that are increasingly becoming the digital scaffold of today’s research infrastructure….Extracting key information from PDF files isn’t trivial. …It would therefore certainly be useful to be able to extract all key data from manuscript PDFs and store it in a more accessible, more reusable format such as XML (of the publishing industry standard JATS variety or otherwise). This would allow for the flexible conversion of the original manuscript into different forms, from mobile-friendly layouts to enhanced views like eLife’s side-by-side view (through eLife Lens). It will also make the research mineable and API-accessible to any number of tools, services and applications. From advanced search tools to the contextual presentation of semantic tags based on users’ interests, and from cross-domain mash-ups showing correlations between different papers to novel applications like ScienceFair, a move away from PDF and toward a more open and flexible format like XML would unlock a multitude of use cases for the discovery and reuse of existing research….We are embarking on a project to build on these existing open-source tools, and to improve the accuracy of the XML output. One aim of the project is to combine some of the existing tools in a modular PDF-to-XML conversion pipeline that achieves a better overall conversion result compared to using individual tools on their own. In addition, we are experimenting with a different approach to the problem: using computer vision to identify key components of the scientific manuscript in PDF format….To this end, we will be collaborating with other publishers to collate a broad corpus of valid PDF/XML pairs to help train and test our neural networks….”

Release ‘open’ data from their PDF prisons using tabulizer | R-bloggers

“As a political scientist who regularly encounters so-called “open data” in PDFs, this problem is particularly irritating. PDFs may have “portable” in their name, making them display consistently on various platforms, but that portability means any information contained in a PDF is irritatingly difficult to extract computationally.”

Ebooks, Innovation, and the Rebel Within – The Scholarly Kitchen

“As with all good innovators, Peter [Krautzberger, project lead for MathJax] is frustrated. He feels, for example, that advocates of open science focus heavily on sharing of supposedly neutral data, but are still not able to see beyond the PDF. For him open science should be more about how the Web can facilitate communications….”

open science – Why don’t publication venues systematically make the LaTeX source of papers available? – Academia Stack Exchange

“I wonder why most publication venues don’t systematically make the LaTeX source for published papers available? (which implies systematically asking authors for the LaTex source)

LaTex source are more machine readable than PDFs, and make it easier for humans to reuse part of it (e.g. math equation or figures), amongst other advantages. I fail to see any downside….”

Nature Publishing Group and ReadCube Unveil Preliminary Results of Scientific Article Sharing Trial

“Nature Publishing Group, part of Springer Nature, has announced the results of its ground-breaking 12-month content sharing initiative to support collaborative research. The trial has concluded with positive results and the initiative to offer on-platform sharing of the full text of nature.com articles using ReadCube’s enhanced PDF technology will continue indefinitely.

In December 2014, a 12-month content sharing trial was set up to enable subscribers to 49 journals on nature.com to legitimately and conveniently share the full text of articles of interest with colleagues without a subscription via a shareable web link on nature.com, enabled by publishing technology company, ReadCube. The trial was also extended to 100 media outlets and blogs around the world that report on the findings of articles published on nature.com, allowing them to provide their own readers with a link to a full text, read-only view of the original scientific paper….”