Unrestricted Text and Data Mining with allofPLOS

Content mining, machine learning, text and data mining (TDM) and data analytics all refer to the process of obtaining information through machine-read material. Faster than a human possibly could, machine-learning approaches can analyze data, metadata and text content; find structural similarities between research problems in unrelated fields; and synthesize content from thousands of articles to suggest directions for further research explorations. In consideration of the continually expanding volume of peer-reviewed literature, the value of TDM should not be underappreciated. Text and data mining is a useful tool for developing new scientific insights and new ways to understand the story told by the published literature. Continue reading “Unrestricted Text and Data Mining with allofPLOS”

PLOS Channels Provide Opportunity for Discovery, Exploration and Contextual Insights

Last month, the new PLOS Cholera Channel joined existing Veterans Disability & Rehabilitation Research, Tuberculosis and Open Source Toolkit Channels in providing distinct and cohesive scholarly homes for research communities. These innovative forums increase the visibility of curated, quality research and reliable news and commentary, bridging a gap in relevance that contributes to public misunderstanding of research.

The Channels Program launched with Veterans Disability & Rehabilitation Research (VDRR), and as Veterans Day in the US approaches it’s an opportunity to take a moment to relay the channels origin story, highlight the latest content and re-introduce the editors behind this program. Continue reading “PLOS Channels Provide Opportunity for Discovery, Exploration and Contextual Insights”

The Scholarship Monopoly

No I don’t mean the game we all played as kids with railroads and hotels and a questionable gentleman in a top hat.

Scholarship monopoly is a very serious concern for academics of all sorts. Really, any monopoly is a concern in any kind of business or industry. It’s a given that competition helps us grow, inspires us to try harder, and pushes the best ideas and products to the fore. Academia is slightly different, in that competition is more about comparing and checking theories and ideas with peers. Rather than directly competing with each other, academics work off each other to verify data and draw conclusions.

So where does the monopoly come into this?

The publishers of academic content, those responsible in a large part for disseminating academic findings and pairing academics with peer reviewers. But what if those publishing were concentrated into a very few, for profit companies? The potential for a monopoly arises.

This is exactly the current dilemma academic publishing is in. Much like the traditional publishing industry, academic publishing is dominated by a “Big 5” group of publishers, accounting for almost 50% of all academic publishing per year.

To get a more complete understanding of the academic publishing and dissemination lifecycle, let’s first break down the stages of this process:

  1. Research
  2. Publishing
  3. Evaluation

Research is the meat of the content creation process, and rests entirely with the academic—be it a professor, researcher, or student. The individual finds and evaluates data, forms a hypothesis, and gathers their conclusions to form their content.

With content gathered, the publishing process begins. Traditionally, this involves sending the content to a publisher, who has a staff of editors and designers to layout and prepare the content. What begins as data ends up a fully formed paper or even a book. In most instances, the content creator is detached from this step.

Finally, the content in it’s completed form is evaluated by other academics. Once the content is deemed as complete by peer reviewers, it becomes a part of the greater body of academic work. Student’s learn from it, professors teach from it. The content takes a place among all other academic material.

The problem academia faces stems from the handling of this three-stage process. From From the “Knowledge Gap” project:

“At first sight, there is an obvious concern of a conflict of interest. This is especially true when the supplier of academic journals is also in charge of evaluating and validating research quality and impact (eg: pure, plum analytics, Sci Val), identifying academic experts to direct to potential employers (eg: Expert Lookup), managing the research networking platforms through which to collaborate (eg: SSRN, Hivebench, Mendeley), managing the infrastructure through which to find funding (eg: plum X, Mendeley, Sci Val), and controlling the platforms through which to analyze and store your data (Eg: Hivebench, Mendeley).”

The acknowledgement is that companies like Elsevier have begun to rebrand themselves as Analytics tools for the gathering and dissemination of academic knowledge materials, distancing themselves from the strictly publishing oriented role they previously focused upon. Because Elsevier (and the other large academic publishers) owns a disproportionate amount of the existing publications of academic value, they are well positioned to capitalize on this content by offering increased analytical data from this content. But the control over such a portion of the academic content creates a monopoly, limits competition, and provides academics no real choice other than to buy into the monopoly.

Glasstree is but one of many alternatives to the traditional academic publishing and review mechanism. I am not writing this piece today as an advertisement for Glasstree in specific terms, as we often have in the past. What’s more important is to acknowledge the process of academic publishing and the stranglehold large academic publishers, under the guise of “Information Analytics Companies” and residing behind a paywall, have on the availability of knowledge.

There have been and continue to be pockets of opposition to the academic publishing model, but the cost of avoiding the mainstream publishing methods is steep. Academics find themselves without the needed means of reviewing and disseminating their data, trapped outside the broader field of knowledge. Research and data published outside of traditional means have a perceived lack of credibility.

Coupled with the reduced cost of digital printing and the connectivity of modern communications tools, the means and costs of academic publishing should be plummeting, while the openness and access to materials should be broader than ever. This is not the case, and one possible (if not likely) cause is the grip large academic publishers have on the entire process. Anytime so much data is concentrated with so few entities, the risk of monopoly is great. This data is crucial, as it represents the broad knowledge of all of academia.

As one of many alternatives to the currently accepted academic normal, Glasstree wholeheartedly encourages all researchers, students, and educators to carefully consider their options when disseminating their knowledge, and to take any opportunity they can to break from the normal models with self-publishing, independent reviews, and institution based printing.

The independent publishing revolution has slowly asserted itself on the traditional publishing industry; now it is widely considered a formidable adversary of the old publishing model, and the publishers of years’ past are scrambling to take on digital printing tools to remain competitive. Academia can learn from this despite their differing needs. The financializing of academic publishing will not stop now that it has proven to be profitable. As such, academia must adapt if the individuals and institutions hope to maintain the standards for their work and to prevent the overwhelming monopoly traditional academic publishers, under their new moniker “Information Analytics Companies,” are quickly attaining.




The vision and reality of soundness-only peer review in open-access mega-journals

Valerie Spezi, Simon Wakeling, Stephen Pinfield, Jenny Fry, Claire Creaser, Peter Willett, (2017) ““Let the community decide”? The vision and reality of soundness-only peer review in open-access mega-journals”, Journal of Documentation, https://doi.org/10.1108/JD-06-2017-0092

“Findings suggest that in reality criteria beyond technical or scientific soundness can and do influence editorial decisions. Deviations from the original OAMJ model are both publisher supported (in the form of requirements for an article to be “worthy” of publication) and practice driven (in the form of some reviewers and editors applying traditional peer review criteria to OAMJ submissions). Also publishers believe post-publication evaluation of novelty, significance and relevance remains problematic.”

Open Access Week 2017 – Open in Order to…

As a proud co-founder of Open Access Week, we hope you will join us in celebrating progress and promoting awareness to help make Open Access – the founding principle of PLOS – the new norm in scholarship and research globally. This year’s theme is “Open in Order to…” and invites the community to focus on what openness enables.

Since PLOS’ beginning, we’ve been open in order to accelerate progress in science and medicine through publishing, advocacy and innovation to benefit the research community and beyond. PLOS is open in order to ensure that: research outcomes are discoverable, accessible and available for discussion; science communication is constructive, transparent and verifiable; and publishing advances reproducibility, transparency and accountability. Continue reading “Open Access Week 2017 – Open in Order to…”

Cross-Journal Initiative Helps Manuscripts Take Flight

All properly executed science deserves to be published as quickly as possible. One common frustration of scientists related to publication speed is the review-rejection cycle that in action resembles a cross between cycling on a hamster wheel and jumping through a hoola-hoop. To offer authors a way out of this cycle of delay, PLOS launched a journal transfer initiative earlier this year that provides authors an alternative to starting from scratch for papers not initially accepted by a subset of PLOS journals. Continue reading “Cross-Journal Initiative Helps Manuscripts Take Flight”

The problem with scientific publishing

And how to fix it

Periodical journals have been the principal means of disseminating science since the 17th century. Over the intervening three-and-a-half centuries journals have established conventions for publication — such as insisting on independent (and usually anonymous) peer review of submissions — that are intended to preserve the integrity of the scientific process. But they have come under increasing attack in recent years. What is wrong with scientific publishing in journals, and how can it be fixed? Continue reading “The problem with scientific publishing”

Using APIs in Academia

Academic publishing is a necessity, yet continues to be a point of concern for institutions and individuals alike. Academics, students, teachers, and researchers all need the ability to publish and share their findings, but the model academic publishers utilize is woefully inadequate. Not only do publishers exploit their authors for profit, they also gate this content, meaning some information may never see publication regardless of how important or valuable the information may be.

Glasstree’s continuing mission is to break down those barriers. We started by introducing self-publishing to academia with Glasstree’s publishing tools. Instead of hoping to be accepted by a publisher, Glasstree empowers academics to take control of their content by publish it themselves!

Lulu is Glasstree’s parent company, and together we aim to make knowledge, literature, and publishing available to everyone. Whatever your story – be it a fictional novel or a dissertation – we are here to help you share.

The next step in our evolution is here: Print API.

What is an API? And how does this new tool benefit academics interested in self-publishing? Keep reading and we’ll explore these questions.


Even if you’re unfamiliar with the technical aspects of APIs for software, you’ve almost certainly encountered them online without realizing. The acronym API stands for “Application Programming Interface.” Most basically, API is code that allows two unique pieces of software to talk to each other. This, in and of itself, is pretty simple.

Retailers, individuals, and institutions all make use of APIs to expand their capabilities and offer their users more options, better pricing, faster shipping and much more. Lulu’s Print API serves the same functionality. Once the API is integrated, users can create unique “buy now” options on their SHOP pages within their websites, and all orders placed are channeled into our global printing network, to be fulfilled by the same process as any order on Glasstree.

Breaking down Boundaries, Creating Partners

From a technical stand point, our Print API service may not seem like an exciting piece of news for the individual author (APIs run in the background and are never seen). API tools are usually meant for web developers, who implement the cross-platform code so the two discrete programs work in harmony. The average author might have little need for an API connection if they don’t want to deal with selling directly from their website.

That being said, publishers and academics need APIs for many things. We understand that need, because we’ve lived in that world for the last fifteen years. We’ve witnessed, year after year, small and independent publishers who start up, bring on a handful of authors, publish a few books, and then eventually fold. Yes, of course, some small publishers succeed, and some even succeed beyond all expectations. We’re more concerned with the publishers who couldn’t keep up.

One of the biggest problems facing many small publishers is the cost associated with printing and fulfilling book orders. The price to print and ship can be prohibitive for small publishers, who likely are operating on a limited budget and need to make the most out of every dollar invested. Print API is an answer to the funding problems these small publishers face. Because the Lulu Print API can be implemented to allow for direct print on demand services at low prices, small publishers can remove the cost of printing and storing books from their budget.

Just like using Lulu’s self-publishing tools, the Print API features all the formats and sizes Lulu has to offer, at the same low prices, and with the same quality and global shipping you’ve come to expect from Lulu. The difference is that publishers the world over can plug into our network while maintaining their brand’s independence.

Harnessing the power of the Web


The API process capitalizes on Internet connectivity to enable collaboration among a variety of companies and individuals, further opening the printing and publishing world to more readers, authors, and publishers.

Pricing is another important aspect to consider with an API connection. Rather than pricing your book on the Glasstree site for your profit and our commission, you price it with 100% return of profits. The price you charge on your site is entirely up to you! With the API integrated, the order bills from Glasstree to you for the printing and shipping, while the amount you charge a customer is entirely on your end. This expands on the already generous and easy to control profit model Glasstree utilizes.

In a university setting, an API tool is a means to offer the institution’s students and teachers a means to publishing and sharing their work all from within the institution. The college bookstore can host these print-on-demand titles on their website, and facilitate printing through the API connection. Costs are minimal, and the bookstore can easily make the necessary profits, all while control overhead and storage.

An API connection completely removes barriers to publishing. The institution need only implement the API and provide the file standards for uploading (the same specifications used for publishing on Glasstree). Students, teachers, and researchers can all publish their works at a minimal expense, while their institutions can list these books via our API on a college bookstore website for anyone to purchase.

Integration is In

Using API integration is more than just the cool new thing happening across the web. Take a look at this article from TechCrunch last year, “The Rise of APIs”. While the title sounds very Terminator-esque, the point the author makes is clear: third-party APIs are the future, and they are here to shake up the way the Internet works. The opening paragraph of the article sums it up; ” there is a rising wave of software innovation in the area of APIs that provide critical connective tissue and increasingly important functionality.”

While a clean and easy-to-navigate interface is always going to be important, the ability to quickly implement a new program through API connections is what will keep web based retailers one step ahead. Adding new features, replacing out of date products, and generally being able to work with the range of other programs on the web is a key to staying relevant; using API connections solves all of these problems. All modern software providers are conscious of API connectivity, and the implications of creating software that does not allow for API integration. The way of the future is sharing, through both open and private API connections, and mutually finding success through shared programming.

Lulu and Glasstree embraces this mentality wholly. From the first day, we’ve been a company designed to help content creators better share their stories and knowledge. Enabling API connections with our print network is a logical and necessary step for us.

Looking to the Future

Academia has always been an institution that had to keep an eye toward the future. Because schools and teachers are the ambassadors of knowledge for generations to come, the means to disseminate and archive knowledge has always been critical.

Look for more from Glasstree in the future, as we continue to make innovations in the publishing community. For now, you can check out our API/Developer’s Portal site at developers.lulu.com to learn more about Print API and see if the tool might be right for you.

In times of geopolitical and economic instability how can innovative technologies drive new revenue opportunities for institutions and research funding in the UK?

By Jean Roberts


This article examines how the emergence of innovative technology platforms, recently introduced by new players in the university services space and public arena, has the potential to open up additional revenue generation opportunities for the university research funding toolkit. How aware are universities of these new technology platforms and their revenue potential? Given anticipated EU funding upheaval (and potential removal/reduction of funding sources), uncertainty surrounding Brexit, and the lack of clarity in the lead-up to Brexit (creating what looks to be a prolonged period of instability and cross-messaging in funding circles), the time is now ripe for university management, financial stewards and library managers to embrace new technology platforms as part of their strategic finance planning in order to take advantage of new emerging revenue models in combination with existing operations.


Read the full article at https://insights.uksg.org

Jean Roberts is Business Development Director for Glasstree Academic Publishing


Your Preprint Questions, Answered


“Early bird” by Katy Warner is licensed under CC BY-SA 2.0.

Last year, we noted that preprints were “having a moment.” Since that time, a number of new discipline-specific preprint servers have launched (PsyArXiv, LawArXiv, and engrXiv), and more are on the way (Chemrxiv, PaleorXiv, and SportRxiv, to name a few). In addition, funding organizations, such as the Chan Zuckerberg Initiative, have begun to provide financial support for preprint servers. Still doubt the rising popularity of preprints? There’s even a new app for rating preprints in the life sciences called Papr, which calls itself “Tinder for preprints.”

Are you thinking of posting a preprint? Here are some things you might be wondering about:

What exactly is a preprint?

A preprint is usually defined as a piece of scholarship that has not been peer reviewed or formally published. Many preprints do go on to be published in academic journals. One 2013 study, for example, found that 64% of the work that is posted in arXiv has been published in academic journals. However, there is also small group of scholars who have begun posting what they call “final version preprints.”

Why should I post a preprint of my work?

Posting a preprint allows you to get your research out into the world quickly and easily. That’s good for the advancement of knowledge, but it’s also good because it enables you to position yourself as the originator of a certain claim or technique, even before your article is formally published. Posting a preprint is also a great way to get feedback on your work from others, and make your scholarship even better.

Can I still submit my manuscript to a journal if I previously posted it on a preprint server?

In most cases, yes. A growing number of journals welcome manuscript submissions that first appeared as preprints. BioRxiv, for example, has a manuscript transfer process which makes it easy for researchers to submit their preprint to over 120 scholarly journals. That having been said, there are still a few journals that consider the posting of preprints to be “prior publication.” Make sure to read the policies of the journal you are interested in submitting to. Wikipedia also has a list preprint policies by journal.

How will people find my preprint?

Many preprint servers assign DOIs (digital object identifiers) to preprints, which make them easier to discover (although the popular arXiv does not). In addition, a number of preprint servers are indexed by Google Scholar. Nevertheless, if you want people to read your preprint, you should be prepared to do your own promotion. Use social media to draw attention to your work.

How should I license my preprint?

As the author, you automatically own the copyright to your work. However, adding a Creative Commons (CC) license tells people how your preprint can be reused. Some preprint servers require a CC license for any work that is posted. Others, such as SSRN or Humanities Commons CORE, do not. We recommend adding a CC license to all preprints you post.

Can I cite a preprint?

Yes. If you have evaluated a preprint and find it to useful to your research, definitely go ahead and cite it. Just make sure to note in your citation that it is a preprint. Also make sure you are citing the version that you actually used. One caveat: there are a few journals that do not allow researchers to cite preprints, although this policy seems to be changing. If you are unsure, ask your editor. Writing a grant application? The NIH recently announced that investigators are free to cite their own preprints in research proposals or projects reports.

Have another question about preprints that we didn’t answer? Let us know in the comments.

Academic Publishing: Then and Now

Education and Academia are an ever evolving organism, changing to fit the times and the demands of the population. In the eighteenth and nineteenth centuries, academic merit and scholarly reputation were tied most closely with social status and not knowledge! Academia grew from a “who you know” institutional structure to a merit based design, emphasizing the recognition of published works as a means of evaluating the scholar.

This model persisted, and eventually gave rise to the need for dedicated academic publishing, to facilitate the many intellectuals, scholars, students, and researchers who wished to both share their knowledge and grow their reputation. Today academic publishing is the standard metric for demonstrating expertise in a given field. It is all but assured that an aspiring academic will publish, and continue to publish throughout their career.

In the last century academic and scholarly publishing has grown tremendously, following the same growth acceleration as the size and enrollment of colleges across Europe and North America. Publishers and educational institutions have scrambled to keep up. In this mix entered the commercial publishers, who prioritized profit and reach over quality. As with any commercial endeavor, the classic goals of university and learned society publishing shifted from a scholarly mission to profit generation.

Glasstree offers itself as a middle ground to this problem. A means to publish important and relevant academic work in a timely and cost effective fashion, without sacrificing the opportunity to realize significant profits for the author(s). We believe that profits are important, but that they should not be controlled by a small number of large commercial publishers.

Academic publishing differs from traditional publishing in important ways, and any publishing company seeking to facilitate academic publishing must operate with these concerns in mind. In particular, peer-review has become a tense subject among individual academics, who fear the profit driven publishers will leverage the importance of peer-review to constrain or control what materials are available.

The alternative is Glasstree, a fully supported publishing company without the constraints traditional publishers impose. Offering all the services a scholar or student will need, with none of the restrictions, Glasstree integrates the independent publishing mentality without sacrificing any of the tools academics need for their work.

Glasstree enables academics to make a significant profit from their own work, reversing the traditional academic publishing revenue model, which typically pays authors an average of just 9% royalties, to offer 70% of the profits from sales. Its accelerated speed-to-market allows academics to publish their research in a matter of days or weeks, sharing their insights in record time.

For more details on Glasstree Academic Publishing, please visit https://www.glasstree.com/

Start-up story: Glasstree Academic Publishing

By Jean Roberts

Glasstree Academic Publishing is a non-licence cloud-based content dissemination platform supporting e-book, print and open access (OA) publishing, which was launched in November 2016. Glasstree is a subdivision of Lulu.com, a large USA-based independent publishing platform which has published more than two million books since 2002. Lulu analyzed their author database and discovered that at least 38 per cent of Lulu’s content was produced by academic authors independently publishing their works. The company was keen to look at ways it could better understand and support this academic community. It became apparent that this pattern of publishing was indicative of an emerging trend, a drive to seek alternative means of getting content into the public domain, embraced by a group of academic entrepreneurial innovators who wanted their work to become accessible and were willing to sacrifice their relationships with traditional publishing in order to do so.

After conducting direct discussions with a representative sample of those academics, Lulu supported the concept that every academic professional in every institution should have the right to publish their monographs, books, articles and papers independently. After major collaboration with these academics, Glasstree Academic Publishing was launched to better support their needs and provide a focused academic content platform, incorporating the same functions and services as a traditional academic publisher would provide. The idea was not only to replicate, but to improve upon the experience that traditional publishers provide to authors, particularly as regards the ability to redirect ownership and revenues back to the author. Glasstree offers print and digital options, copy-editing services, gold OA and peer review, as well as various discoverability and impact metric tools.

The fundamental principles of Glasstree are:

  • providing an equitable profit-sharing model for academics and their supporting institutions
  • providing better control and visibility of content
  • the ability for authors and institutions to set the price of their own work
  • a quicker route to market
  • a fairer profit-sharing model (70 per cent of royalties instead of the industry average of nine per cent).

Read the full article at insights.uksg.org/

Jean Roberts is Business Development Director for Glasstree Academic Publishing

So long static – we now support interactive Ploty figures in our articles!

Plotly enables users to create dozens of different types of charts, networks and maps, all of which have a basic-level of interactivity where you can zoom, pan, rotate (for 3D plots) and hover your cursor over a data point to see its value(s). However, you can add also more interactivity by adding one or more advanced interactive features to your figures such as dropdown options, sliders and dynamic animations.  

To mark the introduction of this new feature, we are reducing Article Processing Charges* for all articles with at least one Plotly figure by 50%. The submission deadline for the APC reduction is December 31st 2017. You can find more information about this and how to submit your Plotly figure at the end of this post.

We plan to feature published interactive figures throughout the year, including a roundup of the best visualizations in late January 2018 on our and Plotly’s blogs.

“Plotly is thrilled to be working with F1000Research as scientific publishing transitions to interactive, online graphics. Plotly charts keep the data and chart intrinsically linked – a major improvement over submitting charts as static image files. Open research is the future and Plotly is proud to lend cutting edge tools to open science publications.” Jack Parmer, Plotly CEO

Finding clarity in interactivity

Scientific publishing made the transition to the web almost two decades ago, and yet we still treat online articles as if they have the same physical limitations as their printed equivalents. We even still use terms such as ‘papers’ and ‘preprints’ to refer to works that only exist online. The same is of course true for elements within articles such as figures, which remain in the same static state since William Playfair drew the first statistical charts in 1786.

The entire purpose of a scientific figure is to help readers understand. When information is visualized graphically it is much easier to comprehend than a table densely packed with numbers or a long tract of text. However, biological and environmental systems are complex and it’s often difficult to represent in a static 2D object. This is especially true if the research involves many variables or large quantities of data. Many readers of scientific articles will have struggled to decipher over-plotted charts, or network graphs crowded with hundreds of nodes all labelled in an unreadable font size so the figure fits with the paper’s margins.  Being able to zoom, filter, and hover over individual data points to see their values, address these challenges and help readers to properly explore data at a much finer scale.

A very densely packed gene expression heatmap. Thankfully, you can select smaller regions of the chart, or use the zoom options in the top right, to get a better idea of what the heatmap shows. Chart from Plotly: https://plot.ly/ipython-notebooks/bioinformatics/


The same data, different visualizations

Interactive and animated figures have other advantages over their static counterparts. If there are several ways to visualize your data, you no longer have to choose just one; if you want to demonstrate how different input values affect a model’s outputs, you can achieve this graphically; and if you want to represent the interplay of many variables, you can make use of dynamic changes in the size, color, shape, and location of data points over time.

This last point is most famously demonstrated by Hans & Ola Rosling’s Gapminder visualization, a dynamic graph showing the changes in life expectancy, income per person and population size for almost every country in the last 215 years. The graph helps tell a rich demographic story, of human progress and inequality in the global distribution of that progress.  Their use of color, size changes and movement help us to emotionally engage with the data, which in turn helps us appreciate the real-world processes that it represents. Hans’ Gapminder lectures might not have racked up the tens of millions of views had it been static (plus it would probably have to be split into several graphs to makes sense). Scientific articles are becoming increasingly difficult to read; used appropriately, interactive figures have the potential to help counteract this trend. This is especially true for communicating findings to policy makers and the wider general public.

A Plotly version of the Gapminder visualization, which shows global changes in wealth, health and population (represented by bubble size) over the last 55 years (N.B. the original visualization covers the last 215 years). Chart created by Plotly.


Partnering for flexibility and scalability

We are excited to partner with Plotly to help researchers visualize their data without the traditional constraints. Some scientific publishers, including us, have experimented with publishing interactive figures before; we even went as far as publishing the first ‘living’ figure. However, these efforts were custom-built attempts that were either scalable but not flexible, or flexible but not scalable. Plotly, which launched the same year as F1000Research, has built a platform that excels at both with elegant aesthetics as an added bonus. So, we are leaving it to the data visualization experts and focusing our efforts on supporting their tech.


Make your data tell a story

We look forward to seeing your creative ways of visualizing your data using this new feature for our articles. In case you needed some inspiration, Plotly’s Modern Data and Medium blogs showcase lots of scientific and non-scientific interactive charts.

Instructions and FAQs for creating and submitting interactive Plotly figures to F1000Research can be found here.

*Articles over 8000 words of main text will still incur the long article surcharge of $1000. For the definition of ‘main text’, see our Article-Processing Charge page. Articles already published on F1000Research can be updated to include interactive figures, but they will not be eligible for the APC reduction.

Knowledge Networking in Scientific Practice

Technology is being incorporated more and more into our daily lives. Social media platforms allow researchers to easily connect with one another and to simply find citations or resources. Artificial intelligence and big data make it relatively easy to obtain the information scientists need to move forward with their project. With the extended push to publish data, large amounts of data can be mined allowing for disparate studies to be combined, bigger patterns to be identified, and potentially further reaching conclusions to be made. With this comes the demand for researchers to, not only stay knowledgeable and on-top-of current research, alongside publishing their own articles. Knowledge networking, a way of compiling and sharing info, can help researchers find their way through the mounds of data and resources in order for these conclusions to be made.

Finding information, be it particular facts or a specific citation, is usually associated with finding the right publication – book or journal to reference – containing the needed information. With an internet based search, instead of discovering information, research has become more about filtering and constructing search queries into something useful. Open access makes it easier to obtain and share knowledge, intellectual resources, and data, but being able to parse through and distinguish between relevant and irrelevant information is crucial.

Knowledge networking, a way of compiling and sharing info, can help researchers find their way through the mounds of data and resources in order for these conclusions to be made.

Knowledge networking is a dynamic process in which knowledge is distributed and developed through increasing access to information and augmented by a community. There are a few different types of communities that exist that enable the spread of knowledge, each of which are expanded on below: publishing/networking, academic platforms, and specialist communities.

Publishing and networking

Journal publications are still the standard format for scientific dissertation and discourse. The way content is published has drastically changed over the past decade, where sharing raw data, presentations, and preprints is becoming more common practice.

Many online publication databases like PubMed and Web of Science, though not necessarily exclusively open access, have search functions that allow the tracking citations, parsing metadata, and filter for authorship. Some also allow users to track a certain topic and get email notifications of new publications. Branching out of the model of user based searches and instead using a more metadata approach, Semantic Scholar, an academic search engine, utilizes artificial intelligence with the goal to “connect the dots between disparate studies to identify novel hypotheses and to suggest experiments which would otherwise be missed.” Similarly, F1000Workspace uses algorithms to cater searches and identify important papers within the field as well as way to organize references and share documents with other researchers.

It is important for scientists to track and communicate with each other, especially when trying to establish a collaboration with another research group, as they need to connect personally as well as intellectually. Author IDs, like those from ORCID, aid in tying the work in a publication to a subject specialist and can be valuable in linking projects to people. In addition to ORCID, social media sites like LinkedIn and even Twitter connect researchers together. Even though these platforms are more geared toward job searches and visibility respectively, they can be valuable in easily connecting people.

It is important for scientists to track and communicate with each other, especially when trying to establish a collaboration with another research group, as they need to connect personally as well as intellectually.

Academic community platforms

Within academic spheres, a myriad of software tools are used to connect researchers and to aid in data hosting and paper writing. Universities frequently use internal private services that require authorization, like DropBox, due to their security. Platforms like Figshare and many other repositories host data and large databanks for any discipline. Many open access data banks, like the Protein Data Bank (PDB), which holds structural information on a protein, are required to be used before publishing a paper ensuring that the data is available for future use.

There are community based platforms like ResearchGate, with forum-like spaces to ask research related questions. On it, individuals can be linked together on projects and publications can be linked, and interesting papers that are hidden behind paywalls can be requested for directly from the author. Site members can follow a research interest, in addition to following individual members. ResearchGate indexes self-published information on user profiles to suggest members to connect with others who have similar interests.

Specialist communities

There are highly specific communities/academic platforms available that cater for specialist interests, such as MalariaWorld. These platforms allow all attention to focus on solving a very specific problem. Moreover, with the drive towards collaboration, the identification of experts within a given field is helpful.  Such specialist communities allow individuals who have a special skill set to be identified and helps with networking communities.

Connecting the networks

Creating a sufficient knowledge network is a significant undertaking. However, when creating a platform an organization does not have to reinvent the wheel necessarily. Instead of each group defining their own metadata algorithms, their own ways of conducting social media, and inventing new methods of commenting or Q&A sections, perhaps what is needed is the combination of these (micro-)services to incorporate the best of what already exists. A significant resource for knowledge networking in this case would not be a singular organization or software that’s able to do it all, but one that links together the best at each service to get experts disseminating information.


I tried using oaDOI.org

I tried using oaDOI.org API to find the amount of Open Access and you won’t believe what I found! (Click bait title)

By now most people would have heard of the very useful Unpaywall service that allows you to bypass many paywalled articles by sending you to free versions.

Unpaywall service

While not perfect and all comprehensive, it’s one of the easiest ways to find if a free version of an article exists. The underlying service of unpaywall is oaDOI.org, which provides a free nifty API service that you can use. Continue reading “I tried using oaDOI.org”

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