Tag Archives: open access week

Faculty Support of Open Data: An Interview with Sergei Pond

Headshot of Sergei Pond

This week is Open Access Week, a yearly international celebration that aims to increase awareness about open access. Most academic work is locked up behind a paywall, available only to those who are affiliated with a college or university. Open access scholarship is completely free to read and reuse.

Professor of Evolutionary Genomics Sergei Pond is one of the many Temple faculty members who support open research practices. Pond recently spoke with Librarian Sarah Jones to discuss his work and his thoughts on how open data can help with the current reproducibility crisis.

Tell us about your recent research on COVID-19. What role did open data play in your work? 

My group at Temple (Institute for Genomics and Evolutionary Medicine) is a computational biology group. We use sequence data to watch what the virus is doing and evaluate how certain intervention efforts are going. Sequence data have never been generated at a faster pace than during the COVID-19 outbreak. As of today, around 130,000 SARS-CoV-2 genomes are available. In March there were 500. The rate of accumulation is really remarkable.

We’ve done a lot of collaborative work to look at the early evolution of SARS-CoV-2. Viral genomes change all the time; the trick is to figure out which changes matter and which ones don’t. At this moment, there are some changes but none that appear to be particularly important. Once we start giving it something to work against, like large scale drugs and vaccines, then we’ll watch it.

Something the public may not appreciate is that you have to do a lot of tedious work to make sure that the data you’re analyzing makes sense. You have to clean it up and make sure that your tools run fast enough. One of the issues everyone has run across is the volume of data–typically you’re talking about hundreds or maybe thousands of sequences, but tens or hundreds of thousands brings it up to a different scale. One of the issues with these large datasets is that they’re so big and the techniques that you use tend to be fairly complicated, so it turns into this hard-to-interpret black box. We’re trying to design something that’s easy to understand.

You recently published an article on the lack of data sharing in COVID-19 research. What problems do you see this causing? Which open tools and practices would you like to see adopted? 

Ideally, what you would like to be able to access are the original files that came off the sequencer. Typically what you see is the final genome; it’s a product of many steps that translate these data from raw sequencing data to genomes. It’s been the bane of computational biology that it’s not very common to share the original data. More importantly, it is next to impossible to find sufficient detail about how people went about processing these data to generate the genome. So basically you receive a genome but you’re missing how it was assembled. This is what creates the crisis of reproducibility. You have to be able to trust the data that you’re putting into your analyses.

There’s absolutely no excuse with modern tool availability not to publish the entire chain. If you’re an experimental scientist and you don’t publish your lab protocol nobody will believe it; it has to be recreatible. But in computational analysis there’s no standard like this. There’s no expectation that you will release the data and the tools that you used to analyse these data.

Tell us about your work with the Galaxy Project. How does this platform encourage open practices? 

Galaxy is a computational framework for open data and democratizing data analysis. Every step from extracting raw data to doing comparative analysis can be done in Galaxy. I think the strongest aspect of it is the longstanding focus on the reproducibility and shareability of research. When you develop a process for doing something, you can publish it and share it. It will record which tools you used, which settings, and how they were connected to each other. Each step you can store and share, so when you publish your work you instantly release your entire workflow.

Are there any misconceptions that you would like to address regarding open data? What do you wish people knew about it? 

There are a few things that tend to slow down or prevent people from doing open data and sharing. One, the logistics of it: will you find the time to annotate and format everything correctly and submit it? That excuse is becoming harder to use because there are large entities that have databases and tools that allow you to do this as easily as possible.

The other issue is data ownership. If you release open data it will be good for science, it will be good for discovery, and it will enable other people to extract more information from it. But as a data producer, how do you get proper credit for it? As a scientist you get rewarded for publishing papers and bringing in grants, but for being a good citizen of the open community, it’s not there.

I want to mention the idea of privacy. Human genomic data is personal health information, which needs to be guarded and protected. Viral data are a little different, you can’t track them down to specific individuals. But nonetheless, that could be a concern. It definitely is a concern in the area of HIV because in many jurisdictions in the United States HIV transmission is still a felony. That’s changing, but it’s still there. You don’t want to have a potential disclosure of an infection route.

Is there anything else you wanted to share? 

I want to emphasize that SARS-CoV-2 genomics has been a unique effort when it comes to collaboration and open science. It’s not ideal and we can improve on it, but compared to previous outbreaks this is probably the most open environment that we’ve had. It’s obviously a necessity, considering how much damage this pandemic has already caused. A truly international, truly open effort is necessary.

Fortunately, a lot of it was set up prior to SARS-CoV-2. There are people that took the time and strategically thought about how they could accelerate all of the necessary steps when the next big pathogen came out, and we’re reaping the benefits now. That really is important and worth emphasizing. That would not have happened without planning.

Thank you Dr. Pond!

Why Temple Researchers Publish OA

promotional banner for open access week

This week is Open Access Week, a yearly international celebration that aims to increase awareness about open access (scholarship that is free to read and reuse). Most academic work is locked up behind a paywall, available only to those who are affiliated with a college or university. Many Temple faculty members and graduate students choose to publish in open access journals in order to make their work more widely available to readers around the world.

The Libraries support open access publishing by Temple researchers through our Open Access Publishing Fund. When faculty and graduate students apply for the fund, we ask them why they have chosen to publish open access. Here are a few of the responses we have received this year:

“I prefer to publish open access because it increases accessibility and visibility. With an open access publication, I can be confident that my lab’s work will be accessible to everyone, free of charge and without having to wait for an embargo period.”
-David Smith, Assistant Professor, Psychology

“The open access nature of the journal is well-suited to our article, which addresses traffic calming via the use of non-asphalt materials for paving road surfaces, making streets safer for pedestrians, bicyclists, and motorized vehicles. Such paving materials are more common in the developing world, which was noted by one of the article reviewers. Publishing in an open access journal enhances access to the article by scholars in developing countries, where access to more conventional academic journals may be restricted due to cost or other barriers.”
-Jeremy Mennis, Professor, Environmental Studies

“This research is about the ecology of invasive species, which are an increasingly urgent problem that affect natural systems across the globe. It is important to make this research accessible to the scientific community and other non-academic stakeholders who are studying or affected by invasive species.”
-Amy Freestone, Associate Professor, Biology

“It is good to publish in an open-access journal because this format allows broader sharing of our studies. In addition, being digital, online article is published faster than the traditional journal article that takes over 4-6 months for printing an issue. Being open access, everyone worldwide can read our article without having to afford a costly subscription.”
-Marion Chan, Associate Professor, Lewis Katz School of Medicine

“The study aims to assess the relative importance of both environmental and socioeconomic neighborhood factors in the prediction of A. albopictus’ (one of the main transmitters of Zika virus) presence in Southeast Pennsylvania using MaxEnt (open source software) machine-learning algorithm. The study uses exclusively free available data and software to provide knowledge about the main drivers and current distribution of a vector species in South East Pennsylvania. This knowledge is relevant not only for academia but for others professionals working or interested on mosquito prevention planning such as public health officials. The free availability of this publication will provide access for these stakeholders to information that otherwise would be restricted for general use. We believe that publication in an open access journal will boost the impact of the article within and beyond academia.”
-Daniel Wiese, PhD student, Geography and Urban Studies

“The paper presents a school-based preventive dental program in the Republic of Armenia, as well as its results and recommendations to local stakeholders. In this middle-income country, most of the universities and public institutions do not have institutional access to mainstream academic journals. Publishing open access will allow readers in Armenia and in other low-income settings to get access to this paper and possibly replicate the intervention and its results.”
-Hamlet Gasoyan, PhD student, College of Public Health

A Brief Introduction to Open Access Journal Publishers

“Types of OA Publishers” by Annie Johnson is licensed under CC BY 4.0.

This week is Open Access Week, a yearly international celebration that aims to increase awareness about open access (scholarship that is free to read and reuse). Most academic work is locked up behind a paywall, available only to those who are affiliated with a college or university. One way researchers can make their work more widely available to readers is by publishing in an open access journal.

Some of the largest publishers of open access journals are actually commercial publishers you’ve probably heard of, like Elsevier and Springer Nature. SAGE, De Gruyter, Taylor & Francis, and Wiley also publish open access journals.

Nonetheless, there are a growing number of exclusively open access journal publishers whose names may be less familiar to researchers. Here’s a brief run down of some of the major open access publishers you might encounter:

Exclusively Open Access Non-Profit Publishers

eLife
eLife is a non-profit OA publisher/journal that was founded by Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust is 2011. They publish scholarship in the life and biomedical sciences. Some articles published in eLife include ancillary materials, such as the decision letter from the editorial team with suggestions for improvement, as well as the authors’ response to that letter. Peer reviewers may also choose to reveal their identities to authors. In addition to traditional journal content eLife runs a magazine which includes editorials, interviews, and podcasts. eLife is one of the most prominent publishers to criticize the journal impact factor. As a result, they do not report on or promote this metric.

PLOS
Founded in 2001, PLOS (Public Library of Science) is a non-profit publisher that publishes seven journals. Its flagship journal, PLOS ONE is known as a “mega journal” because of the large number of articles it publishes (22,054 papers in 2016 alone). In 2014 PLOS implemented a new data policy, in which they require that all researchers make the data underlying their work fully available.

Exclusively Open Access Commercial Publishers

BioMed Central
Based in the United Kingdom, BioMed Central (BMC) was founded in 1999 and publishes over 300 journals. It is now owned by Springer Nature. Temple University Libraries is an institutional member of BMC, and automatically covers 50% of the total APC for all Temple researchers who submit.

F1000 Research
F1000 Research is a scholarly publication platform that was founded in 2000. It is known for its use of open peer review. F1000 Research publishes posters and slides in addition to scholarly articles.

Frontiers
Frontiers Media was founded in 2007 and is based in Switzerland. It currently publishes sixty-three open access journals in a range of disciplines.

Hindawi
Hindawi is an open access publisher based in London. It was founded in 1997, although it did not become an exclusive open access publisher until the 2000s. Hindawi currently publishes over 400 journals.

MDPI
Founded in 1996, the publisher MDPI (Multidisciplinary Digital Publishing Institute) is based in Switzerland and publishes 203 open access journals, mostly in the sciences.

PeerJ
Launched in 2013, PeerJ is a publisher of two journals: PeerJ (which focuses on the biological, medical and environmental sciences) and PeerJ Computer Science. They also have a repository for preprints, called PeerJ Preprints. In the beginning, PeerJ relied on a membership model to make money, in which authors would pay one fee and they could publish for free in PeerJ for the rest of their careers. They have recently changed their model so that authors can pay an article processing charge (APC) instead of purchasing a lifetime membership.

One last note: all the publishers profiled here are members of the Committee on Publication Ethics, and their journals can be found in the Directory of Open Access Journals.

Faculty Support of Open Access: An Interview with David Sarwer

No matter what discipline you are in, it is hard to ignore the major shift from traditional journal publishing to open access publishing. In honor of Open Access Week 2017, we are celebrating faculty at Temple University who support open scholarship in a variety of ways.

One of these faculty members is David Sarwer, the Associate Dean for Research, and Director of the Center for Obesity Research and Education at the College of Public Health. Sarwer is also the Editor-in-Chief of an open access journal, Obesity Science & Practice. He sat down with Biomedical & Research Services Librarian (Ginsburg Health Sciences Library) Stephanie Roth to discuss his experiences as the editor of a new open access journal.

Please tell us more about Obesity Science & Practice. How did you become involved as the Editor-in-Chief?

Obesity Science & Practice is a Wiley journal. They publish four other journals in the area of obesity and were quick to recognize that there was an increasing number of high quality papers not making the cut in those journals. When they approached me about serving as the inaugural Editor-in-Chief, I was still skeptical about publishing in open access journals. The more the Wiley team taught me about their approach, I came to believe that open access publishing was likely to play a significant role in the future of academic publishing.

What gave you confidence to believe in open access?

The early success of the journal has given all of us a great deal of confidence. We have quickly moved to publishing four issues a year. We now receive a steady stream of articles that are either direct submissions to the journal or are referred to us by other Wiley obesity journals. Many of the papers published in the journal have come from internationally recognized authorities in the field of obesity. All of these developments give me a great deal of confidence about the future of the journal and open access publishing more generally.

When you first heard about open access publishing what were your immediate thoughts?

Like everyone else, I was familiar with the old school publishing model. So, I was hesitant and skeptical. The Wiley team did a great job to make me comfortable that open access represented the path to the future.

Did you ever publish to an open access journal prior to becoming the editor of one?

No, but I wouldn’t hesitate to publish in a high quality, reputable open access journal today.

Now as an editor, what are your thoughts about open access publishing?

I am very impressed with open access compared to traditional publishing and especially by our journal. The speed at which we are able to process papers and push them out to our readers is a great strength. We have published a number of high quality, impactful papers in the field. Several of them have received mass media coverage as well, which is an important, yet often overlooked aspect of academic productivity.

What has been your experience with OA journals vs. traditional publishing?

I haven’t noticed much of a difference. Many non open access journals are now putting their papers online. That shows the potential growth and acceptability of open access in the future.

What has contributed to more authors embracing your journal?

It has helped that Wiley is well recognized for their journals. That has helped to increase our journal’s credibility. Wiley has also done a good job identifying high quality submissions that were rejected from one of their four other major obesity journals. When a paper is referred to us from one of those journals, we often use the previous reviews to inform the editorial process and decision making. This has allowed us to move papers through the review process quickly.

What are your future plans for the journal?

I would like to stay on our current path of success. We recently moved to publishing four issues a year and continue to receive a steady stream of papers. I would like to see the first impact factor be appropriately robust and to have it grow over time.

Do you provide tools for graduate students or residents to publish in your journal?

At the journal level, we aren’t doing anything specific for graduate students. We do receive a fair amount of submissions from those who may be working on their first papers and launching their own independent careers and that is also encouraging.

What tips would you give to researchers looking to publish in an OA journal?

I would like to encourage them to make sure they don’t discount them. Be thoughtful. Make sure the journal is a legitimate outlet, and not one associated with predatory publishing. Researchers should see open access as an important and central part of academic publishing in the future.