Open@VT

The University Libraries will be hosting its second Open Data Week on April 10-13 with opportunities to learn more about sharing, visualizing, finding, mining, and reusing data for research. In addition to panel discussions on open research data as well as on text and data mining, there will be two sessions on data visualization. From Tuesday through Thursday, join one or more sessions featuring guests Thomas Arrow and Stefan Kasberger from ContentMine to learn about open source tools in development for mining scholarly and research literature. ContentMine software “allows users to gather papers from many different sources, standardize the material, and process them to look up and/or search for key terms, phrases, patterns, and more.” Be sure to register for limited capacity events (Lunch on Wednesday 4/12, and the in-depth workshop on Thursday 4/13); links and full schedule below. For more information, see our Open Data Week guide, and use our hashtag, #VTODW.

Monday April 10
Open Research/Open Data Forum: Transparency, Sharing, and Reproducibility in Scholarship
6:30-8:00pm, in Torgersen Hall 1100 (NLI credit available)

Join our panelists for a discussion on challenges and opportunities related to sharing and using open data in research, including meeting funder and journal guidelines:

• Daniel Chen (Ph.D. candidate in Genetics, Bioinformatics, and Computational Biology)
• Karen DePauw (Vice President and Dean for Graduate Education)
• Sally Morton (Dean, College of Science)
• Jon Petters (Data Management Consultant, University Libraries)
• David Radcliffe (English)
• Laura Sands (Center for Gerontology)

Tuesday April 11
Introduction to Content Mine – Tools for Mining Scholarly Literature
9:30-10:45am, Newman Library Multipurpose Room (NLI credit available)

Join ContentMine instructors for an overview of text and data mining, and an introduction to ContentMine tools for text and data mining of scholarly and research literature.

Tuesday April 11
Data Visualization with Tableau
10:30 am -12:00 pm, Torgersen 1100 (NLI registration)

With the Tableau data visualization software, you or your students can easily turn research data into detailed, interactive visualizations that tell the story that numbers alone struggle to express. The software can link directly to your data sources so you always have the most up-to-date data on hand without exporting manually, and easily generate hundreds of types of visualizations that include interactive elements.

Wednesday April 12
Introduction to Content Mine: Tools for Mining Scholarly Literature
9:00-9:55am, Newman Library Multipurpose Room (NLI credit available)

Join ContentMine instructors for an overview of text and data mining, and an introduction to ContentMine tools for text and data mining of scholarly and research literature.

Wednesday April 12
Making Visible the Invisible: Data Visualization and Poster Design
9:30-11:00am, Newman 207A (NLI registration)

Visually representing data helps users and readers engage with the content, understand key findings, and retain information. Exploring, creating, and presenting these visual representations is becoming critical for teaching, academic research, and professional engagement. In this session we will explore the basics of data visualization and poster design, and look at a few tools to create different kinds of visualizations. We will also discuss the academic and professional value in visualizing data.

Wednesday April 12
ContentMine and Specialized Tools for Life Sciences Research
11:15-12:05pm, Newman Library Multipurpose Room (NLI credit available)

Join students in a computational biochemistry informatics class session for an introduction to ContentMine open source tools for text and data mining to explore research literature sources, with a focus on tools related to mining and exploring content for Life Sciences research (phylogeny and and visualization).

Wednesday April 12
Lunch with ContentMine guest speakers and program participants
12:30-1:30, Location TBA (Registration required; Limit: 50 participants)

Wednesday April 12
Text and Data Mining Forum
2:30-3:45pm, Newman MultiPurpose Room (NLI credit available)

Join our panelists for a discussion about opportunities and challenges related to text and data mining, with a focus on research purposes and information access. Audience questions are encouraged.

• Tom Arrow (ContentMine)
• Tom Ewing (College of Liberal Arts and Human Sciences, Virginia Tech)
• Weiguo (Patrick) Fan (Pamplin College of Business, Virginia Tech)
• Ed Fox (Computer Science, Virginia Tech)
• Leanna House (Statistics, Virginia Tech)
• Brent Huang (Computer Science, Virginia Tech)

Wednesday April 12
Introduction to Content Mine: Tools for Mining Scholarly Literature
4:00-5:15pm, Newman ScaleUp Classroom (101S) (NLI credit available)

Join ContentMine instructors for an overview of text and data mining, and an introduction to ContentMine tools for text and data mining of scholarly and research literature.

Thursday April 13
ContentMine Tools to Explore Scholarly Literature: A Full Day, Hands-On Workshop
9:00am – 4:00pm, Newman Library 207A (Registration required; also, NLI credit available; Coffee and Lunch provided)

During this workshop participants will: (1) ensure the software is functioning on their laptop computer, (2) participate in individual and group hands-on exercises to become more familiar with ContentMine tools, and (3) have the opportunity to experiment with using ContentMine tools with ContentMine instructors’ support – to mine scholarly literature and explore results specific to their own research project goals. Prior to the workshop, attendees will receive instructions to download software and make any other preparations to get the most of of the workshop.

As part of Open Access Week, the University Libraries and the Graduate School offered two travel scholarships to OpenCon 2016, a conference for early career researchers on open access, open data, and open educational resources. This is the third year we have jointly supported graduate student travel to the conference. From a pool of many strong essay applications, we chose Mayra Artiles, a Ph.D. candidate in Engineering Education, and Daniel Chen, a Ph.D. candidate in Genetics, Bioinformatics, and Computational Biology. In addition, Mohammed Seyam, a Ph.D. candidate in Computer Science, attended. All were in Washington, D.C. for the conference November 12-14, and sent the reports below. Be sure to check out the OpenCon 2016 highlights.

Mayra Artiles writes:

Being as open as possible – OpenCon 2016

This year I had the opportunity to attend OpenCon 2016 in Washington, DC. When I initially applied for the scholarship, I had a vague idea of how the Open agenda tied into my research and why was it important to me. However, I was not prepared for what the conference would spark. While in the US Open is mainly focused on open access to journals, the global idea of open is as diverse as are our problems. Interacting with people from different parts of the globe, who were amazingly passionate about Open in general, I learned that open access to journal articles is relatively a first world problem. While some countries fight for journal access, many more fight for textbooks and others fight for reliable internet. The more people I met, the more I learned how all of these unique issues are all nested under the large umbrella of making knowledge accessible on a global scale. One of the things that came out of these conversations was my involvement in a collaboration to create OpenCon Latin America – a conference similar to the one we had all just attended but held entirely in Spanish, empowering people and spreading the Open ideal in a language spoken mainly by over 425 million people.

This made me think about the following question: How can we, as Hokies, be as open as possible with our research? While fighting the academic tenure process and breaking the paradigms of open access journals is an endeavor of huge proportions, we can take small steps on being more open every day. We need to be as open as possible and as closed as necessary. It is for this reason I have made a list of steps on how we can be open today. The best part is that all these resources are open:

1. Take stock of all your publications and make a list of the journals you’ve published or plan to publish in.
2. Visit Sherpa Romeo and look up these journals. This page will provide information on which parts of your work are shareable and whether or not there is an embargo on your work. If you’re lucky, you can share a copy of your pre-print.
3. Share as much as possible on repositories such as VTechWorks and other sites such as ResearchGate.
4. Create your impact story at ImpactStory – all you need is an ORCID profile. Our work should mean more than amount of times we get cited. This website shows just that: it will give you a score for how ‘open’ is your work, show how many people saved, shared, tweeted, and cited your work and across how many channels, among other great things. As researchers, we are more than our H-index.
5. Have a conversation with your research peers and advisors on the value of open research. While we can’t convince everybody to suddenly publish in open access, we can begin the conversation and break the paradigms. A great resource to learn more about the value of open research is Why Open Research?

Daniel Chen writes:

What is “open”? Merriam-Webster tells us that it is “having no enclosing or confining barrier: accessible on all or nearly all sides”. For OpenCon, access (to academic publications), education, and data lay at the center of its mission.

The conference brings together a select group of like-minded individuals who are all passionate towards openness. Since the conference was single-tracked, it allowed everyone to focus on the various projects, hurdles, and conversations people have about Open around the world. We had plenty of time and space to roam around American University to continue conversations. I was lucky and privileged enough to be one of the select attendees and represent Virginia Tech.

My road to Open revolves mainly though open education and open data. I teach for Software Carpentry and Data Carpentry and support NumFOCUS. It is logical then, that my definition of Open mainly focuses around open source scientific computing. It’s a very specific subset of Open, and OpenCon helped me remember what role I play in the the larger Open movement.

For me Open Education is teaching the Creative Commons-licensed Software Carpentry material the past 3 years. Over the years, my idea of open education revolved around higher education: textbooks for university students, scientific computing materials for graduate students, resources for open source. I was reminded that open education was not just for the graduate students trying to improve the quality of their research, textbooks and educational materials were not just for university students. Open education is used to teach students from all ages, lesson materials and books for elementary school, textbooks for middle school, high school, and university. It allows students and educators to invest resources in other ways to help foster better learning. Here at Virginia Tech, you may notice OpenStax books in the library, but the Rebus Community is another resource and place to get involved with open education materials.

As a data scientist, I am constantly combining disparate datasets from a myriad of sources to answer a research question. I rely heavily on open data sets. Many cities in the United States now have open data portals (e.g., NYC Open Data), and government agencies, such as the Department of Commerce house a plethora of open datasets. These datasets are great for an analyst such as myself, but open data sources such as OpenStreetMap and ClinicalTrials.gov help with urban planning in cities and provide drug trial data and results to people all over the world.

One of my favorite parts of the conference happened on the second day when we shifted from a single-track conference to an un-conference style meeting. Attendees from the conference pitched various discussion topics, and the attendees of the conference dispersed across the American University Law School. I attended a discussion about openness in academia where we talked how we incorporate it in our academic lives. For some of us (including myself), we are lucky that our advisors understand openness. Most, if not all, of my research code has a MIT Open Source License. Others found the challenge of pushing and fighting for ‘openness’ a way of disrupting the traditional ivory tower philosophy. One attendee was an undergraduate freshman who was trying to understand what openness was and how he can incorporate it as he begins his academic career. This was a great metaphor for what OpenCon stands for, empowering and pushing openness to the next generation.

I also attended the breakout discussion about global health, where we talked about how openness plays a role in improving global health. I met many people who work in the health space, and use open data and open access sources to improve health. For example, Daniel Mietchen from the NIH is part of a global infectious disease response team to build the tools and protocols necessary to respond to the next epidemic. The 2014 Ebola and 2015 Zika outbreaks are recent reminders of how much we can improve our global response to infectious disease outbreaks. In this unconference, we also talked about drug results reporting in at ClinicalTrials.gov. The problem is that even though clinical trials are listed there, not all of the results from the trials are reported after the initial trial listing. This takes away the ability for people looking to educate themselves about various treatment options for a disease, and more pressure is needed to make sure this information is adequately distributed in a timely manner.

Our final day at the conference had everyone in the conference work in groups to talk to various funding agencies and senators about openness. Essentially, we became lobbyists for Open. I was lucky enough to be in two groups. My first group talked with Rachael Florence, PhD, the Program Director of the Research Infrastructure program at the Patient-Centered Outcomes Research Institute (PCORI). We talked about how PCORI’s goal is to make study results and data more widely available, brought up the concerns about disseminating clinical trials results, and generally discussed faster reporting, lowering publication bias, reproducible research, and data sharing. We also talked about what OpenCon was, and intrigued Dr. Florence to attend next year.

My next stop was the office of Virginia Senator Mark Warner. We did not get to talk to him directly, but instead talked to his senior Policy Advisor, Kenneth Johnson, Jr. It was during this discussion that I wished we had more training on being an effective lobbyist. We only make 2 passes around the circle during our meeting. The first was introducing ourselves, and the second was how Open played a role in our lives. There was a small conversation about open data, open access, and open education for the state of Virginia, but I wished we were able to have a longer conversation. Senator Warner is already familiar with many aspects of Open, so not too much convincing was needed, but I worried about how other groups fared.

In the end, I felt OpenCon was a great experience. I made new connections with other people from all over the world, and gained new experiences on how to talk about Open. It has also given me some ideas for a side project about using ClinicalTrials.gov data to reporting rates for various clinical trials. I hope I am lucky enough next year to attend as well, and urge everyone at Virginia Tech to learn about Open, and get involved!

Virginia Tech’s fifth observance of Open Access Week took place October 24-28 with seven events, featuring a panel discussion and talks from two visiting speakers.

The first event of the week featured Brian Hole, who is CEO of Ubiquity Press. An archaeologist by training, he had experienced lack of journal access in places like India. Ubiquity Press was begun to provide a good quality, low cost open publishing platform that would be inclusive of the developing world. While the platform does operate using the sometimes controversial APC model, the costs are low ($400 standard, but can be lower depending on services provided) and are often covered by libraries so there is no cost to author or reader. Ubiquity is also involved in publishing books as well as journals for open research software, several for open data, citizen science, and an upcoming open hardware journal. The platform offers an open peer review option, which four journals have implemented. Currently publishing 42 journals, its platform will be open source, and is itself a fork of the Open Journal Systems open source code. It’s an impressive platform and openness is at its core.

On Monday evening, the forum “For the Public Good: Research Impact and the Promise of Open Access” was held, hosted by Peter Potter (Director of Publishing Strategy, University Libraries) and featuring panelists from a variety of perspectives: graduate students Siddhartha Roy (Civil and Environmental Engineering) and Mohammed Seyam (Computer Science) as well as Montasir Abbas (faculty, Civil and Environmental Engineering), Karen DePauw (Dean of the Graduate School), and Brian Hole (Ubiquity Press). The conversation was wide-ranging, covering pre-prints, publishing costs, metrics, and peer review. Other topics included the importance of open licensing for reuse of scholarly material and the role of openness for a public land-grant university. Faculty open access mandates were briefly addressed, with comments focusing on saving faculty time and showing benefits. Transparency of data and code were a theme, as well as the possibility of researching completely in the open. See the video below for the full forum (and here are Peter’s introductory slides).

Thanks to the University Libraries’ Event Capture Service for the video below.

In the session “Where Can I Post My Publications?” Ginny Pannabecker and I covered the landscape for article archiving, including research networking sites, researcher profiles, disciplinary and institutional repositories, and personal and departmental websites. It’s important to know about journal permissions, which sites can host research as opposed to linking to it, and about limits to sharing and preservation on proprietary platforms. We got great feedback on this session, and one faculty member signed up for an ORCID identifier and used the new EFARS system to deposit scholarship to the VTechWorks faculty collection.

“Publishing Services at Virginia Tech,” hosted by Gail McMillan and Peter Potter covered the journal and conference hosting services provided by the Libraries. Attendees showed particular interest in the student journals hosted, such as Philologia and the Virginia Tech Undergraduate Historical Review (and more are on the way).

We were very pleased that our librarian exchange with the Cape Peninsula University of Technology in Cape Town, South Africa coincided with Open Access Week, since Veliswa Tshetsha focuses on scholarly communication there. Her presentation Access to Research in South Africa gave an overview of open access initiatives in that country as well as on the continent. Recently CPUT signed the Berlin Declaration on Open Access, joining 45 other African universities. The main funding body, the National Research Foundation, like funding bodies in the U.S., is requiring article archiving, supporting article processing charges, and developing a policy on data archiving. Paywalls are only one of the problems contributing to what she referred to as an African “access drought.” Others include telecommunications access, high APC charges in some open access journals, embargoes, and researchers submitting to open access journals with little or no peer review.

The week ended with two sessions regularly offered by the Libraries. In “Scholarly Publishing Trends” I covered a lot of ground, from open science to peer review to ORCID, and Gail McMillan introduced attendees to our Open Access Subvention Fund and its guidelines.

Beyond our own events, there were other developments of note:

• There is a survey for Virginia Tech faculty on open access practices and attitudes that is now available. Help a graduate student on this thesis research!
• A great new tool for finding open research was unveiled, oadoi.org. Enter a DOI and be redirected to an open version- give it a try!
• The federal government’s Office of Science and Technology Policy (OSTP) announced new public access policies for three agencies, and a new working group on open science.

Thanks to all who attended an Open Access Week event, and thanks for reading!

Few areas in scholarly publishing are undergoing the kind of examination and change that peer review is currently undergoing. Healthy debates continue on different models of peer review, incentivizing peer reviewers, and various shades of open peer review, among many other issues. Recently, the second annual Peer Review Week was held, with several webinars available to view.

Since peer review is currently such a dynamic topic, the University Libraries and the Department of Communication are especially pleased to host a talk about peer review in science by Dr. Malte Elson of Ruhr University Bochum. Dr. Elson is a behavioral psychologist with a strong interest in meta-science issues. Dr. Elson has created some innovative outreach projects related to open science, including FlexibleMeasures.com, a site that aggregates flexible and unstandardized uses of outcome measures in research, and JournalReviewer.org (in collaboration with Dr. James Ivory in Virginia Tech’s Department of Communication), a site that aggregates information about journal peer review processes. He is also a co-founder of the Society for Improvement of Psychological Science, which held its first annual conference in Charlottesville in June. Details and a description of his talk, which is open to the public, are below. Please join us! (For faculty desiring NLI credit, please register.)

Wednesday, October 12, 2016, 4:00 pm
Newman Library 207A

Is Peer Review a Good Quality Management System for Science?

Through peer review, the gold standard of quality assessment in scientific publishing, peers have reciprocal influence on academic career trajectories, and on the production and dissemination of knowledge. Considering its importance, it can be quite sobering to assess how little is known about peer review’s effectiveness. Other than being a widely used cachet of credibility, there appears to be a lack of precision in the description of its aims and purpose, and how they can be best achieved.

Conversely, what we do know about peer review suggests that it does not work well: Across disciplines, there is little agreement between reviewers on the quality of submissions. Theoretical fallacies and grievous methodological issues in submissions are frequently not identified. Further, there are characteristics other than scientific merit that can increase the chance of a recommendation to publish, e.g. conformity of results to popular paradigms, or statistical significance.

This talk proposes an empirical approach to peer review, aimed at making evaluation procedures in scientific publishing evidence-based. It will outline ideas for a programmatic study of all parties (authors, reviewers, editors) and materials (manuscripts, evaluations, review systems) involved to ensure that peer review becomes a fair process, rooted in science, to assess and improve research quality.

Nicole Cabrera, Jordyn Ostroff, Brianna Schofield, and the Samuelson Law, Technology and Public Policy Clinic. Understanding Rights Reversion: When, Why & How to Regain Copyright and Make Your Book More Available (Berkeley: Authors Alliance, 2015).

Although I am familiar with copyright and licensing agreements for journal articles, I am less familiar with book publishing agreements. Rights reversion for books was a new concept to me, so the first guide published by the Authors Alliance had my attention right away (the group has since published a second guide, Understanding Open Access). This guide is intended for authors who, for whatever reason, may wish to reclaim rights to their books– rights that they transferred to their publishers when they signed a publishing agreement. It’s the result of “extensive interviews with authors, publishers, and literary agents who shared their perspectives on reverting rights, the author-publisher relationship, and keeping books available in today’s publishing environment.” The guide follows an “if-then” organization, referring readers to specific chapters depending on their situation, though I read it straight through (full disclosure: I’m an Authors Alliance supporter).

Early on, the authors define rights reversion and its availability:

“a right of reversion is a contractual provision that permits an author to regain some or all of the rights in her book from her publisher when the conditions specified in the provision are met… in practice, an author may be able to obtain a reversion of rights even if she has not met the conditions stipulated in her contract or does not have a reversion clause.” (p. 6-7)

This guide is intended for authors with publishing agreements already in place; it is not a guide to negotiating contracts (though it may inspire authors to examine the details of rights reversion clauses in new contracts).

The authors note that rights reversion becomes an issue for academic authors especially when their books fall out of print, sales drop, or their publishers stop marketing their books. In such instances, authors may wish to reclaim their rights (so that they can find another publisher to reissue the book or perhaps deposit the book in an open access online repository) but they find themselves constrained by the terms of their publishing agreements or they may not understand how how to go about reclaiming their rights. With these concerns in mind, the Authors Alliance “created this guide to help authors regain rights from their publishers or otherwise get the permission they need to make their books available in the ways they want.”

An important first step in the process is for authors to learn about different ways that they might increase their books’ availability (for example, electronic, audio, and braille versions as well as translations). Next, the guide helps authors determine if they have transferred to their publishers the rights necessary to make their books available in the ways they want. Older contracts may be ambiguous regarding e-book versions; the guide advises authors on how to negotiate the ambiguity. An additional consideration is that permissions for usage of third-party content may no longer be in effect.

Some examples of reversion clauses are provided in chapter 4, pointing out triggering conditions (such as out of print, sales below a certain threshold, or a term of years), written notice requirements, and timelines. It’s important to understand how the triggering conditions are defined, as well as how to determine whether they have been met, and the authors provide good suggestions for finding this information.

The publisher’s plans for the book should be discovered, and the guide emphasizes reasonable, professional conversations with publishers. The success stories throughout the book are particularly valuable in this respect.

Chapter 6 details how to proceed if a book contract does not include a rights reversion clause:

“Ultimately, whether a publisher decides to revert rights typically depends on the book’s age, sales, revenue, and market size, as well as the publisher’s relationship with the author and the manner in which the author presents his request.” (p. 77)

Before requesting reversion, an author should have a plan in place, review all royalty statements, and discover the publisher’s plans for the book. Being reasonable, flexible, creative, and persistent are the golden rules for negotations with a publisher. Precedents can be persuasive, so inquire with friends and colleagues who are authors. If electronic access is important, be aware that many publishers are actively digitizing their backfiles. In this respect, an author might draw a publisher’s attention to the increasing evidence that open access versions don’t harm sales, and can sometimes increase them as a result of improved discovery.

Understanding Rights Reversion is itself an open access book (licensed CC BY) available online in PDF. If you would prefer a print copy, it’s available in Newman Library, or you can order one ($20) from the Authors Alliance. For more information, see the Authors Alliance rights reversion portal, which includes rights reversion case studies that occurred after the publication of this guide. The Guide to Crafting a Reversion Letter, a companion to the guide containing sample language and templates, has just been released.

Thanks to Peter Potter, Director of Publishing Strategy at the University Libraries, for his feedback on this blog post (contact him if you have questions about book publishing- he has a wealth of experience). Thanks also to the Open Library for the cover image.