Open@VT

Open Access, Open Data, and Open Educational Resources

Category Archives: Open Data

OpenCon 2018: Open Space for Critical Discussion

As part of Open Access Week, the University Libraries and the Graduate School offered a travel scholarship to OpenCon 2018, a conference for early career researchers on open access, open data, and open educational resources. From a pool of many strong essay applications, we chose Diana M. Franco Duran, a Ph.D. candidate in Civil Engineering in the Construction Engineering and Management program. Diana attended the conference in Toronto, Canada on November 2-4, and sent the report below. Be sure to check out the OpenCon 2018 highlights.

Diana M. Franco Duran writes:

Diana M. Franco Duran

Diana M. Franco Duran

OpenCon is a community with a culture of openness that seeks everyone who can participate. It promotes an open, safe, and diverse space in which ideas are respected. This year, OpenCon focused the discussion on two main topics: 1) community as the foundation for culture change, and 2) diversity, equity, and inclusion in open research and education. The conference’s goal was to motivate the attendees to change the culture towards a more open research and educational system with diversity, inclusion, and equity.

Open research and open education are about more than sharing the work. Open research and open education are about people. There is no way to make research and education open if we do not know the community. The community must be engaged into the discussion, so we can discover how openness can help them do what they want to do. Openness as a problem solution must work in the context of the community.

During the workshops, two of the topics for discussion were 1) how to motivate students to incorporate open access in research related activities, and 2) how to reward open research and education in higher education institutions.  It is important to communicate open access, open data, and open education to students as well as faculty, and to develop program policies/ strategies to incorporate any form of open access as an objective in the research of graduate students.

Do-a-thon at OpenCon 2018

Do-a-thon at OpenCon 2018

From my point of view, open access, open data, and open research have become significant in higher education in the last few years. However, open education has not reached that status yet. There is still the misconception that open education is only sharing educational resources. Open education is the collaborative development of educational resources to provide everyone access to high-quality resources and experiences. As a younger generation, we live surrounded by technology and unlimited resources provided by the internet. Therefore, we have all the tools to make the academic environment relevant to others by giving them access to education and knowledge.

At OpenCon, the voices and stories of all attendees are heard. I personally connected to the story of one of the panelists, Adbullah Alghurabi, a master’s student in Canada, who developed educational resources for his community in Yemen. He translated scholarship opportunities into Arabic to help students find these opportunities. He also provided students with educational materials they needed to prepare for the TOEFL and IELTS exams that did not require internet access, since students in Yemen often lack an internet connection. Undoubtedly, these stories connect to others.

Thanks to this opportunity, I am now part of the team organizing the OpenCon Latin America 2019 which will be held in Colombia. We want to focus on open education and how it is related to open access and open data, highlighting the Latin American context.

Organizers of OpenCon Latin America 2019

Organizing team for OpenCon Latin America 2019

I am thankful that I had the opportunity to attend OpenCon 2018 and represent Virginia Tech. This is a space where I had the chance to get to know people from all over the world but also I had the opportunity to know how open data, open research, and open education are helping the community. Through the workshops, story circles, open reflections, do-a-thons, and unconferences, OpenCon offers a space to work together and shape ideas to contribute the community by considering openness as an inclusive solution.

OpenCon 2017: The OpenCon Platform

As part of Open Access Week, the University Libraries and the Graduate School offered a travel scholarship to OpenCon 2017, a conference for early career researchers on open access, open data, and open educational resources. From a pool of many strong essay applications, we chose Alexis Villacis, a Ph.D. student in Agricultural and Applied Economics. Alexis attended the conference in Berlin, Germany on November 11-13, and sent the report below. Be sure to check out the OpenCon 2017 highlights.

OpenCon 2017 workshop

Alexis (left) at an OpenCon workshop

Alexis Villacis writes:

The progress of science and access to education varies widely geographically, and sometimes are very limited due to economic, cultural and social circumstances. Open Access, Open Education, and Open Data are key to support those who are left behind and bring empowerment to the next generation. OpenCon brings together the worldwide champions who are working towards the advancement of the Open Movement. Students, early career academic professionals, and senior researchers all come together under one roof to share their initiatives. Participants hear their inspiring stories, from Canada to Nepal, of sparking change during a three-day conference; a conference I am grateful to have had the opportunity to be part of, as a representative of Virginia Tech.

Over these three days, participants showcased how Open is being advanced around the world. The discussion centered on how often higher education models (knowledge access, research questions, and research funding, among many others) marginalize underrepresented scholars and students. It was thought-provoking and sometimes shocking to hear how our western ways of knowing have colonized access to information and how this has impacted the progress of R&D in other parts of the world.

OpenCon 2017 selfie

Sharing with participants from other countries and hearing the challenges they face every day made me contrast our everyday realities and the privilege we have at VT. A privilege we take for granted in our everyday lives, where access to all types of tools, research, and content is one click away through our computers. We, as an institution of higher education, promote and share access to knowledge and new technologies throughout Virginia and beyond. The impact of these transfers is what keeps our society thriving every day, but where would we be if this access were restricted to us? Perhaps, VT as a Land Grant Institution would not exist at all, the state of Virginia would not be what it is today and neither many other parts of the US.

As I walked through the halls of the Max Planck Society, where the conference was held, I kept wondering: is this not what we are doing today? What changes are we withholding from the rest of the world by limiting access to data, knowledge, and education? The essence of this and the significance of Open Access clearly goes beyond journals and data, and it is also about social justice, equity, and the democratization of knowledge. We Hokies can make a difference in Open Access. More importantly, we are the key players called to work towards its advancement.

OpenCon 2017 group photo

Open Data Week Will Feature ContentMine, Data Visualization, Panel Discussions

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.

Open Data Week featuring ContentMine

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)

ContentMine logo

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.

OpenCon 2016 Reports from Virginia Tech Graduate Students

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.

Mohammed Seyam, Mayra Artiles, and Daniel Chen at Sen. Warner's office

Mohammed Seyam, Mayra Artiles, and Daniel Chen at Sen. Warner’s office

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?

OpenCon 2016 logo

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!

Open Science Prize Entries Show the Power of Open Content and Data – Vote for Your Favorite by Jan 6, 2017!

The Open Science Prize, encourages experimentation with open content and open data to enable discoveries that improve health and push research forward. Six finalist projects address: FDA Trials; Emerging diseases; Mental and neurological disease modeling; Open Neuroimaging data; Rare disease research; and Global air quality.

Vote for your favorite project! Voting ends January 6, 2017,11:59pm PST.

The Wellcome Trust, the US National Institutes of Health (NIH), and the Howard Hughes Medical Institute have sponsored this award, “to stimulate the development of novel and ground-breaking tools and platforms to enable the reuse and repurposing of open digital research objects relevant to biomedical or health applications.” Further details about the contest are described in the Open Science Prize FAQ and in this Open Science Prize Vision and Overview from the BD2K Open Data Science Symposium, #BD2KOpenSci.

Presentation videos by each of the 6 finalist groups are available from the BD2K Open Data Science Symposium. The project titles below link to descriptions on the Open Science Prize site. Try them out and learn more about each project before you vote! Or, if you missed the vote, go explore anyway to experience these innovative platforms that make open data and research results work towards our better health:

(*Beyond the Open Science Prize, explore even more topics on Open Data and Open Research for Health via December 2016 All Hands Meeting and Open Data Symposium video archives.)