Open@VT

Open Access, Open Data, and Open Educational Resources

Introducing the Virginia Tech Patents collection in VTechWorks and the patent harvesting software repository, Patent-Harvest

Authors: Philippe Gray and Anne Lawrence

Inspired by the Association of Southeastern Regional Libraries webinar, “Adding Patent Records to Clemson’s IR — Highlighting the University’s Output,” VTechWorks, Virginia Tech’s institutional repository, now offers a similar collection, Virginia Tech Patents. The collection contains 645 U.S. Patents assigned to Virginia Tech at the time of patent application. The dates of issuance span 1919-2016. The collection’s display is customized with fields, search filters, and facets particular to patents, such as patent type, inventor, assignee, patent and application numbers, and patent classifications. Our motivation for creating the collection was that a sizeable collection of useful public domain content could be harvested programmatically and that it provides an opportunity to spotlight how Virginia Tech “invents the future.”

To enable other repositories to develop a similar collection, we offer our software, Patent-Harvest, in a GitHub repository. Patent-Harvest contains a Java program written to harvest all patents with Virginia Tech as the assignee. It can be adapted to harvest patents and associated files for other organizations or search parameters.

The harvesting program uses the PatentsView API to retrieve relevant metadata for all Virginia Tech patents and outputs a CSV spreadsheet. If desired, all the corresponding files for each patent are also downloaded and logically renamed. Since most United States patent documents are image-only PDFs, a script is included that uses optical character recognition to read text content and embed it in the patent documents. This makes the text of the patent documents searchable, but doesn’t change how they appear to the reader.

Open Education Week 2017: The Potential of Open Education

Happy Open Education Week! 2017 marked the fourth year of celebrating international Open Education Week at Virginia Tech. The Open Education Week planning committee set goals to meet felt needs of faculty on campus and to encourage student communication with faculty regarding the impact of learning resources on student learning.

Cost is always an issue. The committee agreed that we wanted to do something more positive than focus on barriers to learning, so we chose the theme “The Potential of Open Education.” What is Open Education anyway?  Open Education includes pedagogies, practices, and resources which reduce barriers to learning.  “Open Education combines the traditions of knowledge sharing and creation with 21st century technology to create a vast pool of openly shared educational resources, while harnessing today’s collaborative spirit to develop educational approaches that are more responsive to learner’s needs.” Source: Open Education Consortium

Two faculty and graduate student oriented events featured local and invited speakers, including live and live-streamed:

Seven Platforms You Should Know About: Share, Find, Author, or Adapt Creative Commons-Licensed Resources

Thanks to Kayla McNabb for setup of the video below and Neal Henshaw for editing.

Creative Commons licenses allow no-cost access, redistribution, remix, and reuse with attribution. This session is for faculty (and others) who want to know about platforms which enable sharing, finding, creating, and/or adapting of openly licensed or public domain resources. This session featured live demos by expert users or creators of VTechWorks, Merlot, the Open Textbook Library, OER Commons, VT’s Odyssey Learning Object Repository, Overleaf (formerly WriteLaTex), Pressbooks, and the Rebus Open textbook editing community.

The event handout “Where to find, share, author and adapt Open Educational Resources? A Selection of No-Cost Platforms” is available here; also check out links from the Seven Platforms program.

The Potential of Open Educational Resources: Virginia Tech Faculty & Student Panel Discussion

Thanks to Digital Media Services for the video below and the University Libraries’ Event Capture Service for video production.

Virginia Tech Open Educational Resource (OER) authors, adapters, and authors and several students discussed the use, benefits, challenges, and opportunities related to using or adapting openly licensed course materials for couse use. Panelists included Jane Roberson-Evia (Statistics), Mary Lipscombe (Biological Sciences), Stephen Skripak (Pamplin), and Anastasia Cortez (Pamplin). Publishing expert Peter Potter (University Libraries), and students Mayra Artiles (Doctoral student, Engineering Education), and Jonathan de Pena (Senior, Finance) also joined the panel, moderated by Anita Walz (University Libraries).

Virginia Tech’s Student Government Association (SGA) designed the Open Education Week exhibit to educate and to solicit visitor input. The interactive exhibit features a range of required student learning materials including textbooks, homework access codes, software, and clickers, visual representations of data related to course material costs and student responses, information about open education options, a new Creative Commons brochure, CC stickers, and several interactive features. Students also have the opportunity to write a personalized message on an SGA-designed postcard to their professor, department head, or whomever they want to contact.

A selection of resources used in the exhibit are linked here:

Florida Virtual Campus (October 7, 2016) 2016 Student Textbook and Course Materials Survey. Available here.

National Association of College Stores (2011) “Where the New Textbook Dollar Goes” Used with Permission of NACS. (No updated data available). Available here.

Senack, Ethan. (January 2014) Fixing the Broken Textbook Market: How students respond to high textbook costs and demand alternatives. U.S. PIRG Education Fund & the Student PIRGs: Washington, DC. Available here.

Senack, E., Donoghue, R. (2016)Covering the cost: Why we can no longer afford to ignore high textbook prices. Student PIRGS: Washington, DC. Available here.

U.S. Bureau of Labor Statistics, as quoted by Popken, B. in “College Textbook Prices Have Risen 1,041 Percent Since 1977“ NBC News (August 6, 2015). Available here.

OEW word cloud

© Anna Pope, CC BY 4.0

OEW word cloud

© Anna Pope, CC BY 4.0

SGA also hosted a Multimedia Event. This student led engagement event featured multiple interactive stations where students could discuss, answer questions, take pictures, and write postcards. Two wordcloud prompts in particular were telling: “Where would your money go if you didn’t have to buy textbooks” — with the top two answers by far reflecting daily living expenses — “food” and “rent.”

Students were also asked to reflect on how they avoid buying full price textbooks. Responses included “Rent [textbooks],” “go without,” “hope for the best,” “borrow them from a friend,” and “buy used.”

OEW whiteboard

© Anna Pope, CC BY 4.0

___________________

The Open Education Week at Virginia Tech planning committee for 2017 included: Anita Walz (Chair), Kayla McNabb, Quinn Warnick, Anna Pope, Anne Brown, Kimberly Bassler, and Craig Arthur.

Exhibit curators: Virginia Tech Student Government Association: Anna Pope, Kenneth Corbett, Spencer Jones, Holly Hunter, and Sydney Thorpe with the University Libraries’: Scott Fralin and Anita Walz

Special thanks for event support: Carrie Cross, Trevor Finney, and Kayla McNabb

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.)

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