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Access Day 1 - 1st Sessions

Cory Doctorow and Richard Akerman Kick Off Access 2009

We got off to a good start with Access today with a keynote from Cory Doctorow. As expected Cory gave a packed session on the latest issues with copyright and the fight for information freedom around the world. I was especially inspired with his rallying cry for libraries and librarians as a critical group that needs to carry the message forward and ensure a balanced approach to copyright. As he said, saying anything bad about a library or a librarian (Margaret Atwood notwithstanding) makes you look like a jerk. So, the key message for me from Cory's piece is to leverage our stereotype an get radical about standing up for informations rights and freedoms - if we don't, then the Cory's and Michael Geist's will be the only voices in a diminishing crowd. And we don't want that. Do we?

Richard Akerman was up next with the Binkley Lecture. Richard's Science Library Pad is a must read blog for academic librarians and scientists in particular. Richard talked about the latest developments in the creation, release and access to data. He had some key points about the move in some jurisdictions to open up government information (e.g. Power of Information Task Force in the UK). His view on data via the 4 categories of Research, Government, Library and Personal data was an effective way to describe the current data landscape and why we need to pay attention. He also provided a number of links to exemplars who are providing access to data. These links will be available in Richard's preso. One of Richard's last points was to contrast making data available via APIs vs Raw Data. Basically, API-accessible data provides you more control over the data, while Raw Data provides greater flexibility re what can be done with the data in a context of a loss of control. To me there is no "2 ways" to provide access to data - Raw Data makes sure that those who can, will find something completely new and innovative in a data landscape which has no walls and chains.

BTW - all Access session are being recorded (video, audio and slide deck feed) and will be made available on the Web as soon as we can get them up there.

Data Deluge Swamps Science Historians

30 TB Per Day in Data

Nice piece about the emerging (sorry, here now) issues related to stewarding large amounts of digital data. It made me realize that in the year that will be 2009 UPEI's own Virtual Research Environment and Digital Library projects will have generated in the order of 30 TB of data that will need to be stewarded in the long term. And this will likely increase 10-fold in the following year.

UPEI Robertson Library Wins CAUBO Award for VRE

The announcement was made this week about the Robertson Library winning the Atlantic Regional CAUBO award for our Virtual Research Environment, or VRE. The text from the award:

The Virtual Research Environment (VRE) is an innovative software system for stewarding research data regardless of the type of data or discipline. The VRE combines a best-practice web-based content management system (Drupal) with a state-of-the-art data repository system (Fedora) via an open source application suite (Islandora) developed at UPEI. Together, these components help solve one of the most important and challenging aspects of any research-intensive institution: the reliable stewardship of research data throughout the life-cycle of a research program and beyond.

The VRE provides a wealth of social software tools and techniques to provide a highly-functional environment that encourages collaboration. It allows users to create workflows that can transform data into more usable formats and ensure that accessible versions of research assets are available to collaborators and/or the broader public. Over 50 research groups currently use the VRE system, representing all disciplines and research approaches, including interdisciplinary projects with international communities of interest. Examples include the Mollusc Health Lab, Marine Natural Products Lab, Marxism and Psychology Research Group, Advancing Interdisciplinary Research in Singing, and the L.M. Montgomery Institute. The VRE software is also the basis of the library’s digital collections, including newspapers, magazines, books, audio and video.

The flexible architecture of the VRE system means that any digital file can be stored, described and accessed in a variety of ways, accommodating the requirements of individual researchers, while building a generalized framework which adapts to more uses. By bringing the core philosophies of the open source community to the research effort, the VRE also provides a transformative landscape on which to build UPEI’s research excellence and outreach. By distributing the open source software behind the VRE to the larger community, these same benefits will be available to the larger Canadian and international research communities. Emerging partnerships with other institutions (e.g., University of New Brunswick) and vendors (Sun Microsystems Inc.) point to the success of the VRE and related development efforts at UPEI’s Robertson Library.

The other winners are available from the CAUBO site. You can get more information on the VRE and the software that sits behind it at our VRE and Islandora sites.

Revisiting Potential Research-Support roles for the Library

Why We Need to Embrace Research

Richard Akerman continues to be one of the few bloggers I follow in a full day full of meetings that has no opportunity for me to read, let alone write, tweets and posts. In this piece Richard highlights 3 key areas where academic libraries can take a leadership role in the research domain, redefining what we do and how the research enterprise can best be supported. It will come as no surprise that I think this is the only emerging service for academic libraries which will allow us to grow and prosper. Without this we will fade slowly into the world of print embalming and coffee shop-equipped study halls. Don't get me wrong - these traditional and newer functions are and will remain critical to our mission, but they will not help us remain a healthy and core part of the academic institution. The Library needs to be the information crossroads for all information management functions on campus: research, learning and administration. For now all the low-hanging fruit are in the research landscape, so go there we must.

I had the pleasure of speaking with external reviewers looking at our Chemistry department from a couple of perspectives (accreditation and new program) and it is clear to me from our discussions that that our research-intensive faculty colleagues want our expertise and support, but we are not responding. While some institutions in Canada, like UPEI, are responding with extensive partnerships between researchers and the library, we are failing from a community perspective to develop a clear and effective strategy. Where is the leadership in the Canadian library community for these efforts? Richard points to CISTI's Research Data Canada initiative, an important project which we should all support, but there is nothing else beyond individual efforts. I would suggest what we need is a national summit which pulls all the players together with the specific goal of developing that national approach. The ICSTI Conference in Ottawa may well be the best place to try and plan something, so I would hope that the academic library community is able to attend.

CLIR Report on Transforming Research Libraries

Audio and Slides from Recent Cyberinfrastructure Sessions

Some very interesting and topical sessions from the recent ARL/CNI Fall Forum. The sessions hit on a number of the key issues highlighted in the recent special Nature issue on Bog data, including how libraries can respond to the opportunity, how we educate the future data curation workers and more.

Text Mining for Biology

Exploring the Possible in Biological Sciences

This is a fascinating article that provides examples from leading researchers in the biological sciences of how applying information management/data curation/semantic technologies to the scientific literature (as well as workflows and research data) can facilitate discovery and new research. Some of the best example I have seen to date from the practitioners themselves of how the new tools can transform the creation of new knowledge. From the intro:

This supplement has focused on progress in text mining applied to biology, and genomics in particular, as reflected in the BioCreative II results. There is a growing demand to 'translate' information from text into more computable forms and to cross-link the information with relevant biological databases. This linkage has the potential to improve the connection between the annotations in biological databases and the supporting evidence contained in the literature. Current biological databases rely heavily on expert human curation, which requires that PhD level biologists read the (relevant) literature carefully, extract specific kinds of information, and encode each snippet of information into an entry in a database using an ontology or controlled vocabulary (see article by Chatr-aryamontri and coworkers [1] in this supplement). Given the growing volume of literature and new high-throughput methods, it is becoming urgent to provide tools that can reduce time and cost of curation, increase consistency of annotation, and provide the linkages to supporting evidence in the literature that make the annotations useful to researchers. Indeed, the distinction between biological databases and the literature is becoming increasingly blurred [2-4], and there is active discussion about whether capture of information from free text can be done before publication or extracted from the literature after publication. In addition, we are seeing the emergence of new tools to aid in massive extraction of information from both literature and biological databases (for example, WikiProfessional [5]) or on-demand extraction of information from the literature (Information Hyperlinked Over Proteins [iHOP] [6]). These tools will provide improved access to different classes of users, who need different types and granularities of information, ranging from retrieval of relevant articles, to identification of passages or individual sentences, to phrases or biological facts, generally encoded in a controlled vocabulary or ontology.

And thanks to Open Access this article is available to all now, not 1 year from now, ensuring that the world evolves at a pace faster than any proprietary system would allow.

Red Island Repository Institute

UPEI is hosting a new workshop - register now for The Red Island Repository Institute on Prince Edward Island - August 11-15, 2008

Register by May 16 and reserve your spot at the Fedora-focused Repository Institute on Prince Edward Island, one of Canada’s premiere travel destinations known for its sandy beaches, golfing, seafood and iconic red dirt roads. The 1-week hands-on workshop will be led by well-known Fedora “natives” Sandy Payette, Fedora Commons Executive Director; Richard Green, Manager, RIDIR, REMAP and RepoMMan Projects, e-SIG, Academic Services, University of Hull, and; Matt Zumwalt, MediaShelf.

The Institute is hands-on and is targeted at individuals from institutions planning or running a repository program and is intended for users with a wide range of experience, from managers to programmers. Attendees will be provided all the information and tools needed to implement and maintain a flexible repository program using Fedora. Since the Institute is a combination of lecture and hands-on experience, we encourage all participants to bring their own laptops. This will allow participants to return to their place of work with a fully-functional Fedora installation for further development and testing. Those participants who are not able to bring a laptop will be provided with one to use for the duration of the Institute.

Register by May 16 for the reduced early-bird fee of $1,500 - after that the fee is $1,800. Registration includes meals (except dinners for Tuesday to Thursday), special events and all materials. A preliminary workshop agenda and registration form are now available at http://vre.upei.ca/riri/.

If you have questions about the Red Island Repository Institute, please contact Mark Leggott at riri@upei.ca.

Science Library Pad: E-Science and libraries

More On Cyberinfrastructure

Further to my earlier post on the new D-Lib issue Richard Akerman has a post with some additional and useful links. Richard os one of the better bloggers following the whole library/science thing so it is worth keeping an eye on his posts.

D-Lib Issue on Networked Science

CyberInfrastructure and Libraries

The latest issue of D-Lib is on eScience/Networked Science/VRE/cyberinfrastructure, or whatever you like to call this stuff. This should be required reading for everybody working in an academic library since cyberinfrastructure is our future. The set of articles by Anna Gold are a particularly good review of the landscape. Anna says:

As roles and responsibilities get sorted out, librarians are testing the waters to identify what present and future roles they may have in these developments; but these are early days, and it is still unclear what those roles may be.

If you are testing the waters I think you need to rethink that strategy and put all 10 toes and the rest of your body in the water. Libraries have a critical role to play in defining a new ecological framework for stewarding and working with research output, whether in science, social science or the humanities. Anna also suggests:

While this [steep] learning curve is one factor, a second challenge adds to the difficulty that librarians have engaging in these issues: data science and data management are an awkward fit with the text-oriented constructs and systems that still dominate library relationships with science communication and publishing.

So true and so unfortunate. The UPEI Library has embarked on an innovative project we call the VRE (Virtual Research Environment) and although it is early days, it is clear that not only is our role critical, but we can and should be in the lead in terms of defining how this will all play out. s we move ahead with the VRE project it is clear that the knowledgebase libraries have developed in dealing with textual data is directly relevant and transferrable to cyberinfrastructure. As more and more data assets are describe using complex metadata schemas and application profiles libraries represent a natural partner in managing this data and the activities they encourage.

myExperiment - share scientific workflows

VREs Evolving...Or Is That Punctuating the Equilibrium?

One thing Science like to be is big and nothing shows that better than the big Grid computing efforts. Like the revolution that open source and Small Code is Beautiful brought to the software world, projects like myExperiment will bring a similar shift to how we do science. The goal of a Semantic Web framework for conducting/re-using experiments is, I think, the way to go in building eScience solutions. From the myExperiment site:

myExperiment makes it really easy for the next generation of scientists to contribute to a pool of scientific workflows, build communities and form relationships. myExperiment enables scientists to share, re-use and repurpose workflows and reduce time-to-experiment, share expertise and avoid reinvention.

Not a lot of code and detail yet, but there are some presentations that provide a good background.

Scraped from Science Library Pad