LoomWare

US NSF Data Dissemination and Sharing

The NSF policy framework for sharing/disseminating research data is worth a look, of only as a best-practice approach for any research program. Some quotes from the site:

Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants. Grantees are expected to encourage and facilitate such sharing.

Beginning January 18, 2011, proposals submitted to NSF must include a supplementary document of no more than two pages labeled “Data Management Plan”. This supplementary document should describe how the proposal will conform to NSF policy on the dissemination and sharing of research results.

via www.nsf.gov

If you're going to do good science, release the computer code too!

Support for Data Stewardship

A brief article drawing attention to the issue of poor (or non-existent) data stewardship and what happens without open data and peer review of research elements like computer programs.

Summary of Recent Workshop

Main Drivers for Successful Re-use of Research Data

Summary from the report:

On 23-24 September 2009 an international discussion workshop on “Main Drivers for Successful Re-Use of Research Data” was held in Berlin, prepared and organised by the Knowledge Exchange Working Group on Primary Research Data. The main focus of the workshop was on the benefits, challenges and obstacles of re-using data from a researcher’s perspective. The use cases presented by researchers from a variety of disciplines (13 presentations) were supplemented by two keynotes and selected presentations by specialists from infrastructure institutions, publishers, and funding bodies (national and European level, 8 presentations). By choosing this design the workshop was able to provide a critical evaluation of what lessons have been learned concerning sharing and re-using research data from a researcher’s perspective and what actions might be taken to encourage and facilitate more successful re-use. Despite the individual differences characterising the diverse disciplines, it became clear that important issues are comparable. Apart from several technical challenges such as metadata exchange standards and quality assurance it was obvious that the most important obstacles to re-using research data more efficiently are socially determined. It was agreed that in order to overcome this problem more effort should be made 1) to raise awareness and 2) to encourage stakeholders to combine forces in order to support and stimulate sharing and re-use of research data on all levels (researchers, institutions, publishers, funders, governments).

Cybera/CANARIE National Summit | Summit 09: Partnerships in CI Development | Banff, Canada | Oct 12-16, 2009

Cybera/CANARIE National Summit

Some of the papers from the latest Cybera/CANARIE National Summit are available. My only observation is why can't the cyber-dudes that put sessions like this on also provide full streaming video of the sessions? Next time?

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.