LoomWare

Access Day 2 - Morning Sessions #2

Gwendolyn MacNairn and William J. Turkel Close Access 2009

Gwendolyn MacNairn talked about her work with Zotero, including: how there seems to be a divide between the CompSci students (Zotero) and the rest of campus (RefWorks); students do not like to pay attention to the quality of the citation ("it is good enough"); both Zotero and RefWorks are good products with their own advantages and disadvantages. Gwendolyn also have an update on the legal issues Zotero had (and that are now gone) and the future functionality of this great product.

Bill Turkel provided a fascinating view on technology and history from a tech-saavy historian's viewpoint - and it . Bill does an exercise with his students where he asks them to think up a piece of technology that would allow you to experience the past, in the context of the Star Trek holodeck, but not using that piece of technology. What if you had a pair of knitting Needles that would remember very pattern they ever created. What about a Reverse Babel Fish that made it seem like every person around you was speaking Middle English. What if you had a tangible spray that allowed you to reach into the cloud and feel what the past felt like. Bill brings the scientific and historic together to make the humanities come alive. He summed up the Access 2009 Conference by saying that playing with the real world, one that pushes back and challenges, we learn in a much more effective way because we become the doers and makers of things.

I want to go back to school and I want Bill to be my teacher. Please!

Finding a fair price for free knowledge

Knowledge in a Brave New World

A thoughtful opinion piece from the best magazine in the world.

Open Repositories 2009 Day 1 - Group 3

The afternoon session featured John Kunze and Sayeed Choudhury talking on NSF DataNet: Curating Scientific Data. John started out with a number of examples of big data examples from the climate change arena. The 4 challenges he highlighted re this domain are:

• Dispersed Sources - agencies, data centres, individuals
• Diversity of Data Types
• Poor Practice
• Data Loss

He also described the DataONE project, which is designed to provide access to data about life on earth. The project will look at data types from biological and environmental domains and it looks like they will join substantial existing research groups into one data curation context. "Data is like software, but even more sophisticated" was one quote to illustrate the complexities of the data curation challenges. John talked about the idea of digital preservation being about building an outcome, not a place with a "deadly embrace". He talked about their efforts to in essence build a repository using the simple and effective tools available to them at the operating system level. I may have missed something but it sounded suspiciously like they were kinda rebuilding Fedora? I'm sure there are good reasons for going where they did, but I would be interested to see an initiative like this consider working with something like Fedora to effect what they are looking for as an outcome: an open and flexible repository of research data. The benefit to the larger community would be considerable.

Sayeed talked about the Data Conservancy project, which I unfortunately missed :-(

The EOL.org codebase is now open source

My Fave Web App now OS

I haven't done any research on this one yet, but I thought I would flag it as an example of a great mash-up website. The EOL site is built in Ruby and MySQL. At one point I thought the site was based on Fedora, but that seems not to be the case any longer.

Reinventing Science Librarianship: Models for the Future

eScience and Cyberinfrastructure

There are enough good sessions (most with audio and PPTs) in this ARL forum to keep you busy on a stormy winter day. There are also some good sessions on what we need to do to make sure the new information professional receives the kind of education they need to keep libraries in the forefront of this important area.

Spoken Web

The October 25 issue of New Scientist has an interesting piece on the Spoken Web, a new kind of Internet for cellphones that IBM is developing in India. It has a number of fascinating aspects, including HSTP (HyperSpeech Transfer Protocol) and the ability for users to create "sites" of information using voice only. A fascinating alternative to the visual web in countries where simple cell phones are everwhere. Also proof of the old "simple is best adage".

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.

Is the Web Dumbing Down Research?

Interesting Research on Research

An interesting Economist post on research done to look at the citation impact of having more and more scholarly output available to researchers.

What he discovered was that, for every additional year of back-issues of a journal available online, the average age of the articles cited from that journal fell by a month. He also found a fall, once a journal was online, in the number of papers in it that got any citations at all. Indeed, he predicts that for the average journal today, five extra years’ worth of online availability will cause a precipitous drop in the number of articles receiving one or more citations—from 600 to 200 a year. Rather than measuring the length of the tail, then, it seems that modern science is actually focusing on a tiny bit of it.

The original article (needs a Science subscription) is worth reading, as the Economist piece does over-simplify the conclusions. For example, the author also discusses other work that disagrees with the article under discussion - science in action :-)

Also worthwhile is this user comment from the perspective of a student doing research in the modern library

XML Schemas and Bioinformatics

Making Sense of the Bioinformatics XMl Landscape

As UPEI develops support for bioscience data in our VRE project, we have delved into the rather daunting world of bioscience XML schemas and related tools. This article is a good intro (although a bit out of date) and a useful start if you are looking to build data repositories in this area.

Organic Better for Bee Growers?

ECOLOGY UNDERNEWS: ORGANIC BEE GROWERS REPORT NO COLONY COLLA

This on is beyond my area of expertise, but I have been following the reports of bee colony die-offs (or Colony Collapse Disorder) with some interest. This blog post from Sharon Labchuk here in PEI provides some anecdotal evidence that organic hives are not suffering from the same problem. As the post suggests, the farming practices of many big bee operations are not necessarily that different from any big farming operation, where pesticides and pharmaceuticals are in heavily used. Most of not all the reports do come from commercial operations, so this would not be surprising. One item reports that "Among [the likely factors] are mites and associated diseases, some unknown pathogenic disease and pesticide contamination or poisoning." In an interesting Library-ish twist to this story I encountered this same issue at a presentation at the Manitoba Libraries Conference last week. Rae Bridgman and 2 other authors were discussing their books and writing in general and Rae's latest is called Amber Ambrosia:

Ten-year-old cousins Sophie and Wil face a long and endless summer, until they find out MiddleGate’s honeybees are falling sick. Even the Secretariat on the Status of Magical Creatures seems unable to solve the mystery. Fearing for Aunt Rue’s position at the Secretariat, Wil and Sophie decide to find out who – or what – is attacking the insects after the symbol of a golden bee suddenly appears on Wil’s black medallion.

Rae said the story and the current real-life mystery were a coincidence, but it is an excellent example of how important literature can be to a society that sometimes puts too much emphasis on science and high production, rather than a more ecological and balanced approach to life Maybe if more kids read this one they can help convince their bee-farming parents to adopt more balanced approach.