LoomWare

DataRSS an Example of Emerging Semantic Frameworks

Next Step in Semantic Web?

I was intrigued by a couple of references in articles I was reading to Yahoo's DataRSS, which is essentially an ATOM feed with an RDF triple for a resource, or the metadata that accompanies a digital resource. The extension of this, as represented by Yahoo's SearchMonkey, is the ability for search engines to index the metadata embedded in webpages which points to individual digital assets making up complex objects, providing one way to get at the richness of the information on the Web. I get the feeling that the Semantic Web has just become a toddler :-)

Report from W3C Workshop on the Future of Social Networking

Efforts to Weave a More Cohesive Social Web

A recent W3C Workshop highlighted the challenges and opportunities with the evolving social web. I was heartened by the recognition that somebody needs to step into this arena and provide some level of standards, or the plethora of social networking sites will get even more confusing. From the conclusions:

• Given the growing number and maturity of data interoperability formats and protocols, there is a significant opportunity for social networks to reduce the detrimental effects of architectural silos by opening their closed communities for the benefit of users. Totally distributed social networking is a possible future scenario.

  A W3C Incubator Group will review and map the data interoperability technologies available, including technologies developed outside the W3C, to identify potential gaps and illustrate how to use these technologies together, supported by an open source implementation of a decentralized architecture.

• There is a significant risk level and a lack of awareness among users surrounding the risks associated with social networking activity and social media publishing.

  Work on privacy best practices, both for users and providers, and further interaction with the existing W3C Policy Languages Interest Group, will continue the discussions on the preservation of privacy.

• Context is playing a large and increasingly important role in the social networking industry. Context has many elements and sources which at this time are poorly understood and managed (by users or the providers of social networks).

  The existing W3C work on deepening the integration of sensors and user contexts in the Web will be fed by specific use cases and requirements of social networks providers, as part of an incubator group.

• Many future business opportunities are (or will soon be) stifled by the lack of a convention and/or widely adopted protocol for the exchange of value for goods and services within communities.

  The revival of past work or initiation of new work on a micropayments protocol, seen as an important enabler for the social networking industry, will be explored as part of an incubator group.

• There is need for specific outreach on social network feature/service accessibility and mobility matters to address the disparity between current implementations of social networks and the devices or capabilities of all users of the Web.

  The relevant W3C groups will be informed of the need for specific outreach on accessibility and mobility matters for social networking.

Freebase Investment Points to Promising Semantic Repository

Freebase Takes $42 Million

Freebase is one of the most interesting of the emerging Semantic Repositories, wrapping a Wikipedia-like editing philosophy around highly structured data. The fact that the project received an investment of over $40 million last year suggests that they are on to something. Freebase represents one way to build the Semantic Web: an open, centralized repository containing the world's knowledge in a framework that encourages lining to/from other semantic systems. The alternative is a distributed network of repositories - I suspect the Semantic Web will evolve with both models as necessary to building the next stage of the Web.

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.

Some Interesting User-Centric Feedback

BiblioCommons and Queens

I thought there were some interesting gems in this piece from Martha Whitehead and Steve Toubon on user-genrated content in the library catalogue. Some examples:

Non-librarians do not limit (i.e., use facets) very much. Librarians want to help; users want to be independent. For recently-returned books, user can say how useful it was and for which course (from list). Provide brief survey of what user used in the book (whole thing, just a chapter and which one), etc. "How is this related to other texts"?

This brings to mind some of the discussion we are having here at UPEI with respect to the OPAC and the new things we can do with our open source framework. Finding a way for students to add value to the kernel which is a bib record is key to that innovation. For example, finding an easy way for students to submit their bibliographies from papers (ideally in something like RefWorks which can then be linked to specific items) I think would be an incredibly powerful addition to a bib entity. Combined with an "exit interview" re value of the item as this piece discusses would be very powerful indeed. Now, we just need to work out HOW...

Scraped from

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.

RDF API for Drupal 6.x

Drupal to Be/Support Semantic Datastores?

It's still not entirely clear to me how this new Drupal module will position Drupal in the emerging Semantic Web landscape, but from what I can gather it would allow Drupal to act as an RDF-smart semantic datastore as well as to integrate with external repositories, such as Fedora. I also understand that Drupal will take the Semantic Web functionality to a new level. Good stuff all and another reason to keep your eye on Drupal and Fedora. Arto's subsequent posting on this issue is well worth reading and highlights a number of reasons why UPEI is working with Drupal and Fedora - the future is semantic!

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.

Hung Up On the Semantic (Web)

Utne Tackles the Semantic Web

My favorite magazine has a short piece on the Semantic Web with some interesting links.

Freebase Available for Public Access

The Freebase site has opened up to public access (read only) and I suggest you check it out. I have mentioned Freebase on Loomware before, especially in the context of its Semantic Web/Wikipedia aspects. From the e-mail:

Freebase.com is now in "public alpha". Anybody in the world can search and browse the site. All applications based on the Freebase API have public read access.

Also, thanks to great feedback from an active alpha community, the Freebase site has improved quite a bit, and there is a growing group of enthusiastic contributors and developers. There is a lot of new data -- over 30,000 films, 500,000 notable people, more sports, businesses, science and so on.