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For those who want to take a glimpse at where science and scientific discourse are going, take a look at some of the papers at this workshop: Workshop on Semantic Web Applications in Scientific Discourse , October 26, 2009, Proceedings ), part of The 8th International Semantic Web Conference (ISWC 2009) Keynote: Enabling Semantic Publication and Integration of Scientific Information David Shotton. Presentation . A Short Survey of Discourse Representation Models Tudor Groza, Siegfried Handschuh, Tim Clark and Simon Buckingham Shum Paper Presentation Strategic Reading and Scientific Discourse Allen Renear and Carole Palmer Paper 'Confortation': about a new qualitative category for analyzing biomedical texts Delphine Battistelli, Antonietta Folino, Patricia Geretto, Ludivine Kuznik, Jean-Luc Minel and Florence Amardeilh Paper Presentation Hypotheses, Evidence and Relationships:The HypER Model of Representing Scientific Knowledge Anita de Waard, Simon Buckingham Shu...

CISTI (Canada Institute for Scientific and Technical Information) is hosting the ICSTI (International Council for Scientific and Technical Information) conference " Managing Data for Science " here in Ottawa at the LAC (Library and Archives Canada). The conference is June 9-10, 1 1/2 days long with an excellent international single stream program structured into four sessions, " Foundations ", " Libraries ", " Data Services " and " Semantic Science ". I will be attending all sessions and will also be moderating the " Semantic Science " session.

The January 2009 issue of IEEE Intelligent Systems is a special issue on the Semantic Web and science knowledge integration: The Emerging Field of Semantic Scientific Knowledge Integration . McGuinness, Deborah L.; Fox, Peter; Brodaric, Boyan; Kendall, Elisa Ontology Design for Scientific Theories That Make Probabilistic Predictions . Poole, D.; Smyth, C.; Sharma, R. Semantic Support for Quantitative Research Processes . Rijgersberg, H.; Top, J.; Meinders, M. MatSeek: An Ontology-Based Federated Search Interface for Materials Scientists . Cheung, Kwok; Hunter, Jane; Drennan, John Annotation and Image Markup: Accessing and Interoperating with the Semantic Content in Medical Imaging . Rubin, Daniel L.; Mongkolwat, Pattanasak; Kleper, Vladimir; Supekar, Kaustubh; Channin, David S. Enabling Cross-Disciplinary E-Science by Integrating Geoscience Ontologies with Dolce . Brodaric, B.; Probst, F.

Uncertainty Reasoning for the Semantic Web I, ISWC International Workshops, URSW 2005-2007, Revised Selected and Invited Papers. DOI http://dx.doi.org/10.1007/978-3-540-89765-1 , Lecture Notes in Computer Science . Of note: Towards Machine Learning on the Semantic Web. http://dx.doi.org/10.1007/978-3-540-89765-1_17 Author copy: http://www.cs.ubc.ca/spider/poole/papers/SemSciChapter2008.pdf Semantic Science: Ontologies, Data and Probabilistic Theories. http://dx.doi.org/10.1007/978-3-540-89765-1_2 Analogical Reasoning in Description Logics . http://dx.doi.org/10.1007/978-3-540-89765-1_19 Table of Contents: Fernando Bobillo, Miguel Delgado, Juan Gómez-Romero. 2008. A Crisp Representation for Fuzzy with Fuzzy Nominals and General Concept Inclusions. http://dx.doi.org/10.1007/978-3-540-89765-1_11 Mauro Mazzieri, Aldo Franco Dragoni. 2008. A Fuzzy Semantics for the Resource Description Framework . http://dx.doi.org/10.1007/978-3-540-89765-1_15 Matthias Nickles, Ruth Cobos. 2008. An Approa...

Rod Page 's demo for his Elsevier Grand Challenge submission (" Towards realising Darwin’s dream: setting the trees free ") shows the type of enrichment of biological - if not all research - articles that is quickly becoming possible. Taking a published article (" Mitochondrial paraphyly in a polymorphic poison frog species (Dendrobatidae; D. pumilio "), various additional biological, geographical and other metadata are extracted and added to a web page for the article. These include: Map showing all localities mentioned in the paper, with their enclosing polygon List of other studies which have samples in area enclosed by the study polygon Each of the following are linked through to their underlying databases (such as NIH accession number and NCBI nucleotide viewer or linked to ubio taxonomic name viewer record: List of sequence features (such as genes) in the article List of taxa sequenced in the article List of gene sequences cited by the article An image c...

Proceedings of the 11th International Conference on Asian Digital Libraries, ICADL 2008 , Bali, Indonesia, December 2-5, 2008 are now available: DL2Go: Editable Digital Libraries in the Pocket . Hyunyoung Kil, Wonhong Nam, Dongwon Lee. Hierarchical Classification of Web Pages Using Support Vector Machine . Yi Wang, Zhiguo Gong. The Prevalence and Use of Web 2.0 in Libraries . Alton Yeow Kuan Chua, Dion Hoe-Lian Goh, Chei Sian Lee. Usability of Digital Repository Software: A Study of DSpace Installation and Configuration . Nils Körber, Hussein Suleman. Developing a Traditional Mongolian Script Digital Library . Garmaabazar Khaltarkhuu, Akira Maeda. Weighing the Usefulness of Social Tags for Content Discovery . Khasfariyati Razikin, Dion Hoe-Lian Goh, Chei Sian Lee, Alton Yeow Kuan Chua. A User Reputation Model for DLDE Learning 2.0 Community . Fusheng Jin, Zhendong Niu, Quanxin Zhang, Haiyang Lang, Kai Qin. Query Relaxation Based on Users Unconfidences on Query Terms and Web K...

I am looking forward to getting a hold of this just announced book, Semantic Digital Libraries , Editors: Sebastian Ryszard Kruk , DERI NUI, Galway, Bill McDaniel , DERI NUI, Galway. Springer-Verlag, Heidelberg (DE) 2009, XVI, 246 p. 1 illus., Hardcover ISBN: 978-3-540-85433-3. The site for the book includes Tutorial on Semantic Digital Libraries , a tutorial presented at JCDL2008 , as well as a faceted searchable interface to the (extensive and useful) links described in the book. Contents Introduction Part I - Introduction to Digital Libraries and Semantic Web Digital Libraries and Knowledge Organization Semantic Web and Ontologies Social Semantic Information Spaces Part II - A Vision of Semantic Digital Libraries Goals of Semantic Digital Libraries Architecture of Semantic Digital Libraries Long-time Preservation Part III - Ontologies for Semantic Digital Libraries Bibliographic Ontology Community-aware Ontologies Part IV - Prototypes of Semantic Digital Libraries JeromeDL...

The FP6 CINeSPACE project, Experiencing Urban Film and Cultural Heritage project ( article ) creates an augmented reality by combining GIS information with semantic technology. The results are a location-/ orientation-aware binocular-like device which overlays multimedia information based on - among other things - what the user is looking at: This is a great concept and prototype, but could we take it a little further and generalize it? Say, to semantically enhanced reality goggles that allow you to select a particular semantic view of the world, including scientific and social views? Put them on and toggle the " Biological taxonomy " semantic view while you are walking through the rainforest and you have species names overlaid on your enhanced reality; identified poisonous plants and animals are marked with a bright red " Do not eat " and " Avoid ", respectively; identified endangered species are marked with an " Endangered: Do not step-on / tou...

This paper takes a more semantic web and forward looking view than recent cyberinfrastructure articles: Stein, L. D. (2008).Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges Nat Rev Genet, 9(9) , 678-688. DOI: 10.1038/nrg2414 Things like Semantic Web Pipes - missing from the article - can be found on the wiki page for the article (Thanks Matthias Samwald). Related recent articles: Goble, C., Stevens, R. (2008). State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics DOI: 10.1016/j.jbi.2008.01.008 Stockinger, H., Attwood, T., Chohan, S.N., Cote, R., Cudre-Mauroux, P., Falquet, L., Fernandes, P., Finn, R.D., Hupponen, T., Korpelainen, E., Labarga, A., Laugraud, A., Lima, T., Pafilis, E., Pagni, M., Pettifer, S., Phan, I., Rahman, N. (2008). Experience using web services for biological sequence analysis. Briefings in Bioinformatics DOI: 10.1093/bib/bbn029 Garciasanchez, F., Fernandezbreis, J., Valenciagarcia...

The Economist has a good article ( The Semantic Web: Start Making Sense , April 6, 2008) on the Semantic Web (Web 3.0?). One of the technologies they describe for automatically semantically marking-up structured and unstructured text is Calais from Reuters: " Reuters, however, believes it has overcome this problem. It recently launched a service called Calais[1] that takes raw web pages (and, indeed, any other form of data) and does the marking up itself. The acronyms can then get to work. That promises to imbue the streams of unstructured text and data sloshing around the internet with almost instant meaning. The idea is that any website can send a jumble of text and code through Calais and receive back a list of "entities" that the system has extracted--mostly people, places and companies--and, even more importantly, their relationships. It will, for instance, be able recognise a pharmaceutical company's name and, on its own initiative, cross-reference that agai...

Related to my last posting ( FREE THE ARTICLES! (full-text for researchers & scientists and their machines) ) and in the light of Peter Murray-Rust's recent annoying discovery that he cannot text-mine Pubmed Central ( Can I data- and Text-mine Pubmed Central? ), I would like to suggest an additional criterion to the definition of Open Access: Open Access must include access by machines : At minimum one must allow crawls of the site/content or (to reduce the impact of badly configured crawlers) create a compressed XML file containing all metadata and either content, or direct links to content and make it available for download (and if bandwidth is still an issue put it on a P2P network like BitTorrent ). Preferable is to offer some kind of API (OTMI) or protocol (OAI-PMH) to get at content and metadata and citations. Better is to offer access to the XML of the articles in addition to the PDF and/or HTML; if the XML actually has some semantic content, then we are approaching th...

The W3C has just released three SPARQL -related proposed recommendations: SPARQL Query Language for RDF SPARQL Query Results XML Format SPARQL Protocol for RDF

I am at WWW2007 only for today (Thursday) after attending the W3C meeting on Sunday -- Tuesday. I must say that I regret not registering for the rest of the WWW2007 conference, as it has moved to what I believe to be a more relevant, robust venue for web research and activities. This morning I attended the panel session " Building a Semantic Web in Which Our Data Can Participate " session, moderated by Paul Miller of Talis, with panelists Steve Coast (OpenStreetMap) Peter Murray-Rust (University of Cambridge) Rob Styles (Talis) Jamie Taylor (Metaweb) It was a very good panel, although the discussion revolved more around getting access to data as opposed the the Semantic Web aspect.

In IEEE Internet Computing , Ora Lassila and James (Jim) Hendler discuss Web 3.0 in their Embracing Web 3.0 as a union of (some) parts of Web 2.0 and the Semantic Web.

USC 's Information Sciences Institute has been awarded $13.8M for this project , which aims to solve the massive data glut that swamps many disciplines by automating scientific workflows . Using grid computing and other advanced technologies (such as A.I. and Semantic Web ), a workflow architecture allows for the capture of complex scientidic workflows and their application in a distributed fashion on data sets in an efficient manner. This is a very ambitious (and well funded) project. Some of the (even more) interesting parts of this project include (from the article): "...investigate mechanisms to support autonomous and robust execution of concurrent workflows over continuously changing data...learning techniques to improve the performance of the workflow system by exploiting an episodic memory of prior workflow executions." episodic memory (Wikipedia)

AAAI2007's workshop on Semantic e-Science CFP deadline extended I see that the CFP for this workshop at AAAI 2007 (in Vancouver, July 22-26) has been extended until April 12 2007.

Wiki for Professionals : VERY ambitious & exciting While the name does not really inspire me ;-) this is an amazing initiative and the various quotes by researchers describing Barend Mons ' project as visionary are completely justified. He (they) are trying to pull together the Semantic Web with a variety of biological databases and PubMed in a suped-up semantically-enhanced Wiki environment that is meant to be used by -- and be useful to -- biological researchers.

Quote Prospect An earlier posting ( Royal Society of Chemistry Semantic Publishing ) of mine has been quoted by the RSC on their Project Prospect ...

Royal Society of Chemistry Semantic Publishing Project Prospect is an exciting effort by the RSC where "... journal papers will be enhanced so that their data can be read, indexed and intelligently searched by machine, a first step towards the "semantic web" ." As someone working in the area of text retrieval and semantic web, this is a very exciting prospect. RSC's Project Prospect is reminiscent of Nature's Open Text Mining Interface (OTMI) effort -- in which I am also participating -- but in the case of Project Prospect, more semantic content will be exposed.