The research world and Wikipedia

April 28, 2009

In a post on the Wikimedia Blog Erik Moeller writes about feedback from the scholarly community regarding participating in improving Wikipedia. In his words (excerpt):

At Wikimedia, we’ve been thinking for a while about ways to directly work with scientists and open access journals. While scientists already contribute to Wikipedia in a self-organized manner (an example being the Gene Wiki effort), we have never made a systematic, large-scale effort to invite them to participate. Our exploratory survey indicates that such an invitation would be welcomed with open arms.

I feel this might be of interest to readers of this blog as well. More can be found on the Wikimedia Blog.

Jan Velterop


Royal Society of Chemistry changing the face of publishing

April 27, 2009

In an editorial for the new RSC journal Integrative Biology, Richard Kidd says

“RSC Prospect has taken elements of semantic web developments—structuring documents to enable meaning to be interpreted—and applied them to the scientific content of our articles to show the possibilities of applying standard identifiers to chemicals and concepts. Identifying the real content of published science opens up possibilities for new ways to discover, reuse, understand and analyse articles that werent previously possible.”

Sounds like CWA stuff. The journal is freely accessible upon registration.

Jan Velterop


Semantic publishing 2

April 24, 2009

Another article by David Shotton worth reading:

“Semantic Publishing: the coming revolution in scientific journal publishing” (to appear in Learned Publishing Volume 22, No 2, 85–94, April 2009; doi:10.1087/2009202.

A preprint is available for download.

Jan Velterop


Semantic publishing

April 20, 2009

A few new papers on the subject of semantic publishing were brought to my attention today. First this one:

David Shotton, Katie Portwin, Graham Klyne and Alistair Miles (2009) Adventures in semantic publishing: exemplar semantic enhancements of a research article. PLoS Computational Biology 5 (4): e1000361. http://www.ploscompbiol.org/doi/pcbi.1000361

In the words of the author: “This article describes exemplar semantic enhancements we made to an original epidemiological research article. We wished to create an example of what we hope will become mainstream in publishing of on-line scientific research articles. So we took an original article: Reis et al. (2008) Impact of Environment and Social Gradient on Leptospira Infection in Urban Slums PLoS Neglected Tropical Diseases 2: e228, doi:10.1371/journal.pntd.0000228, and published a semantically enhanced version of this article on the Web at http://dx.doi.org/10.1371/journal.pntd.0000228.x001.”

“This enhanced article includes interactive figures, mashups with Google Maps and with data from related publications, live links to full-text references, downloadable datasets in Excel files relating to figures in the paper, downloadable RDF metadata files describing the publication and the references it cites, and a separate Document Summary, all with their own DOIs.”

And then this one:

David Shotton (2009) CiTO, the Citation Typing Ontology, and its use for annotation of reference lists and visualization of citation networks. Paper submitted to the BioOntologies SIG at ISMB2009, Stockholm, June 2009. Preprint at

http://imageweb.zoo.ox.ac.uk/pub/2008/publications/Shotton_ISMB_BioOntology_CiTO_preprint.pdf

Author’s comment: “CiTO, the Citation Typing Ontology, is an ontology for de-scribing the nature of reference citations in scientific re-search articles and other scholarly works, and for publishing these descriptions on the Semantic Web. Citation are described in terms of the factual and rhetorical relationships between citing publication and cited publication, the in-text and global citation frequencies of each cited work, and the nature of the cited work itself, including its peer review status. This paper
describes CiTO and illustrates its usefulness, both for the annotation of bibliographic reference lists and for the visualization of citation networks.”

David Shotton can be reached by email (david DOT shotton AT zoo DOT ox DOT ac DOT uk), and at the Image Bioinformatics Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. Tel: Plus Forty-Four-1865-271193.

Jan Velterop


The future SAN-itized

April 13, 2009

This chapter on Semantic Association Networks by Katy Börner is worth reading by everyone interested in the Concept Web. From the concluding remarks:

Somewhere in the not too distant future, reporting a scholarly result might not involve writing a paper. Instead, scholars may add a “knowledge nugget node” or an “association link” to a complex semantic association network of humanity’s knowledge – some Bloggers are already practicing this today. The nodes in this network will describe tangible objects (e.g., a pottery piece found at a certain place by an archeologist together with information about its origin and intermediate positions/usages up to today) or intangible objects (e.g., a formula). Links will represent associations of diverse types (e.g., causal ones such as “ozone is created electrically in nature during active thunderstorms”). Each node and each link would have information on who added, modified or deleted it. A scholar’s reputation would depend on the number of nodes and/or links s/he contributed and their usefulness for humanity.
Scholars would navigate, mine, and add to this vast network of humanity’s knowledge using the information associated with nodes and links and data about the usage of nodes and links. If a scholar adds a new “knowledge nugget” or “association link” the network would be ‘re-compiled’ with the new node leading to

  • the identification of redundant data/algorithm/results,
  • a confirmation of existing facts improving the correctness of humanity’s knowledge,
  • a confirmation of the novelty of a fact increasing humanity’s knowledge, or
  • a conflict with existing facts.

In the latter case, either the new nugget or link is wrong, or other nodes/links are wrong, alternative interpretations/views are acceptable, or the entire conceptualization is not working and a scientific revolution [link added] in Kuhn’s sense (1962) is needed.

The full article: Katy Börner. (2006) Semantic Association Networks: Using Semantic Web Technology to Improve Scholarly Knowledge and Expertise Management. In Vladimir Geroimenko & Chaomei Chen (eds.) Visualizing the Semantic Web, Springer Verlag, 2nd Edition, chapter 11, pp. 183-198.

Jan Velterop


Inaugural meeting shaping up

April 7, 2009

Attendance for the inaugural meeting on May 8, 2009, is shaping up nicely. Under the ‘Conferences‘ tab you can view the names of participants and supporters, and their affiliations. We will update this information weekly between now and the meeting.

Jan Velterop


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