Web Taxonomy Creation

An important contribution to Public Understanding of Science and for enabling of new insights would be creation of an online systematic representation of scientific information that gives a holistic view of related knowledge. This would reuse information and ideas provided by other researchers. These systems organise and visualise information. Letondal [1] of the Pasteur Institute provides a tool to generate web interfaces for molecular biology programs using an end-user programming approach. TreeBASE [2] is a relational database of phylogenetic information hosted by the Yale Peabody museum. Hughes [3] of the Computational Biology Unit (CBU) University of Bergen has investigated visualisation of phylogenetic trees and written an application that converts the NCBI (National Center for Biotechnology Information) [4] taxonomic data into a format that makes it possible to visualise the whole of the NCBI tree of life. Klyne [5] of the Image Bioinformatics Research Group, Zoology Department, Oxford University makes use of Semantic Web technology to build an image publication repository. UK Moths [6] online guide to the moths of Great Britain and Ireland illustrates the role of amateurs who send in pictures to be categorised. Mammals Family tree [7] provides an innovative way of visualising complex trees as a taxonomy on a wheel, this is a technique which could be developed as an interactive visualization. Fishbase [8] is a web accessible and searchable resource for accessing fish information by various categories. IHOP (Information hyperlinked over Proteins) by Hoffman [9] provides a gene network for navigating more than ten million abstracts in PubMed [4]. By using genes and proteins as hyperlinks between sentences and abstracts, this converts the information in PubMed into one navigable resource. Proviision of 3D hyperbolic representations of trees is investigates by Hughes et al [10]. This capability could be provided on the web using Semantic Web Technologies [11] [12] and this would enable others to edit and interact with these represenatations.

Web Taxonomy Creation - http://userdrivenmodelling.blogspot.com/2008/01/web-taxonomy-creation.html

References

[1] Letondal C. - http://www.pasteur.fr/~letondal/ - Pasteur Institute, Computing Center.
[2] TreeBASE - http://www.treebase.org/treebase/index.html - a Database of Phylogenetic Knowledge.
[3] Hughes T. Phylogenetic tree visualisation - Tim's Home Page - http://www.ii.uib.no/~tim/frontPages/treesPage.shtml.
[4] Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4
[5] Klyne G, 2007, Building a Semantic Web accessible image publication repository - http://imageweb.zoo.ox.ac.uk/drupal/files/20071002-SWeb-applications.pdf - Image Bioinformatics Research Group - Zoology Department - Oxford University.
[6] UKMoths - http://www.ukmoths.org.uk/ - Welcome to UKMoths, your online guide to the moths of Great Britain and Ireland.
[7] Mammals family tree - Use zoom tool to see mammal details on the circle's edge - http://news.bbc.co.uk/1/hi/sci/tech/6503045.stm - BBC News Science - Mammal rise 'not linked' to dinos - PDF Family tree visualisation.
[8] Fishbase - http://www.fishbase.org/search.php.
[9] Hoffman R, Information hyperlinked over Proteins - http://www.ihop-net.org/UniPub/iHOP/ - A gene network for navigating the literature.
[10] Hughes T, Hyun Y and Liberles, 2004. Visualising very large phylogenetic trees in three dimensional hyperbolic space. DA. BMC Bioinformatics. BMC Bioinformatics Apr 29;5:48.
[11] Eklund P, Roberts N, Green S, 2002. OntoRama: Browsing RDF Ontologies using a Hyperbolic-style Browser, The First International Symposium on Cyber Worlds, CW02, Theory and Practices, IEEE Press. (2002) pp 405-411.
[12] Talis Engage - http://www.talis.com/engage/ - Community information at your fingertips - an online community information solution that allows citizens to organise, create and publish details of their events, organisations and groups.