Web Taxonomy Creation

An important contribution to Public Understanding of Science and for enabling of new insights would be creation of an online methodic 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 inventive way of visualising complicate trees as a taxonomy on a wheel, this is a technique which could be developed as an interactive visualization. Fishbase [8] is a web easy to reach 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 permit others to edit and interact with these represenatations.

To unprotected to the above a collaborative modelling approach is required. The literature on collaborative modelling is extensive. Huhns [13] and Paternò [14] both explain that alternatives to current software development approaches are required for ease of form creation. The need is to translate from a form-based visual representation understood by users to software. This makes it possible to include with end-users and non-specialists in general. Johnson [15] explains that successful interaction requires mapping between levels of abstractions and that translation between these abstraction levels required by people and computers is difficult. Johnson explains that this problem often method systems are produced that make users cope with the problems of mis-translation. The representation of rules and information can be illustrated diagrammatically and it is possible to describe algorithms by concrete examples instead of abstractly. Models must be designed and visualised so that they convey to users a representation of a problem that assists with their vision of it. This modelling approach is explored by Crapo et al [16] and is the basis of our visualisation techniques allowing the creation and understanding of taxonomies and models.

Scaffidi et al [17] show that most people who develop software are de-facto programmers lacking a formal computing background, this will often be the case for scientists and the public contributing to taxonomies. End-user programming is particularly important in this research as we are making software development easy to reach to non-experts. Research by Ko [18] explains the need for engagement of end-users, including non-specialists by providing them with the capability to interact and amend software. An e-science interactive ecosystem is ideal for involving anyone interested in science to amend or produce personal content. The ecosystem will assistance from an interactive e-learning approach influenced by ‘Semantic Learning Webs’ [19]. The capabilities we will provide over the web are similar, but more collaborative and progressive than provided by spreadsheets for modelling, and web editors for knowledge sharing. We will produce an different methodology for scientific modelling that hides the complexity of low-level programming code from users. This is a kind of meta-design, as explained by Fischer [20] that can be standardised to create a collaborative ecosystem for sharing information among scientists. This builds on research we have undertaken to permit end-user programming. We will visualise scientific information and make this editable online. The system produced must be judged easy to reach and user friendly by users. In addition, it must proportion information successfully with other software and people. So interoperability is extremely important, examples of interoperability research we will make use of are INTEROP [21] and MOMOCS [22], and combine this with a form pushed approach. In order to unprotected to interoperability, the utilisation of open formats should be favoured in order to maximise chances of forward compatibility with evolving scientific models. We will also create or customise editing tools such as wikis blogs, and Semantic Web editors [23] to document the models and collect user’s feedback. We will visualise scientific information and make this obtainable online.


[1] Letondal C. – http://www.pasteur.fr/~letondal/ – Pasteur Institute, Computing Center.

[2] TreeBASE – 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 easy to reach image publication repository – Image Bioinformatics Research Group – Zoology Department – Oxford University.

[6] UKMoths – Welcome to UKMoths, your online guide to the moths of Great Britain and Ireland.

[7] Mammals family tree – Use speed tool to see mammal details on the time of action’s edge – http://news.bbc.co.uk/1/hi/sci/tech/6503045.stm – BBC News Science – Mammal rise ‘not connected’ to dinos – PDF Family tree visualisation.

[8] Fishbase – Taxonomy of Fish Species.

[9] Hoffman R, Information hyperlinked over Proteins – 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 include 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.

[13] Huhns M, 2001, Interaction-Oriented Software Development, Journal of Software Engineering and Knowledge Engineering.

[14] Paternò F, 2005, form-based tools for pervasive usability, Interacting with Computers Vol 17(3), pp 291-315.

[15] Johnson P, 2004, Interactions, Collaborations and breakdowns, ACM International Conference Proceeding Series, 3rd annual conference on Task models and diagrams Vol 86.

[16] Crapo A W, Waisel L B, Wallace W A, Willemain T R, 2002, Visualization and Modelling for Intelligent Systems, Intelligent Systems: Technology and Applications, 1, pp 53-85.

[17] Scaffidi C, Shaw M, Myers B, 2005. Estimating the Numbers of End Users and End User Programmers. IEEE Symposium on Visual Languages and Human-Centric Computing, 21-24 September, Dallas, USA.

[18] Ko A J, 2007. Barriers to Successful End-User Programming. End-User Software Engineering Dagstuhl Seminar.

[19] Stutt A, Motta E, 2004. Semantic Learning Webs. Journal of Interactive Media in Education, 2004(10), Special Issue on the Educational Semantic Web.

[20] Fischer G, 2007. Meta-Design: A Conceptual Framework for End-User Software Engineering. End-User Software Engineering Dagstuhl Seminar.


[22] MOMOCS – form pushed MOdernisation of complicate Systems.

[23] Quint V, Vatton I, 2005. Towards Active Web Clients. DocEng Bristol United.

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