Postgraduate Conference for Computing: Applications and Theory (PCCAT 2011)

I have submitted a paper to this conference at Exeter University in June. These are the details of the conference - http://www.pccat.ex.ac.uk/ -

"Home Page
Welcome to the website of the second Postgraduate Conference for Computing: Applications and Theory (PCCAT 2011). Following the great success of PCCAT 2010, we are pleased to announce that the University of Exeter will host PCCAT on 8th June 2011.

PCCAT 2010 proved a great success, both in terms of networking and introducing the vital world of conferencing to postgraduate students.

We are inviting the submission of abstracts, which if accepted will be extended into either a short paper or a poster for presentation on the day. More details can be found on the Submissions Page

In the new year, we will be inviting interested parties to join the paper review panel, which will be responsible for reviewing and providing feedback for short papers. If this is something you feel you would be interested in, please contact us (details of how to contact the committee are here

We hope to see you at PCCAT 2011, and look forward to hearing from you.


Max Dupenois and David Walker
(PCCAT 2011 Programme Chairs)"

This is my Abstract for the paper -

"Abstract: This paper is about potential to provide an interactive visual taxonomy management system. It has been and is part of efforts to structure, manage, and enable understanding of complex engineering, business and/or scientific information to enable those involved to collaborate using a systems approach. The aim and objectives are to close the link between requirements gathering and end-user modellers. The main subject will be editing and display of product data structures (already implemented), business process modelling, and discussion of possible application to phylogenic/phylogenetic (biology taxonomy) knowledge. Modelling in all these areas could make possible new insights. This approach could also be used for public understanding work and visualisation, e-science, and information management. The aim is to apply novel end-user programming research to enable the editing, management, and representation of anything tree/taxonomy based by uniting the software taxonomy structure with the taxonomy structure of the domain to be modelled and visualised, and using Semantic Web technologies to link this with overall ontologies then to end-users for visualisation.

The purpose of this work is to ease management of development use, and re-use of software and make this a continuous integrated process.

To achieve the above aim what is necessary is to establish or link to a computing infrastructure for representation of complex, engineering, business, and scientific information. This kind of Computer Science/Software Engineering research allows for bringing together related fields of Semantic Web and ontology/taxonomy management, end-user programming, and visualisation and interaction with complex information. Then management of software development with and for such professionals can be eased and all be involved via the web.

Further, the structure and accessibility of Semantic Web technologies may also assist with broadening this approach to accessibility for people with various disabilities, and also for environmental modelling."

Abstract and Poster - BBSRC (Biotechnology and Biological Sciences Research Council) AHRC (Arts & Humanities Research Council) Workshop

BBSRC (Biotechnology and Biological Sciences Research Council) AHRC (Arts & Humanities Research Council) Workshop - 16th and 17th November 2010 - Abstract and Poster - Requirements for Phylogenetic Tree Visualisation - A User Driven Approach - Authors: Peter Hale, Tony Solomonides, Ian Beeson, Neil Willey, Karen Bultitude, Darren Reynolds

Abstract: This poster presentation is about potential to provide an interactive visual taxonomy management system. It will be part of our efforts to structure, manage, and enable understanding of complex scientific information to enable scientists to collaborate using a systems approach. The main subject will be editing and display of phylogenic/phylogenetic knowledge, this could make possible new insights. The project will build on the knowledge of the Faculty of Health and Life Sciences (FHLS) in this biological field, the FHLS Science Communication Unit’s excellent public understanding work and the visualisation, e-science, and information management abilities of the Centre for Complex Cooperative Systems (CCCS) The CCCS team will apply novel end-user programming research to enable the editing, management and representation of biological and environmental information including phylogenetic trees.

UWE has established a computing infrastructure for representation of complex scientific information, has in depth experience in applied scientific research, and on public understanding of science outreach. UWE Computer Science research allows for bringing together related fields of Semantic Web and ontology/taxonomy management, end-user programming, and visualisation and interaction with complex information.

Although web based taxonomies already exist, there are still opportunities to improve the visualisation and interactivity capabilities of taxonomy representation. In addition, Semantic Web techniques can enable automated structuring and management of information.

This research in management, structuring, and visualisation of information will enable visualisation of complex e-science problems to assist in enabling understanding of them, and the CCCS centre has many years of experience in gathering and enabling representations of such problems. This will enable the UWE Science Communication Unit to manage a process of making information managed in this project public. The main scientific information will be based on the work of experienced Faculty of Applied Science (FAS) researchers in Biology and Environmental Sciences. These staff have many years of research experience and much research data to make publicly available, such as phylogenetic information. The taxonomy management system will enable the use of such information and a methodology for its representation and contextualisation in varied interactive ways, according to what is most useful for particular people and types of information. This could be applied to the field of phylogenetic systematic in order to combine biological and environmental approaches and solutions.

UWE has used this technology and approach to visualise engineering product data structures and processes, but there is no reason why this strategy could not be applied to visualisation of phylogenetic taxonomy structures and to the debate on how to classify life forms which is an ontology matter. The use of visualisation via end-user HCI advances and the Semantic Web can widen this debate.

Poster - https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0Bx_KguSfl6vSZDM2ZGY3ZjMtOTNlZi00YmJjLWI2MWItODJjNWRmYmVmNzNh&hl=en.

User Driven Modelling/Programming - Overall Aims

The aim for this research has for some time been to enable empowerment and indepedence of people creating models/programs within their team from :-

• Changes in the strategy of the organisation or the environment in which it operates.
• Changes in the software environment, e.g. what software the IT services will allow.
• Problems in having time and skills for learning and using computer languages.
• Difficulties in visualising and representing the software created.
• Difficulties in enabling collaboration.
• Inaccessibility of software created, caused by use of proprietary, department only, or specialist software.
• Maintenance problems.
• Mistakes in reuse, caused by lack of visualisation and representation of previous use.

The means for this is development of diagrammatic visualised software over the web as far as possible, where the visualisation matches the structure and therefore enables the collaborion by cutting through uneccessary barriers.

The main possible uses so far are models/problems that suit a tree/network based structure, such as process modelling, business modelling, and scientific taxonomies, and family trees.

Unified Computing For Engineering, Business and Science

The research undertaken and described here crosses the boundary between engineering and computing. This is achieved by reusing the same approach for computer modelling and engineering modelling, thus applying computing use case and tree based node and object design. This approach is usable for any kind of tree and network based modelling e.g. engineering process modelling, workflow, business process modelling. The approach makes use of nodes linked by equations, or pure taxonomies if equations aren't required, thus making this useful for taxonomies, and useful for representing computing structures, biology, and engineering structure. When these taxonomies are linked up, they can then be used for a colour coded visualised ontology super taxonomy, of sub taxonomies e.g. processes, materials, components (engineering or computer software), resources, and cost rates.

The visualisation represents the structure of the model, and the structure of the problem, creating a unified approach for systematic program and model, computing and engineering, business, and biology structure representation. This makes structured representation much clearer than it can be in a flat structure such as a spreadsheet, and makes auditing and keeping track of changes easier.

This unified approach then enables representation of the problem at a high level of abstraction and if the optional equations are included aids process modelling and decision support. This high level of abstraction and structured representation and visualisation makes errors more obvious and findable, aiding auditing. Semantic Web and Web 2.0/3.0 technologies make this approach feasible for moving this approach from more complex to simple low end computing and networking the approach where useful or necessary.

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.

Objectives for future development of Ontologies

My next posts outline future research that is required for the advancement of representation, search, and visualisation of information, and at recent and future developments in the use and representation of taxonomies and ontologies, and visualisation tools that can aid in their use. Berners-Lee et al (2006) explain the importance of visualisation for navigation of information "Despite excitement about the Semantic Web, most of the world's data are locked in large data stores and are not published as an open Web of inter-referring resources. As a result, the reuse of information has been limited. Substantial research challenges arise in changing this situation: how to effectively query an unbounded Web of linked information repositories, how to align and map between different data models, and how to visualise and navigate the huge connected graph of information that results."

Horrocks (2002) explains the advantages of moving towards a more formal ontology. Making use of a more formal ontology is the next major aim for my research. Creation of a formal ontology, while at the same time creating applications that model problems such as early stage design and cost, and interactive modelling environments for students, will widen the applicability of the research. This would enable further testing on ways ontologies can be used to solve problems, and are meaningful to people as well as being searchable by computer software. My intention is to enable tagging of this ontology and eventually editing of it by users, in order to allow users and domain experts to be involved in the ontology construction.

So far the taxonomies used in my thesis include traditional object oriented relationships such as child, parent, sibling, attribute, and instance. There are other types of relationship that would need to be modelled in order to maximise the capabilities of software that would use the taxonomies. Key relationships used within the object oriented programming domain between objects have been modelled. These key relationships depict families and aggregations of objects that may share attributes and methods through inheritance. When physical items are represented, this can be translated to geometric diagrams. Semantic descriptions with more relationship types than the ones modelled so far allow a more expressive depiction of a problem domain, and can aid some forms of search within a model. One of the main advantages of a semantic net description, in terms of automated model generation, is that labelling relationships between objects allows the depiction of a number of aspects of a domain in one model, and with a consistent syntax. Ciocoiu et al (2000) explain how an engineering ontology can be made more rigorous in order to facilitate interoperability. This allows representation of, say, a product structure and its manufacturing processes together. A single node then is the only representation of that node within the model, with all its relationships depicted as arcs emanating/terminating at the node. More expressive semantic descriptions are possible through the use of the standard OWL dialects. These more expressive descriptions require sophisticated visualisation tools which will be the subject of the next post.

My Pages on this subject

Semantic Web - http://www.cems.uwe.ac.uk/amrc/seeds/PeterHale/RDF/RDF.htm.
Semantic Web Modelling - http://www.cems.uwe.ac.uk/amrc/seeds/ModellingSemanticWeb.htm.

References

Berners-Lee, T., Hall, W., Hendler, J., Shadbolt, N., Weitzner, D. J., 2006. Creating a Science of the Web. Science 11 August 2006:Vol. 313. no. 5788, pp. 769 - 771. - http://www.sciencemag.org/cgi/content/full/313/5788/769?ijkey=o66bodkFqpcCs&keytype=ref&siteid=sci.

Ciocoiu, M., Gruninger, M., Nau, D. S., 2000. Ontologies for Integrating Engineering Applications. Journal of Computing and Information Science in Engineering, 1(1) pp 12-22. - http://www.cs.umd.edu/~nau/papers/ontologies-JCISE-2001.pdf.

Horrocks, I., 2002. DAML+OIL: a Reason-able Web Ontology Language. In: proceedings of the Eighth Conference on Extending Database Technology (EDBT 2002) March 24-28 2002, Prague. - http://www.cs.man.ac.uk/~horrocks/Publications/download/2002/edbt02.pdf.

Translation for Visual End User Programming

Research Theory influencing this Translation Mechanism

The use of the Semantic Web in my thesis is to be a means for open standard representation of information (built on XML), transformation into different representations as required, and for provision of a high level interface as a tool for model creation, and translation to program code. An 'elaborator', is used, this is a translator that converts the diagrammatic representation of the problem into software code. Translations can be performed into any programming or meta-programming language or open standard information representation language, the visualisation of the model created can be displayed on the web. This translation builds on research in program and model transformation. The translation software performs transformations as required between different programming languages and visual model views. This has been prototyped, but it is important to further this research in order to establish a user base, and make the translation generic. Figure 1 shows the process.

Figure 1 - Translation Process

Implementation

Translation Process

This research involves finding alternative ways of representing models, which do not require the user to write code. The intention is to make it easier to interact with and change the models, and to share information with colleagues. The information used in the models resides in an ontology, and from this ontology models can be automatically produced via a recursive translation tool that has been prototyped.

The research for my thesis uses a technique of interpreting information in order to create decision support programs automatically in response to user choices. This technique is then extended for use in the automatic creation of programs in other computer languages and systems. This can be achieved by automated translation of the Vanguard Studio information into other languages. The basis of this is that elaborators are nodes in the tree, which are automatically created and dynamically write objects. This allows the wing box definition to be translated to the decision support system for costing and then to other software such as web pages for further processing or visualization. An open standard semantic editor Protégé created by Stanford University (2007) was used to structure this information into related taxonomies. This ontology holds the definitions of nodes representing information, and calculations to be performed. Taxonomies are created in Protégé for 'Parts', 'Materials', 'Consumables', 'Processes', 'Rates', and 'Tooling' for a prototype costing system. 'Parts' is the core taxonomy. New categories can be produced as required. Domain experts would edit the taxonomies; these experts can specify the relationships of classes and the equations to be used via a visual user interface in Protégé. These relationships are evaluated and translated to produce computer code. Figure 2 illustrates how code is produced from the semantic relationships.

Figure 2 - Translation Process Implementation

This model can be used as it is, or be a template for the generation of a further model(s). An example interface, a section from a model produced automatically, is shown in figure 3. This information is saved using a generic structure based on keys that define all relationships, into a relational database. This enables storage of hierarchical data in a relational database and also allows for separation of information into tables according to category, and the use of SQL (Structured Query Language) to automatically query and structure the information as required. Vanguards' tree based decision support tool Vanguard Studio (2007) reads this information and represents it as colour-coded nodes. The code written for this thesis automatically queries the taxonomies that make up the ontology and links the information as required for the model. The code builds in all the links required for the equations and thus links up information from different taxonomies, the information is colour coded according to which taxonomy it is from. This same code can be reused for any modelling problem, it builds the equations and follows the links to build each equation tree, and attach this to the rest of the tree. The decision support tool can perform calculations and so output results. Figure 3 shows how the decision support tool can automatically construct and represent a branch in the tree, visualize an equation and calculate a result. Red nodes represent processes, green nodes represent the part definition and magenta nodes represent resources. This illustrates how 3 taxonomies have been automatically linked because they are needed in this calculation. In this prototype hundreds of calculations have been related to each other, this example illustrates that 'Area' was also calculated, and that this forms part of the tree for the 'Hand Layup Tool Cleaning Cost', which in turn is passed into other calculations. Hundreds of calculations using information from all the taxonomies are linked as required in this costing example. The time taken to perform the translation from the ontology and to perform all the calculations is a less than a second.

Figure 3 Ontology to Model Conversion

References

Stanford University, 2007. Welcome to protégé - http://protege.stanford.edu/.

Vanguard Studio, 2007. Global Knowledge Portal http://wiki.vanguardsw.com/.

My Research - http://www.cems.uwe.ac.uk/~phale/.

Modelling - http://www.cems.uwe.ac.uk/amrc/seeds/Modelling.htm

Semantic Web Modelling - http://www.cems.uwe.ac.uk/amrc/seeds/ModellingSemanticWeb.htm

Visualization - http://www.cems.uwe.ac.uk/amrc/seeds/Visualisation.htm

Structured Representation of Information

The Need for Ontologies

Information is scattered within organisations and often not held in such a structured way as to be easily accessed by employees or software. This problem was examined by Lau et al (2005) using the example of McDonnell Douglas (now part of Boeing), that demonstrated how difficult it is to gather unstructured knowledge. Therefore, it is important that research is undertaken into methods of capturing, structuring, distributing, analysing, and visualising information.

Taxonomies, Ontologies and Structuring of Information

An ontology is a classification structure. A taxonomy can be just a convenient structure to assist programmers, or part of an overall 'thesaurus' which describes and agrees the meaning of things. This 'thesaurus' structure is the ontology and may contain one or more taxonomies. Engineers may have different names for the same thing, e.g. wing skin stiffeners may be referred to as stringers, but rib stiffeners are never called stringers. There is a relationship of stringer to stiffener, which needs to be defined, and this definition depends on the context. A classification scheme or ontology is necessary in order to make communication precise. Such an ontology can also be used to help non-specialists to understand the terminology of a particular domain. The ontology can also enable communication between the computer systems and users. Hunter (2002) explains how taxonomies can be the basis of the definitions for an ontology, and that commercial software is available. Hunter gives examples of the Ministry of Defense technology taxonomy, and the Boeing online ontology. The taxonomy "Type-Of" and "Part-Of" relationships can indicate how to construct the taxonomy. Veryard (2001) and McGuinness (2000) provide useful guides on how ontologies can assist in linking distributed data. This linking and connectivity is also explained in 'Ontologies and Semantics for Seamless Connectivity' Uschold and Gruninger (2004).

Knowledge based systems need to allow a variety of people in different disciplines to share knowledge across functional, departmental, and disciplinary boundaries. Consideration is needed of the further problem that certain knowledge should be shared with others outside the organisation such as suppliers, and customers.

There is a strong need for uniting of the approaches of top down ontology definition by a small group of experts with that of the bottom up approach of allowing all users to define the ontology. Software applications are needed that allow users with little software knowledge to edit and update ontologies themselves. The extent to which an organisation allows this depends on its structure but if this is completely prevented or not enabled in the first place, there will be user dissatisfaction resulting from their lack of involvement. It is also likely that progress in defining and editing the ontology would be delayed.

The varied user base of knowledge systems results in a further problem, which is that of fragmentation of the language itself. As the users are in different trades and professions they will not necessarily understand the same words, or assign to them the same meaning. Again this makes it necessary to structure the information in a knowledge-based system carefully, to ensure it can be well visualised, and agreements can be reached.

Relationships between terms such as type-of, and part-of become more important than the term itself, as the relationship defines the meaning of the term by relating it to the other terms. These relationships can then be represented in diagrammatic form and navigated, in order to allow the meaning of terms to be agreed and explained. A classification structure such as this is termed the ontology.

My objective is to build a catalogue and make use of it for decision support and costing systems, while demonstrating that the same approach could be used for other types of system(s). It is essential that this catalogue can query information from organisations' existing database systems. Most large organisations have key operational knowledge and information dispersed across different types of information systems, often in relational databases. This has the advantage of allowing the use of the standardised language Structured Query Language (SQL) to access this information.

This research is explained in greater depth at http://www.cems.uwe.ac.uk/amrc/seeds/ModellingSemanticWeb.htm and http://www.cems.uwe.ac.uk/amrc/seeds/PeterHale/RDF/RDF.htm.

References

Hunter, A., 2002. Engineering Ontologies http://www.cs.ucl.ac.uk/staff/a.hunter/tradepress/eng.html.

Lau, H. C. W., Ning, A., Pun, K. F., Chin, K. S., Ip, W. H., 2005. A knowledge-based system to support procurement decision. Journal of Knowledge Management, 9(1), pp 87-100.

McGuinness, D. L., 2000. Conceptual Modeling for Distributed Ontology Environments. Proceedings of the Eighth International Conference on Conceptual Structures Logical, Linguistic, and Computational Issues (ICCS 2000), Darmstadt, Germany. August 14-18, 2000.

Uschold, M., Gruninger, M., 2004. Ontologies and Semantics for Seamless Connectivity, Association for Computer Machinery - Special Interest Group on Management of Data - SIGMOD Record December, 33(4).

Veryard R., 1994. Data Mappings http://www.users.globalnet.co.uk/~rxv/infomgt/datamapping.pdf - Soap Box Blog, 2006 http://www.users.globalnet.co.uk/~rxv/so/2006/11/semantic-coupling.htm.