C. Maria Keet
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Dr. C. Maria Keet
Senior Lecturer
School of Mathematics, Statistics, and Computer Science
University of KwaZulu-Natal
Westville Campus (block H1)
Durban
South Africa
Tel: (+27) 031 260 1035
Fax: (+27) 031 260 7001
Home: www.meteck.org
Blog: keet blog
email: keet at ukzn.ac.za
linkedIn

CV and publications


1. Research interests and activities
2. Seminars and presentations
3. Organisational activities, reviewing etc
4. Teaching and tutorials

 

1a. Research Interests

- Logic-based knowledge representation, focussed on representing biological knowledge (biological reality)
     - conceptual modelling & ontology languages (Description Logics (& OWL), Object-Role Modeling, etc.)
     - relations in (bio-)ontologies, such as parthood and other part-whole relations
- Granularity
- Ontology development
- Biological data characteristics

1b. Research Activities

The main thread across my research activities is ontology, ontologies, logic, and conceptual data modelling. They are divided into three paragraphs for presentation convenience, and a final paragraph on participation in funded projects.

Granularity
     The development of a formal theory of granularity (TOG), my PhD thesis topic, covers subtopics such as mereology, indistinguishability, types of granularity, abstraction and expansion, and formal ontology. With the thesis completed, the focus is shifting toward its application in/with modularization, ontologies (elaborating on chapter 5 of the thesis), formal conceptual data models, developing an ontology of granularity (an extension of chapter 2 of the thesis), elaborating on part-whole relations (mainly with Alessandro Artale and Nicola Guarino), and exploring its relation with rough sets.

CS and logic-based bio-ontologies
     In this strand of investigation, I consider automated reasoning for formal (FOL, DL and OWL-ized) bio-ontologies, formal properties of relations in bio-ontologies (e.g. part-of and transformation-of), ontology engineering, and biological data characteristics. Some of those CS & bio problems feed into the granularity research activities so as to solve real problems. In addition, I was involved in OBDA testing with bio-ontologies and bio-databases for the EU FP6 FET TONES Project and I coordinated and contributed to an extension of this work to achieve in silico hypothesis testing using the horizontal gene transfer database (HGT-DB) as case study (with Mark van Passel, Santi Garcia-Vallve, Werner Nutt, Diego Calvanese, Mariano Rodriguez, and Giorgio Stefanoni)

Formal and ontology-driven conceptual data modeling
     Automated reasoning over conceptual data models that have a formalization in Description Logics in the background, mainly focussed on the DLR flavours and properties of Object-Role Modeling languages and various extensions, such as formal temporal conceptual data modelling. One of the application scenarios for the TOG is to add most of it to formal conceptual data models and/or to the language (and then also to, say, OWL 2). In addition, I was involved in the project "Technologies for Conceptual Modelling and Intelligent Query Formulation" between the Free University of Bozen-Bolzano in Italy (coordinator Prof. Enrico Franconi) and the Meraka Institute at CSIR in Pretoria South Africa (coordinator Dr. Thomas Meyer).


Participation in funded projects

- Participation (researcher) in the Marie Curie action funded by the EC under ICT Call 3 FP7-PEOPLE-2009-IRSES on a Network for Enabling Networked Knowledge (NET2). Project duration: 2010-2012.

- Participation (researcher) in the Italy-South Africa collaboration project Technologies for Conceptual Modelling and Intelligent Query Formulation, within the Executive Programme of Scientific and Technological Co-Operation between the Italian Republic and Republic of South Africa 2008-2010.

- Participation (tester and report writing) in the EU FP6 FET TONES Project (nr FP6-7603) concerning Ontology-Based Data Access for databases in the subject domain of people with disabilities and of horizontal gene transfer. Project duration: 2006-2008.



2. Seminars and Presentations

Invited talks Other talks
  • Ontology-driven formal conceptual data modelling for biological data analysis. Presentation given at the Research Session of the Masters Artificial Intelligence spring School 2011 (MAIS'11), Durban, South Africa, d.d. 27 Sept., 2011.
  • Ontology engineering with rough concepts and vague instances. KRDB Lunch Seminar, 15 June 2010.
  • Comparing and unifying industry-grade conceptual data modelling languages. KRDB Lunch Seminar, 2 December 2008.
  • Some logical and ontological aspects of part-whole relations. KRDB Lunch Seminar 19 February 2008.
  • Current characteristics and historical perspective on 'CS and IT with/for Biology'. Presentation given on 20 October 2005 at the KRDB Research Centre, Free University of Bozen-Bolzano, Italy. An introductory overview for the thematical Seminar Series CS and IT with/for Biology.
  • Factors affecting ontology development in ecology. Presentation given on 1 July 2005 at the KRDB Research Centre, Free university of Bozen-Bolzano, Italy.
  • Ontologising Bioscience: a niche. Presentation given on 1 July 2004 at the Laboratory of Applied Ontology, Trento, Italy.
  • Development of ontologies for the sciences. ISTC-CNR Laboratory for Applied Ontology, Trento, Italy, 10 March 2004.

  • Talks of accepted papers at conferences and workshops: Interjoven04, MIE05, DILS05, ORM05, KWEPSY06, WSPI06, GrC06, ORM06, OWLED07, SeS07, AI*IA07, DL07, GrC07, DL08, WORM08, EMMSAD08, KR08, OWLED08, Geomatics09, RST09, GrC09, MTSR09, ORM09, AI*IA09, DL10, EKAW10, ORM10, ESWC11, AFRICON11, SAICSIT'11.

3. Organisational activities, reviewing etc

4. Teaching


 

Microbiology & Biochemistry
MSc Food Science free specialisation (graduated 1-'98): Microbiology & Biochemistry (including related philosophy and politics), Wageningen Agricultural University, the Netherlands. www.wau.nl

Overview of the theses carried out during my MSc degree

Effect of maize rhizosphere on degradation of 3-chlorobenzoate by Pseudomonas B13 or Alcaligenes L6
    Investigation into in situ bioremediation, by aforementioned bacteria, of soil contaminated with 3CBA (an intermediary in degradation of PCBs in soil). Also with drawings of the biochemical structures of the 7 possible aerobe degradation pathways of 3CBA and the involved enzymes. The research was carried out at the Department of Microbiology, Wageningen University and Research Centre, the Netherlands.

In vitro digestibility of weaning food based on sweet potato (products)
or: Digestibilidad in vitro de la comida de destete en base de (harina de) camote.
    Mimicking the digestive tract in the lab with relevant enzymes and bacteria, using sweet potato varieties and weaning food based on sweet potato as samples to be 'digested'. The research was carried out at the Centro Internactional de la Papa [International Potato Centre], Peru.

Microbial cyanide assimilation on behalf of detoxification of cyanogen glycosides
or: Mikrobiele cyanide-assimilatie t.b.v. ontgifting van cyanogene glykosiden
     The search for micro-organisms to achieve biotechnological detoxification of cyanogen glycosides, like amygdalin, or the hydrogen cyanide that is released when processing cassava and apricot seeds. The research was carried out at the Department of Food Science, Section Food Microbiology, Wageningen University and Research Centre, the Netherlands.

Akseptatie van genetisch gemodifceerde mikro-organismen op basis van verschillende levensbeschouwingen
    Een studie naar de motieven van vegetariers, new Age-ers, moslims en de mensen met een christelijke moraal om genetisch gemodificeerde mikro-organismen geheel of gedeeltelijk af te wijzen dan wel toe te staan.
A spin-off is a summarized translation of one section of a chapter about an immanent or transcendent god. The research was carried out at the Department of Applied Philosophy, Wageningen University and Research Centre, the Netherlands.



Peace & Development
MA Peace and Development Studies (graduated 12-'03), Department of Government & Society, University of Limerick, Ireland. www.ul.ie

Publications

MA Dissertation (grade A): Terrorism and Game Theory
An analysis of the causes, goals and actors involved in the 'terrorist theatre' and on the possibilities of Game Theory (coalitions, negotiations and audience costs) as a more rational approach to this emotion-laden topic.
The aim of the research was to investigate theories of terrorism and its changes over time and apply this to game theory, in particular the concept of audience costs and coalition formation within the game theoretical framework.
Causes and goals of terrorism were identified and modifications of ideas of terrorism in time observed, accompanied with an analysis of involved actors.
Based on a premise of justification derived from the Just War theory, negotiations with aggrieved groups (terrorists) can be a rational approach to such type of protracted conflicts and uncovered dynamics based on the composition and character of organised actors. This includes averting the joint bargaining paradox when asymmetric actors cooperate to achieve a joint goal, governments who may fare better from their point of view when dividing up refugees into geographically separate areas to decrease the possibility of cooperation between aggrieved groups and recognising two-speed negotiations, which can have a (detrimental) effect on (deadline) negotiations. Secondly, an adaptation of the audience cost model explained the "war of nerves" of the terrorist theatre involving the generation of fear amongst its targets and the updating of information on moderate actors by action of extremists. Several mutations of the Prisoner's Dilemma were discussed as options to prevent mutual harm. Summary - Conclusions - full report (PDF, 763kb).
The research was carried out at the Department of Government and Society, University of Limerick, Ireland.

A selection of essays written during the first and second semester (academic year 02/03):
Democracy in the European Union
    I compare ideas about modern democracy as surfaced in the 18th century, with the EU and the nations that make up the EU, and the validity/sustainability of claims to introduce democracy as a means to achieve lasting peace in non-Western nations.
Neo-Marxist Dependency Theories
    An overview of Neo-Marxist Dependency theories and a brief discussion of Cuba as case study on how to end the dependency trap via its 'greening of the socialist revolution'.
Women's Rights in Islamic Marriage
    I'm outlining the situation in the pre-Islamic era, and the women's current position when establishing a marriage contract, polygamy, divorce and the relation to conflict and peace.

Three presentation write-ups:
EU Policies towards the Middle East (pdf): A synopsis of the policies resulting from the Barcelona Declaration and the subsequent bilateral Association Agreements, with a focus on Lebanon.
Aspects of the agricultural sector on development issues: The analysis starts with the Green revolution (post-colonial situation), moves into the international political and economical arena and ends with current and emerging technologies in agriculture, in what can be described as a neo-colonial situation.
Towards a Theory of Terrorism: Basic theory, categorisation of involved actors, terrorist activities and main responses on those actions. Some suggestions on possibly more constructive responses are discussed as well.



Research projects carried out as part of the BSc IT & Computing degree
BSc(hons), first class, IT and Computing (graduated 3-'04), Open University UK (Programme B13, minus level 1 courses and additional level 3 courses). Passed courses (grade 1 or 2): object-oriented analysis, design and programming (Smalltalk), microprocessor-based computers, relational databases, digital communications, C++, database computer project, AI for technology and software systems & development (resp. M206, T223, M358, T305, MT262, TM422, T396 and M301). www.open.ac.uk

Publications

Project (grade 1): Bacteria and bacteriocins in the food industry - modelled and documented in a relational database
The report provides an overview of the main issues in bioinformatics and outlines five main challenges in modelling biological data characteristics before modelling the semantics of bacteriocins (non-therapeutic antibiotics applied in the food industry for safety and preservation) in ER and, improved, in ORM. The main modelling considerations are discussed. Through the iterative database development process, the "bacteriocin database" has been successfully implemented to the satisfaction of the customer.
This research was carried out at the Department of Computing, Faculty of Mathematics and Computing, Open University UK. The database is developed for University College Dublin, Faculty of Agriculture, Department of Food Science.
Project report available upon request; related papers online:
Keet, C.M. Biological Data and Conceptual Modelling Methods. Journal of Conceptual Modeling, Issue 29, October 2003.
Keet, C.M. Conceptual Modelling and Ontologies for Biology: experiences with the bacteriocin database. Agropecuaria Conference (Interjoven 2004). 3-6 June 2004, San Jose de las Lajas, Cuba.
Keet, C.M. (2003). Conceptual Modelling for Applied Bioscience: the Bacteriocin Database. CSPS/computational intelligence/0310001. article

Small irrelevant but funny programs I wrote:
Easter (197kb) - Calculates easter in any given year, alsmede carnaval voor degene die daarin geinteresseerd is.
Squareball (204kb) - I needed to program something with "moving objects" for a course assignment (C++); I came up with this lame game.
GAS (288kb) - Graphing Acoustic Stability. The resulting pictures look like nice fractals; options include zooming and changing the colours of the stable and instable areas.

In case you are wondering about the difference in given name that appears in publications, C. Maria, and my regular name, Marijke: this is due to some odd naming conventions in the country I grew up (the Netherlands); Marijke is derived from Maria. I use my official name for scientific publications, and normal name for other activities


For comments:
send an email to keet at ukzn dot ac dot za.

This page was last updated on January 2, 2012