C. Maria (Marijke) Keet
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Assistant Professor (temporary contract)
KRDB Research Centre
Faculty of Computer Science
University of Bozen-Bolzano
Piazza Domenicani 3
39100 Bozen-Bolzano
Italy
Uni: http://www.inf.unibz.it/krdb
Home: www.meteck.org
Blog: keet blog
tel: +39 0471 016 127
fax: +39 0471 016 009
email: {surname}@inf.unibz.it
linkedIn

CV and publications and, since recently, also:

Keet, C.M. A Formal Theory of Granularity. PhD Thesis, KRDB Research Centre, Faculty of Computer Science, Free University of Bozen-Bolzano, Italy. 2008. PDF


 

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, ontology integration
- Biological data characteristics, bioinformatics, and ecoinformatics
- Game Theory as applied to politics and terrorism

 

Overview of main activities & deliverables of research projects

1. Research Activities
2. Publications and Technical Reports
3. Seminars and tutorials
4. Organisational activities, reviewing etc
5. Teaching


1. Research Activities

Granularity
     Development of a formal theory of granularity (TOG), my thesis topic, which 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 formal conceptual data models and ontologies (elaborating on chapter 5 of the thesis), as well as developing an ontology of granularity (an extension of chapter 2 of the thesis).

CS and bio
     Automated reasoning for formal bio-ontologies, formal properties of relations in bio-ontologies (e.g. part-of and transformation-of), biological data characteristics. Some of those CS & bio problems feed into the granularity research activities so as to solve real problems. In addition, I'm involved in OBDA testing with bio-ontologies and bio-databases for the EU FP6 FET TONES Project.

ORM and DL
     Automated reasoning over conceptual data models that have a DL in the background, mainly focussed on the DLR flavours and properties of Object-Role Modeling languages. 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 1.1). In addition, I'm 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).


2. Technical reports

Within the scope of the TOG
Below you will find two technical reports about a few experiments carried out, a mapping ORM-DLRifd, comparison of 9 Description Logics languages -- which eventually will be useful for moving toward an implementation stage of the theory -- and some philosophical considerations in the light of 'emergence' (see my blog for a summary of the latter): Tutorial material on part-whole relations
C.M. Keet. Introduction to part-whole relations: mereology, conceptual modelling and mathematical aspects. KRDB Research Centre Technical Report KRDB06-3, Faculty of Computer Science, Free University of Bozen-Bolzano, Italy. October 2, 2006. 32p. pdf

Usability/HCI
M. Jarrar, C.M. Keet, and P. Dongilli. Multilingual verbalization of ORM conceptual models and axiomatized ontologies. STARLab Technical Report, Vrije Universiteit Brussels, Belgium. February 2006. see also tech reports for the supported 10 languages

Ontology Integration
C.M. Keet. Aspects of Ontology Integration. Technical Report, Napier University, Edinburgh, Scotland. 2004.
On data characteristics and heterogeneity, ontology types and a discussion on different methodologies of ontology integration. The examples are related to the subject domain of biology and ecology.

- Ontology development and integration for the biosciences - summary
    Technical report consisting of the main and improved content of the previous two reports (on ontology integration and development of ontologies for the biosciences) extended with integration challenges and goals. Further, it includes mappings between STELLA ecological modelling and ontology elements, facilitating bottom-up ontology development focussed on representing the flow in the chosen subject domains pollution (owl) and microbial loop (owl) in marine ecosystems (created in Protege; the 'ontologies' are preliminary and experimental).
- Ontologising bioscience: a niche
    The first chapter looks into implications for developing ontologies for the biosciences; then the ecological niche was analysed and (partially) formalised. Carried out while doing an internship at the LOA in Trento. The latest version of the formalization and description of the ecological niche is published in the WSPI06 article.


3. Seminars and Presentations

Invited talks
- On modelling and formally representing granularity. Fondazione Bruno Kessler (ITC-IRST), 3 December 2007, Trento, Italy. - Europeanization of education. International Workshop on the Impact of EU Education Policy and Educational System Reforms on Youth and Society, 29/30 March 2006, Brussels, Belgium. keynote speech
- Using bio-ontologies in RDBMSs for querying granular information. Bioinformatics, Ontologies and databases Seminar day, 13-2-2006, LBD, EPFL, Lausanne, Switzerland. extended abstract
- Data and ontology integration issues in the biosciences. Seminar given on 23-8-2004 at the Micro-Array Department, Integrative Bioinformatics Unit, University of Amsterdam, The Netherlands.

Other talks
- Some logical and ontological aspects of part-whole relations. KRDB Lunch Seminar d.d. 19-2-2008.
- Current characteristics and historical perspective on 'CS and IT with/for Biology'. Presentation given on 20-10-2005 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 1-7-2005 at the KRDB Research Centre, Free university of Bozen-Bolzano, Italy.
- Ontologising Bioscience: a niche. Presentation given on 1-7-2004 at the Laboratory of Applied Ontology, Trento, Italy.
- Development of ontologies for the sciences. Laboratory of Applied Ontology, Trento, Italy, d.d. 10-3-2004.


4. Organisational activities, reviewing etc

- Program Committee member of ESAS 2006, NETTAB 2007, ESAS 2007; ESAS 2008; Semantic Web for Health Care and Life Sciences Workshop 2008, KROW08
- Reviewing also for journals (IEEE TFS, J. AIIM, BMC Bioinformatics, Applied Ontology) conferences (ODBASE05, CBMS06, ODBASE06, ESWC07, ESWC08), and workshops (DL08), external reviewer REWERSE deliverable.
- Program Committee co-Chair of the KRDB PhD Workshop, 11 May 2007, KRDB Research Centre, Free University of Bozen-Bolzano.
- Coordinator KRDB Seminars. Oct. '07 - present.
- Organiser CS and IT with/for Biology, Seminar Series at the KRDB Research Centre, Free University of Bozen-Bolzano. Oct-Dec 2005. (co-oragnised with Enrico Franconi)
- Co-organiser KRDB Seminar Series 2006, KRDB Research Centre, Free University of Bozen-Bolzano. (main organiser Rosella Gennari)
- PhD students representative CS Faculty (Nov. '06 - Dec. '07); see also the FUB CS PhD students website.


5. Teaching

- Logic (course code 70014, BSc-level). Exercises and supplementary material.
- Semantic Web for the Life Sciences. Guest lecture d.d. 23-5-2007 as part of the course 'Semantic Web Technologies' (course code: 70175, MSc-level), Free University of Bozen-Bolzano, Italy.
- Introduction to part-whole relations: mereology, conceptual modelling and mathematical aspects. Tutorial given on 23-10-2006 at the KRDB Research Centre, Free University of Bozen-Bolzano, Italy.
- ORM introduction. Seminar given on 27-4-2004 at the Laboratory of Applied Ontology, Trento, and Free University Bolzano/Bozen, Italy.


Summer Schools attended

- EDBT Summer School 2007, 3-7 September 2007, Bolzano, Italy.
- ReasoningWeb 2006, 4-8 September 2006, Lisbon, Portugal.
- BIT PhD Summer School, 3-7 July 2006, Brixen-Bressanone, Italy.
- Ontological Spring II, 21-24 May 2006, Dagstuhl, Germany.
- Biology, Computation and Information, 11-16 September 2005, Dobbiaco, Italy.
- ICCL Summer School on Logic-based knowledge Representation, 2-15 July 2005, Dresden, Germany.
- Summer School & Workshop Semantic Interoperability and Data Mining in Biomedicine, 2-11 July 2004, Balatonfüred, Hungary. (with a grant from the Semantic Mining NoE)


 

Microbiology & Biochemistry
Overview of the theses carried out during my MSc degree2

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
Research projects carried out as part of the MA in Peace & Development Studies3

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.

Essays written during the first and second semester (academic year 02/03):
The blind leading the blind?
    A comparison of EU and US policy relations with the Middle East.
Master of Arts, What's in a Name?
    Discussing the question "what is scientific knowledge, as opposed to pseudo-scientific?"
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 degree1

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 technical report online:
Keet, C.M. (2003). Conceptual Modelling for Applied Bioscience: the Bacteriocin Database. CSPS/computational intelligence/0310001. article

More or less related to previous courses:
Genetic Algorithms - An overview
A Genetic Algorithm for DNA?
Communication: the last mile and some light-years
Software:
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.



Other research carried out in my spare time
(ok, attempts to satisfy my own curiosity, to some extend)

Prions
    What researchers think they know about prions (thought to be the main culprit of BSE et al), what they suspect about the physiology of prions and on aspects they don't really have a clue about. written a while ago.

The French paradox - Red Wine
    This page deals with the physiological and biochemical aspects of the benefits of red wine to maintain good health. Not everybody likes to hear it, but really, wine is not bad for you, not at all.

An overview of Genetic Algorithms
    One of my courses (of the BSc one) was about artificial intelligence, on which I tried to make a head start looking into what genetic algorithms are. By now, it is probably outdated.

Many more information about various IT topics
    It started off (whilst being employed by Compaq back in 1999) with describing the technology, and providing comparison tables, on High Availability and Clustering; but I've included information on file systems, NetWare and RAID usage later as well.

Decision making process in the European Union
    Extract from course material 'European Union and agricultural politics' on the structure of the decision making process, though it may not be up-to date anymore when the Nice Treaty is ratified by all its member states (by the end of 2002); see, for instance, also the references of the wikipedia entry on the EU.



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

________________________
1. BSc IT and Computing, 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

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

3. MA Peace and Development Studies, Department of Government & Society, University of Limerick, Ireland. www.ul.ie

4. PhD at Department of Computer Science, Knowledge Representation meets DataBases (KRDB) group, Free University of Bolzano-Bozen, Italy. www.unibz.it

For comments:
send an email to keet at inf dot unibz dot it.

This page was last updated on 28 April 2008