Guy De Tré

Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides

Quorum-sensing (QS) peptides are biologically attractive molecules, with a wide diversity of structures and prone to modifications altering or presenting new functionalities. Therefore, the Quorumpeps database (http://quorumpeps.ugent.be) is developed to give a structured overview of the QS oligopeptides, describing their microbial origin (species), functionality (method, result and receptor), peptide links and chemical characteristics (3D-structure-derived physicochemical properties). The chemical diversity observed within this group of QS signalling molecules can be used to develop new synthetic bio-active compounds.

Alkamid database: chemistry, occurrence and functionality of plant N-alkylamides

ETHNOPHARMACOLOGICAL RELEVANCE N-Alkylamides (NAAs) are a promising group of bioactive compounds, which are anticipated to act as important lead compounds for plant protection and biocidal products, functional food, cosmeceuticals and drugs in the next decennia. These molecules, currently found in more than 25 plant families and with a wide structural diversity, exert a variety of biological-pharmacological effects and are of high ethnopharmacological importance. However, information is scattered in literature, with different, often unstandardized, pharmacological methodologies being used. Therefore, a comprehensive NAA database (acronym: Alkamid) was constructed to collect the available structural and functional NAA data, linked to their occurrence in plants (family, tribe, species, genus). MATERIALS AND METHODS For loading information in the database, literature data was gathered over the period 1950-2010, by using several search engines. In order to represent the collected information about NAAs, the plants in which they occur and the functionalities for which they have been examined, a relational database is constructed and implemented on a MySQL back-end. RESULTS The database is supported by describing the NAA plant-, functional- and chemical-space. The chemical space includes a NAA classification, according to their fatty acid and amine structures. CONCLUSIONS The Alkamid database (publicly available on the website http://alkamid.ugent.be/) is not only a central information point, but can also function as a useful tool to prioritize the NAA choice in the evaluation of their functionality, to perform data mining leading to quantitative structure-property relationships (QSPRs), functionality comparisons, clustering, plant biochemistry and taxonomic evaluations.

Brainpeps: the blood–brain barrier peptide database

Peptides are able to cross the blood–brain barrier (BBB) through various mechanisms, opening new diagnostic and therapeutic avenues. However, their BBB transport data are scattered in the literature over different disciplines, using different methodologies reporting different influx or efflux aspects. Therefore, a comprehensive BBB peptide database (Brainpeps) was constructed to collect the BBB data available in the literature. Brainpeps currently contains BBB transport information with positive as well as negative results. The database is a useful tool to prioritize peptide choices for evaluating different BBB responses or studying quantitative structure–property (BBB behaviour) relationships of peptides. Because a multitude of methods have been used to assess the BBB behaviour of compounds, we classified these methods and their responses. Moreover, the relationships between the different BBB transport methods have been clarified and visualized.

Handling Bipolarity in Elementary Queries to Possibilistic Databases

Making data-querying and representation easier and more human consistent is an important research topic. In this context, fuzzy logic with its capability to model linguistic expressions provides an interesting framework, which has been adopted by many researchers. However, there are still some aspects that have not been adequately covered. In particular, it becomes widely advocated that while communicating, humans give both positive and negative information to state what they desire and what they reject. Because positive and negative statements do not necessarily mirror each other, this results in so-called heterogeneous bipolar information. Traditional fuzzy approaches do not adequately support the handling of heterogeneous bipolar information in information systems. Therefore, there is a need for more advanced techniques. In this paper, how bipolarity can be dealt with in the formulation and evaluation of selection conditions in fuzzy querying within a possibilistic, relational database framework is presented. Three novel query-evaluation techniques based on interval-valued fuzzy sets, Atanassov fuzzy sets, and twofold fuzzy sets are presented and compared with each other. Possibility theory is used to deal with uncertainty. Special attention is paid to the description of the semantics, use, benefits, and drawbacks of each formalism.

Extended possibilistic truth values

A problem with the modeling of uncertainty within the context of an information or knowledge‐based system is the handling of missing information. In this article, extended possibilistic truth values are introduced as a formal means to cope with this problem. The notion of an extended possibilistic truth value has been obtained from the assumption that the truth value of a proposition can be undefined. This is the case if the proposition cannot be evaluated due to the non‐applicability of (some of) its elements. By definition, an extended truth value can either be true, false, or undefined. Using these three values, a ternary strong Kleene propositional logic has been built. An uncertainty model for this logic is proposed, in order to model (linguistic) uncertainty concerning the extended truth value of a proposition. This uncertainty model is based on possibility measures, and leads to the concept of an extended possibilistic truth value. Finally, the algebraic properties of extended possibilistic truth values are presented.

Bipolar query satisfaction using satisfaction and dissatisfaction degrees: bipolar satisfaction degrees

Since many years, research on flexible querying of regular databases aims at making database systems better accessible, and this by allowing queries to be formulated in a more human consistent manner. In general, this is done by allowing the user to express preferences, which are not necessarily strict, but can be approximately specified. As a result, a satisfaction degree can be calculated for each record in the database, expressing the degree to which the particular record satisfies the users preferences. In addition to this, bipolar querying adds the notion of both positive and negative preferences in handling flexible queries. The reason for this is that it is sometimes more feasible for a user to express what is undesirable than to express what is desirable. Moreover, satisfactory and unsatisfactory cases do not necessarily have to be each others reverse, which is called heterogeneous bipolarity. To deal with this heterogeneous bipolarity, this paper introduces a new bipolar query satisfaction modeling framework, where, besides a satisfaction degree, also an independent dissatisfaction degree is used.

Level-2 fuzzy sets and their usefulness in object-oriented database modelling

Abstract In the real world information is, for the most part, available in an imperfect form. Managing this kind of information with classical database systems brings a disadvantageous loss of data semantics along. Therefore, advanced database modelling techniques are necessary. This paper deals with a uniform and advantageous representation of both perfect and imperfect ‘real world’ information in object-oriented databases. An object-oriented data(base) modelling technique, based on the concept ‘level-2 fuzzy set’, is presented. Hereby, the focus is on the semantic definitions of the structural, as well as on the behavioural aspects of the data. It is shown how level-2 fuzzy sets can be used to generalise the concept ‘type’. Since types are generally recognised to be the basic building blocks of object-oriented database models, generalised types can be used as basic notions of fuzzy object-oriented database models. Finally, it is illustrated and discussed how the ODMG data model can be generalised to handle ‘real world’ data in a more advantageous way.

Multicriteria methods and logic aggregation in suitability maps

In this paper, we identify and describe fundamental logic properties of multicriteria methods for land‐use suitability analysis and the design of suitability maps. The existing multicriteria methods can be evaluated from the standpoint of their ability to support the necessary logic properties that affect the expressive power of evaluation methods. The paper investigates and compares simple additive scoring, multiattribute value technique, multiattribute utility technique, analytic hierarchy process, ordered weighted average, outranking methods, and logic scoring of preference (LSP). We introduce canonical forms of logic aggregation in suitability maps and show how to use canonical aggregation structures to design LSP suitability maps that evaluate distributions of points of interests (POIs) in urban areas.

Viewpoints on emergent semantics

We introduce a novel view on how to deal with the problems of semantic interoperability in distributed systems. This view is based on the concept of emergent semantics, which sees both the representation of semantics and the discovery of the proper interpretation of symbols as the result of a self-organizing process performed by distributed agents exchanging symbols and having utilities dependent on the proper interpretation of the symbols. This is a complex systems perspective on the problem of dealing with semantics. We highlight some of the distinctive features of our vision and point out preliminary examples of its application.

Field Based Methods for the Modeling of Fuzzy Spatial Data

In this chapter, two different field based techniques for the modeling of fuzzy information spread over a geographic region, are presented and are compared regarding their applicability. The first one is a vector-mode approach, using triangulated irregular networks (or TINs), the second one is a raster (bitmapmode) approach. Appropriate aggregation operators are defined in both approaches and illustrated by means of examples. The feasibility of the implementation of the operators (by approximation whenever required) is studied. Attention has been paid to the applicability, advantages and disadvantages of both methods in flexible querying.