Nizar Messai

Querying a bioinformatic data sources registry with concept lattices

Bioinformatic data sources available on the web are multiple and heterogenous. The lack of documentation and the difficulty of interaction with these data banks require users competence in both informatics and biological fields for an optimal use of sources contents that remain rather under exploited. In this paper we present an approach based on formal concept analysis to classify and search relevant bioinformatic data sources for a given user query. It consists in building the concept lattice from the binary relation between bioinformatic data sources and their associated metadata. The concept built from a given user query is then merged into the concept lattice. The result is given by the extraction of the set of sources belonging to the extents of the query concept subsumers in the resulting concept lattice. The sources ranking is given by the concept specificity order in the concept lattice. An improvement of the approach consists in automatic refinement of the query thanks to domain ontologies. Two forms of refinement are possible by generalisation and by specialisation.

Using Domain Knowledge to Guide Lattice-based Complex Data Exploration

In this paper we propose an approach which combines semantic resources and formal concept analysis to deal with heterogenous data sets represented as many-valued (MV) formal contexts. We define a new Galois connection considering the semantic relationships between attribute values in a MV context. The semantic relationships are used to calculate the similarity between attribute values to decide whether an attribute is shared by a set of objects or not. Then, based on this Galois connection, we define MV formal concepts and MV concept lattices. Depending on a chosen similarity threshold, MV concept lattices may have different levels of precision. We take advantage of this feature to browse the content of a biological databases repository in a dynamic and progressive way. The browsing process combines the navigation in several MV concept lattices and allows zooming operations by switching between MV concept lattices with higher or lower precision.

BioRegistry: a structured metadata repository for bioinformatic databases

One of the major challenges in the post genomic era consists in exploiting the vast amounts of biological data stored in the numerous heterogeneous biological databases distributed worldwide. Most research projects in bioinformatics start with data retrieval from selected sources. However, identifying appropriate data sources is not trivial and requires the representation of the knowledge about data sources. We present here the BioRegistry project which aims at providing means to represent and exploit knowledge associated with biological databases. As a first step, a repository structure has been designed to organise metadata associated with databases consisting of five metadata categories: database identification, topics covered, quality information, access/availability, and tracking of the metadata. The BioRegistry model and its relationships with the DCMI (Dublin Core Metadata Initiative) are described. Prototypes with various functionalities to feed, maintain and exploit the repository are presented.

Backing composite web services using formal concept analysis

A Web service is a software functionality accessible through the network. Web services are intended to be composed into coarser-grained applications. Achieving a required composite functionality requires the discovery of a collection of Web services out of the enormous service space. Each service must be examined to verify its provided functionality, making the selection task neither efficient nor practical. Moreover, when a service in a composition becomes unavailable, the whole composition may become functionally broken. Therefore, an equivalent service must be retrieved to replace the broken one, thus spending more time and effort. In this paper, we propose an approach for Web service classification based on FCA, using their operations estimated similarities. The generated lattices make the identification of candidate substitutes to a given service straightforward. Thus, service compositions can be achieved more easily and with backup services, so as to easily recover the functionality of a broken service.

Extending Attribute Dependencies for Lattice-Based Querying and Navigation

In this paper we study dependencies of attributes in the context of Formal Concept Analysis. These dependencies allow to define a hierarchy of attributes reflecting the importance or interest in attributes. A hierarchy of attributes is a set of attributes partially ordered with respect to their importance. It represents domain knowledge used to improve lattice-based querying and navigation. Actually, in lattice-based querying, hierarchies of attributes are used to define complex queries containing attributes with different levels of importance: more important attributes define the focus of the retrieval while less important ones define secondary information whose presence is desirable in the answers. Furthermore, the relation between attributes in a complex query represents implicit or explicit knowledge units that must be considered while computing answers. Similarly, in lattice-based navigation, the choice of moving to a particular concept rather than to another is influenced by the higher importance of the attributes in the concept intent. Hence, the design and use of a hierarchy of attributes leads to a navigation guided by domain knowledge.

BioRegistry: automatic extraction of metadata for biological database retrieval and discovery

Biological databases are blooming today at an increasing rate to deal with the huge amount of data produced by genomic and post-genomic research. The need for a well-maintained searchable directory is therefore an important issue for a good exploitation of these databases. The BioRegistry repository is automatically generated from a publicly available list of biological databases (The Molecular Biology Database Collection published in Nucleic Acids Research) and aims at associating content metadata with each database in view of database retrieval and/or discovery. Such content metadata are either simple keywords or terms belonging to a medical thesaurus. Querying modalities including a search by semantic similarity are described. The use of conceptual clustering methods is proposed to build a semantic classification of biological databases enabling browsing through the BioRegistry repository and discovering previously unknown databases.

Two complementary classification methods for designing a concept lattice from interval data

This paper holds on the application of two classification methods based on formal concept analysis (FCA) to interval data. The first method uses a similarity between objects while the second considers so-called pattern structures. We deeply detail these methods in order to show their close links. This parallel study helps understanding complex data with concept lattices. We explain how the second method obtains same results and how to handle missing values. Most importantly, this is achieved in full compliance with the FCA-framework, and thus benefits from existing and efficient tools such as algorithms. Finally, an experiment on real-world data in agronomy has been carried out for decision helping in agricultural practices.

SCoME: A Web Services Composition Modeling and Engineering Framework

To exploit the true potential of Web services, it is critical to develop technologies and tools for composing new services from existing ones. Indeed, to reduce development time and integration efforts, this process of service composition requires an effective development environment to facilitate quick and simple composition of Web services, and remains a key challenge to realize the true potential of Web services. While numerous composition approaches have been developed, very little has been done towards providing an Integrated Development Environment to ease the process of composition. In this context, this paper introduces a new incremental approach to service composition engineering and considers the composition global life-cycle, i.e. specifying, composing, verifying, deploying, monitoring, and analyzing to achieve a full governance of the composition.

Using formal concept analysis to discover patterns of non-compliance with clinical practice guidelines: a case study in the management of breast cancer

Clinical decision support systems (CDSSs) may be appropriate tools to promote the use of clinical practice guidelines (CPGs). However, compliance with CPGs is a multifactorial process that relies on the CPGs to be implemented, the physician(s) in charge of the decision, and the patient to manage. Formal concept analysis (FCA) allows to derive implicit relationships from a set of objects described by their attributes, based on the principle of attribute sharing between objects.We used FCA to elicit patient-based formal concepts related to the non-conformity of multidisciplinary staff meetings (MSMs) decisions with CPGs in the domain of breast cancer management. We developed a strategy for selecting attributes and make lattices manageable. We found that when not using the guideline-based CDSS OncoDoc2, patients with bad prognostic factors were associated with non-compliant decisions. This was corrected when the system was used during MSMs.

Diamond - A Cube Model Proposal based on a Centric Architecture Approach to Enhance Liquid Software Model Approaches.

The adoption of multiple connected devices in our lives is a reality which the available technology is not able to deal with. The concept of Liquid Software emerged in the end of the 90s, however, its full potential of a unified interface which can drift between different connected devices and bring with its behavior and complexities is still not fully applied. Thus, enhancements of current Web application architecture, in other words, a new approach able to deal with our technology requirements is required. In this context, we propose a centric-basic architecture to deal with Liquid Software principles and constraints. The CUBE, once built, should be able to deal with all these requirements, making use of best practices from different technologies.