Christelle Vangenot

A conceptual view on trajectories

Analysis of trajectory data is the key to a growing number of applications aiming at global understanding and management of complex phenomena that involve moving objects (e.g. worldwide courier distribution, city traffic management, bird migration monitoring). Current DBMS support for such data is limited to the ability to store and query raw movement (i.e. the spatio-temporal position of an object). This paper explores how conceptual modeling could provide applications with direct support of trajectories (i.e. movement data that is structured into countable semantic units) as a first class concept. A specific concern is to allow enriching trajectories with semantic annotations allowing users to attach semantic data to specific parts of the trajectory. Building on a preliminary requirement analysis and an application example, the paper proposes two modeling approaches, one based on a design pattern, the other based on dedicated data types, and illustrates their differences in terms of implementation in an extended-relational context.

GIS Databases: From Multiscale to MultiRepresentation

Cartography is one of the major application areas using geographical databases. Whether it is for the business of producing paper maps for sale, or whether it is for displaying maps on a screen to visualize the result of a query, we need computer systems that know how to represent the same geographical area at different scales. The concept of multiscale database has become popular in the GIS domain as a way to enforce consistency between representations and reduce the global update load. Scaling, however, is just one of the facets that may lead to keeping several representations for the same real-world object. Viewpoint and classification are two major abstractions in the design process that also generate multiple representations. This paper investigates the generic issues and solutions to achieve flexible support of multiple representation in a GIS database.

Semantic mappings in description logics for spatio-temporal database schema integration

The interoperability problem arises in heterogeneous systems where different data sources coexist and there is a need for meaningful information sharing. One of the most representive realms of diversity of data representation is the spatio-temporal domain. Spatio-temporal data are most often described according to multiple and greatly diverse perceptions or viewpoints, using different terms and with heterogeneous levels of detail. Reconciling this heterogeneity to build a fully integrated database is known to be a complex and currently unresolved problem, and few formal approaches exist for the integration of spatio-temporal databases. The paper discusses the interoperation issue in the context of conceptual schema integration. Our proposal relies on two well-known formalisms: conceptual models and description logics. The MADS conceptual model with its multiple representation capabilities allows to fully describe semantics of the initial and integrated spatio-temporal schemas. Description logics are used to express the set of inter-schema mappings. Inference mechanisms of description logics allow us to check the compatibility of the semantic mappings and to propose different structural solutions for the integrated schema.

Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA‐NET methodological recommendations

HLA‐NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user‐friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1‐4) of the HLA‐NET network at the mid‐term of its activities. WG1 (Population definitions and sampling strategies for population genetics’ analyses) recommends avoiding outdated racial classifications and population names (e.g. ‘Caucasian’) and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. ‘pan‐European’). A standard ‘HLA‐NET POPULATION DATA QUESTIONNAIRE’ has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in ‘HLA‐NET GUIDELINES FOR REPORTING HLA TYPINGS’. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide‐binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable of dealing with ambiguous data, such as the ‘gene[rate]’ computer tools to estimate frequencies, test for Hardy–Weinberg equilibrium and selective neutrality on data containing any number and kind of ambiguities. WG4 (Ethical issues) proposes to adopt thorough general principles for any HLA population study to ensure that it conforms to (inter)national legislation or recommendations/guidelines. All HLA‐NET guidelines and tools are available through its website http://hla‐net.eu.

Modelling and Manipulating Multiple Representations of Spatial Data

One of the requirements which is poorly supported by spatial data models is a consistent management of different representations of the same spatial phenomena from different viewpoints or at different resolutions. This need is well known by users and designers. Modelling of applications, where users share the same database for different contexts and cartographic applications are examples of environments where such a need arises. This paper proposes a conceptual data model providing full support for multiple representations of the same real world data. The model addresses two complementary aspects: the integrated approach, that leads to the definition of customised database items, and the inter-relationship approach, where the representations are linked through inter-representation links. Both approaches use the stamping technique to differentiate among multiple representations of a given phenomenon and to access a particular representation. Finally, we focus on consequences of multiple coexisting representations on data manipulation. This proposal has been tested and validated with users, and implemented as a front-end to existing DBMS 1 .

Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques

The Mamu-A, Mamu-B, and Mamu-DRB genes of the rhesus macaque show several levels of complexity such as allelic heterogeneity (polymorphism), copy number variation, differential segregation of genes/alleles present on a haplotype (diversity) and transcription level differences. A combination of techniques was implemented to screen a large panel of pedigreed Indian rhesus macaques (1,384 individuals representing the offspring of 137 founding animals) for haplotype diversity in an efficient and inexpensive manner. This approach allowed the definition of 140 haplotypes that display a relatively low degree of region variation as reflected by the presence of only 17 A, 18 B and 22 DRB types, respectively, exhibiting a global linkage disequilibrium comparable to that in humans. This finding contrasts with the situation observed in rhesus macaques from other geographic origins and in cynomolgus monkeys from Indonesia. In these latter populations, nearly every haplotype appears to be characterised by a unique A, B and DRB region. In the Indian population, however, a reshuffling of existing segments generated “new” haplotypes. Since the recombination frequency within the core MHC of the Indian rhesus macaques is relatively low, the various haplotypes were most probably produced by recombination events that accumulated over a long evolutionary time span. This idea is in accord with the notion that Indian rhesus macaques experienced a severe reduction in population during the Pleistocene due to a bottleneck caused by geographic changes. Thus, recombination-like processes appear to be a way to expand a diminished genetic repertoire in an isolated and relatively small founder population.

16(th) IHIW: analysis of HLA population data, with updated results for 1996 to 2012 workshop data (AHPD project report).

We present here the results of the Analysis of HLA Population Data (AHPD) project of the 16th International HLA and Immunogenetics Workshop (16IHIW) held in Liverpool in May–June 2012. Thanks to the collaboration of 25 laboratories from 18 different countries, HLA genotypic data for 59 new population samples (either well‐defined populations or donor registry samples) were gathered and 55 were analysed statistically following HLA‐NET recommendations. The new data included, among others, large sets of well‐defined populations from north‐east Europe and West Asia, as well as many donor registry data from European countries. The Gene[rate] computer tools were combined to create a Gene[rate] computer pipeline to automatically (i) estimate allele frequencies by an expectation‐maximization algorithm accommodating ambiguities, (ii) estimate heterozygosity, (iii) test for Hardy–Weinberg equilibrium (HWE), (iv) test for selective neutrality, (v) generate frequency graphs and summary statistics for each sample at each locus and (vi) plot multidimensional scaling (MDS) analyses comparing the new samples with previous IHIW data. Intrapopulation analyses show that HWE is rarely rejected, while neutrality tests often indicate a significant excess of heterozygotes compared with neutral expectations. The comparison of the 16IHIW AHPD data with data collected during previous workshops (12th–15th) shows that geography is an excellent predictor of HLA genetic differentiations for HLA‐A, ‐B and ‐DRB1 loci but not for HLA‐DQ, whose patterns are probably more influenced by natural selection. In Europe, HLA genetic variation clearly follows a north to south‐east axis despite a low level of differentiation between European, North African and West Asian populations. Pacific populations are genetically close to Austronesian‐speaking South‐East Asian and Taiwanese populations, in agreement with current theories on the peopling of Oceania. Thanks to this project, HLA genetic variation is more clearly defined worldwide and better interpreted in relation to human peopling history and HLA molecular evolution.

MurMur: a research agenda on multiple representations

One of the most publicized goals of modern computer society is to provide flexible access to information for everybody, anywhere, anytime. To make data management systems successful in satisfying a users quest for information, an absolute requirement is the capability of tailoring the information to the peculiar needs of the targeted user. Unfortunately, this is a domain where current technology fails to support adequate functionality. Basically, existing approaches to such versatility rely on the idea that all possible views of a piece of information can be derived from a single ultimate representation. This may work in a centralized setting, but it is definitely unlikely to provide a sufficient framework in distributed, interoperable environments. This paper presents a research and development project that intends to explore the issues related to representation and management of multiple representations of the same reality. A specific focus of the project is spatio-temporal information and the support of multi-scale geographic databases, where objects are represented at many different resolution levels.

Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

BackgroundDietary changes associated to shifts in subsistence strategies during human evolution may have induced new selective pressures on phenotypes, as currently held for lactase persistence. Similar hypotheses exist for arylamine N-acetyltransferase 2 (NAT2) mediated acetylation capacity, a well-known pharmacogenetic trait with wide inter-individual variation explained by polymorphisms in the NAT2 gene. The environmental causative factor (if any) driving its evolution is as yet unknown, but significant differences in prevalence of acetylation phenotypes are found between hunter-gatherer and food-producing populations, both in sub-Saharan Africa and worldwide, and between agriculturalists and pastoralists in Central Asia. These two subsistence strategies also prevail among sympatric populations of the African Sahel, but knowledge on NAT2 variation among African pastoral nomads was up to now very scarce. Here we addressed the hypothesis of different selective pressures associated to the agriculturalist or pastoralist lifestyles having acted on the evolution of NAT2 by sequencing the gene in 287 individuals from five pastoralist and one agriculturalist Sahelian populations.ResultsWe show that the significant NAT2 genetic structure of African populations is mainly due to frequency differences of three major haplotypes, two of which are categorized as decreased function alleles (NAT2*5B and NAT2*6A), particularly common in populations living in arid environments, and one fast allele (NAT2*12A), more frequently detected in populations living in tropical humid environments. This genetic structure does associate more strongly with a classification of populations according to ecoregions than to subsistence strategies, mainly because most Sahelian and East African populations display little to no genetic differentiation between them, although both regions hold nomadic or semi-nomadic pastoralist and sedentary agriculturalist communities. Furthermore, we found significantly higher predicted proportions of slow acetylators in pastoralists than in agriculturalists, but also among food-producing populations living in the Sahelian and dry savanna zones than in those living in humid environments, irrespective of their mode of subsistence.ConclusionOur results suggest a possible independent influence of both the dietary habits associated with subsistence modes and the chemical environment associated with climatic zones and biomes on the evolution of NAT2 diversity in sub-Saharan African populations.

On Using Conceptual Modeling for Ontologies

Are database concepts and techniques suitable for ontology design and management? The question has been on the floor for some time already. It gets a new emphasis today, thanks to the focus on ontologies and ontology services due to the spread of web services as a new paradigm for information management. This paper analyzes some of the arguments that are relevant to the debate, in particular the question whether conceptual data models would adequately support the design and use of ontologies. It concludes suggesting a hybrid approach, combining databases and logic-based services.