Étude des anomalies du développement humain# un modèle d’analyse phénotypique

Depuis le début des années 90, le projet génome humain a permis l’émergence de nombreuses techniques globalisantes porteuses du suffixe –omique : génomique, transcriptomique, protéomique, épigénomique, etc.… L’étude globale de l’ensemble des phénotypes humains (« phénome ») est à l’origine de nouvelles technologies constituant la « phénomique ». L’approche phénomique permet de déterminer des liens entre des combinaisons de traits phénomiques. Nous voulons appliquer cette approche à l’étude des malformations humaines en particulier leurs combinaisons, ne formant des syndromes, des associations ou des séquences bien caractérisés que dans un petit nombre de cas. Afin d’évaluer la faisabilité de cette approche, pour une étude pilote nous avons décidé d’établir une base de données pour la description phénotypique des anomalies foetales. Nous avons effectué ces étapes : o Réalisation d’une étude rétrospective d’une série d’autopsies de foetus au CHU Sainte- Justine (Montréal, QC, Canada) entre 2001-2006 o Élaboration de trois thésaurus et d’une ontologie des anomalies développementales humaines o Construction une base de données en langage MySQL Cette base de données multicentrique accessible sur (http://www.malformations.org), nous permet de rechercher très facilement les données phénotypiques des 543 cas observés porteurs d’une anomalie donnée, de leur donner une description statistique et de générer les différents types d’hypothèses. Elle nous a également permis de sélectionner 153 cas de foetus malformés qui font l’objet d’une étude de micropuce d’hybridation génomique comparative (aCGH) à la recherche d’une anomalie génomique.

A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation

The Neotropical evaniid genus Evaniscus Szepligeti currently includes six species. Two new species are described, Evaniscus lansdownei Mullins, sp. n. from Colombia and Brazil and E. rafaeli Kawada, sp. n. from Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under E. rufithorax Enderlein. An identification key to species of Evaniscus is provided. Thirty-five parsimony informative morphological characters are analyzed for six ingroup and four outgroup taxa. A topology resulting in a monophyletic Evaniscus is presented with E. tibialis and E. rafaeli as sister to the remaining Evaniscus species. The Hymenoptera Anatomy Ontology and other relevant biomedical ontologies are employed to create semantic phenotype statements in Entity-Quality (EQ) format for species descriptions. This approach is an early effort to formalize species descriptions and to make descriptive data available to other domains.

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

BACKGROUND: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. DESCRIPTION: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. CONCLUSIONS: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.

A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of similar to 240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resources are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, "preferred terms", and "structural equivalency". We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the "URI table") by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the "Analyzer") to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.

Enhancing the Expressiveness of the Bunge-Wand-Weber Ontology

In practical terms, conceptual modeling is at the core of systems analysis and design. The plurality of modeling methods available has however been regarded as detrimental, and as a strong indication that a common view or theoretical grounding of modeling is wanting. This theoretical foundation must universally address all potential matters to be represented in a model, which consequently suggested ontology as the point of departure for theory development. The Bunge–Wand–Weber (BWW) ontology has become a widely accepted modeling theory. Its application has simultaneously led to the recognition that, although suitable as a meta-model, the BWW ontology needs to be enhanced regarding its expressiveness in empirical domains. In this paper, a first step in this direction has been made by revisiting BUNGE’s ontology, and by proposing the integration of a “hierarchy of systems” in the BWW ontology for accommodating domain specific conceptualizations.

Using ontology for the representational analysis of process modelling techniques

Selecting an appropriate business process modelling technique forms an important task within the methodological challenges of a business process management project. While a plethora of available techniques has been developed over the last decades, there is an obvious shortage of well-accepted reference frameworks that can be used to evaluate and compare the capabilities of the different techniques. Academic progress has been made at least in the area of representational analyses that use ontology as a benchmark for such evaluations. This paper reflects on the comprehensive experiences with the application of a model based on the Bunge ontology in this context. A brief overview of the underlying research model characterizes the different steps in such a research project. A comparative summary of previous representational analyses of process modelling techniques over time gives insights into the relative maturity of selected process modelling techniques. Based on these experiences suggestions are made as to where ontology-based representational analyses could be further developed and what limitations are inherent to such analyses.

Building an ontology and process architecture for engineering asset management

Historically, asset management focused primarily on the reliability and maintainability of assets; organisations have since then accepted the notion that a much larger array of processes govern the life and use of an asset. With this, asset management’s new paradigm seeks a holistic, multi-disciplinary approach to the management of physical assets. A growing number of organisations now seek to develop integrated asset management frameworks and bodies of knowledge. This research seeks to complement existing outputs of the mentioned organisations through the development of an asset management ontology. Ontologies define a common vocabulary for both researchers and practitioners who need to share information in a chosen domain. A by-product of ontology development is the realisation of a process architecture, of which there is also no evidence in published literature. To develop the ontology and subsequent asset management process architecture, a standard knowledge-engineering methodology is followed. This involves text analysis, definition and classification of terms and visualisation through an appropriate tool (in this case, the Protégé application was used). The result of this research is the first attempt at developing an asset management ontology and process architecture.