A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database

The CEREALAB database aims to store genotypic and phenotypic data obtained by the CEREALAB project and to integrate them with already existing data sources in order to create a tool for plant breeders and geneticists. The database can help them in unravelling the genetics of economically important phenotypic traits; in identifying and choosing molecular markers associated to key traits; and in choosing the desired parentals for breeding programs. The database is divided into three sub-schemas corresponding to the species of interest: wheat, barley and rice; each sub-schema is then divided into two sub-ontologies, regarding genotypic and phenotypic data, respectively

How to quickly detect the overlap and the consistency between LADM with LandInfra and LandXML : application of schema matching techniques.

In this paper, we explore the schema matching techniques to compare the content of three geospatial standards which are LADM, LandInfra (InfraGML) and LandXML. Those standards all refer to the concept of “land” and we will try to quantify the similarity of them based on syntax and semantic comparison of the class names exposed in their respective schema. Consequently, we will demonstrate the applicability, the accuracy and the usefulness (rapidity and automation) of schema matching techniques for comparing the content of standards. The comparison is performed with XSD (XML Schema Definition) files that describe the schema in English. The results show that syntactic match rate between LADM-LandInfra (54%) is higher than LADM-LandXML (10%). In adding the semantic information extracted from Wordnet, the match rate between LADM-LandInfra goes to 84% and 59% for LADMLandXML. In comparing our matching results with two independent sources of information that already and manually compared these three standards, we obtained distinctive results. The correctness of LADM-LandInfra is 60%, while the correctness of LADM-LandXML is only 20%. The applicability of schema matching is positively demonstrated while the usefulness and the accuracy still need further improvements in order to make any statement.Dans ce papier, nous explorons les techniques d’appariement de schémas pour comparer le contenu de trois standards géospatiaux soit LADM, LandInfra (InfraGML) and LandXML. Ces trois standards réfèrent au concept de « land » et nous allons tenter de quantifier leur similitude en tenant compte de la syntaxe et de la sémantique des noms de classe contenu dans leur schéma respectif. Nous allons ainsi démontrer l’applicabilité, l’exactitude et la facilité (rapidité et automation) des techniques d’appariement de schémas. La comparaison est effectuée à partir des fichiers XSD (XML Schema Definition), qui présentent la modélisation en anglais des standards. Les résultats montrent que, lorsqu’uniquement la syntaxe est prise en compte, le taux d’appariement de LADM-LandInfra (54%) est plus élevé que celui de LADM-LandXML (10%). En tenant compte des relations sémantiques possibles extraites de Wordnet, le taux d’appariement de LADM-LandInfra grimpe à 84%, alors qu’il revient à 59% pour LADMLandXML. En comparant nos résultats avec des sources d’information externes qui ont déjà comparées manuellement ces trois standards, nous obtenons un taux d’exactitude de 60% pour LADM-LandInfra et de 20% pour LADM-LandXML. L’applicabilité des techniques d’appariement de schémas est démontrée par nos expérimentations tandis que l’exactitude et la facilité montrent des résultats divergeant qui nécessiteront d’autres tests et analyses

Development and Application of Comparative Gene Co-expression Network Methods in Brachypodium distachyon

Gene discovery and characterization is a long and labor-intensive process. Gene co-expression network analysis is a long-standing powerful approach that can strongly enrich signals within gene expression datasets to predict genes critical for many cellular functions. Leveraging this approach with a large number of transcriptome datasets does not yield a concomitant increase in network granularity. Independently generated datasets that describe gene expression in various tissues, developmental stages, times of day, and environments can carry conflicting co-expression signals. The gene expression responses of the model C3 grass Brachypodium distachyon to abiotic stress is characterized by a co-expression-based analysis, identifying 22 modules of genes, annotated with putative DNA regulatory elements and functional terms. A great deal of co-expression elasticity is found among the genes characterized therein. An algorithm, dGCNA, designed to determine statistically significant changes in gene-gene co-expression relationships is presented. The algorithm is demonstrated on the very well-characterized circadian system of Arabidopsis thaliana, and identifies potential strong signals of molecular interactions between a specific transcription factor and putative target gene loci. Lastly, this network comparison approach based on edge-wise similarities is demonstrated on many pairwise comparisons of independent microarray datasets, to demonstrate the utility of fine-grained network comparison, rather than amassing as large a dataset as possible. This approach identifies a set of 182 gene loci which are differentially expressed under drought stress, change their co-expression strongly under loss of thermocycles or high-salinity stress, and are associated with cell-cycle and DNA replication functions. This set of genes provides excellent candidates for the generation of rhythmic growth under thermocycles in Brachypodium distachyon

A framework for analyzing changes in health care lexicons and nomenclatures

Ontologies play a crucial role in current web-based biomedical applications for capturing contextual knowledge in the domain of life sciences. Many of the so-called bio-ontologies and controlled vocabularies are known to be seriously defective from both terminological and ontological perspectives, and do not sufficiently comply with the standards to be considered formai ontologies. Therefore, they are continuously evolving in order to fix the problems and provide valid knowledge. Moreover, many problems in ontology evolution often originate from incomplete knowledge about the given domain. As our knowledge improves, the related definitions in the ontologies will be altered. This problem is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations, and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies, and interactions with other existing ontologies have been widely neglected. In this research, alter revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, RLR (Represent, Legitimate, and Reproduce), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general, and aids in tracking and representing the changes, particularly through the use of category theory. Category theory has been used as a mathematical vehicle for modeling changes in ontologies and representing agents' interactions, independent of any specific choice of ontology language or particular implementation. We have also employed rule-based hierarchical graph transformation techniques to propose a more specific semantics for analyzing ontological changes and transformations between different versions of an ontology, as well as tracking the effects of a change in different levels of abstractions. Thus, the RLR framework enables one to manage changes in ontologies, not as standalone artifacts in isolation, but in contact with other ontologies in an openly distributed semantic web environment. The emphasis upon the generality and abstractness makes RLR more feasible in the multi-disciplinary domain of biomedical Ontology change management

A knowledge-based system for automated discovery of ecological interactions in flower-visiting data.

Doctor of Philosophy in Mathematics, Statistics and Computer Science. University of KwaZulu-Natal, Durban 2017Studies on the community ecology of flower-visiting insects, which can be inferred to pollinate flowers, are important in agriculture and nature conservation. Many scientific observations of flower-visiting insects are associated with digitized records of insect specimens preserved in natural history collections. Specimen annotations include heterogeneous and incomplete, in situ field documentation of ecologically significant relationships between individual organisms (i.e. insects and plants), which are nevertheless potentially valuable. A wealth of unrepresented biodiversity and ecological knowledge can be unlocked from such detailed data by augmenting the data with expert knowledge encoded in knowledge models. An analysis of the knowledge representation requirements of flower-visiting community ecologists is presented, as well as an implementation and evaluation of a prototype knowledge-based system for automated semantic enrichment, semantic mediation and interpretation of flower-visiting data. A novel component of the system is a semantic architecture which incorporates knowledge models validated by experts. The system combines ontologies and a Bayesian network to enrich, integrate and interpret flower- visiting data, specifically to discover ecological interactions in the data. The system’s effectiveness, to acquire and represent expert knowledge and simulate the inferencing ability of expert flower-visiting ecologists, is evaluated and discussed. The knowledge-based system will allow a novice ecologist to use standardised semantics to construct interaction networks automatically and objectively. This could be useful, inter alia, when comparing interaction networks for different periods of time at the same place or different places at the same time. While the system architecture encompasses three levels of biological organization, data provenance can be traced back to occurrences of individual organisms preserved as evidence in natural history collections. The potential impact of the semantic architecture could be significant in the field of biodiversity and ecosystem informatics because ecological interactions are important in applied ecological studies, e.g. in freshwater biomonitoring or animal migration

Plant Genetics and Molecular Biology

This book reviews the latest advances in multiple fields of plant biotechnology and the opportunities that plant genetics, genomics and molecular biology have offered for agriculture improvement. Advanced technologies can dramatically enhance our capacity in understanding the molecular basis of traits and utilizing the available resources for accelerated development of high yielding, nutritious, input-use efficient and climate-smart crop varieties. In this book, readers will discover the significant advances in plant genetics, structural and functional genomics, trait and gene discovery, transcriptomics, proteomics, metabolomics, epigenomics, nanotechnology and analytical & decision support tools in breeding. This book appeals to researchers, academics and other stakeholders of global agriculture

27th Fungal Genetics Conference

Program and abstracts from the 27th Fungal Genetics Conference Asilomar, March 12-17, 2013

27th Fungal Genetics Conference

Program and abstracts from the 27th Fungal Genetics Conference Asilomar, March 12-17, 2013

Book of Abstracts of MICROBIOTEC09

Sítio da conferência: http://www.deb.uminho.pt/microbiotec09/This book contains the abstracts presented at the 3rd joint meeting of the Portuguese Society of Microbiology and The Portuguese Society of Biotechnology - MicroBiotec09, held in Vilamoura, Portugal, over 3 days, from the 28th to the 30th of November, 2009. MicroBiotec09 comes in the sequence of previous conferences organized by each society, since 1982, date of the I Encontro Nacional de Biotecnologia (Lisbon), till 2005, date of the first joint meeting - MICRO'05 + BIOTEC'05 (Póvoa de Varzim). Following this joint meeting, another - MICRO 07 + BIOTEC 07 + XXIII JPG took place in Lisbon (2007). MicroBiotec09 is a joint organization of “Sociedade Portuguesa de Biotecnologia”, “Sociedade Portuguesa de Microbiologia”, Institute for Biotechnology and Bioengineering (Universidade do Minho – Departamento de Engenharia Biológica) and Centro de Recursos Microbiológicos (Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia – Departamento de Ciências da Vida). MicroBiotec09 brings together both young and established researchers and end users to discuss recent developments in different areas of Biotechnology and Microbiology. The conference program has thus been divided in 8 major sessions: Microbial Physiology, Molecular Biology and Functional Genomics; Cell and Tissue Engineering, Biomaterials and Nanobiotechnologies; Clinical Microbiology and Epidemiology; Environmental Microbiology and Biotechnology; Health and Pharmaceutical Biotechnology; Cellular Microbiology and Pathogenesis; Industrial and Food Microbiology and Biotechnology; Bioinformatics, Comparative Genomics and Evolution. A special session to celebrate the 200th anniversary of Charles Darwin's birth and the 150th anniversary of the publication of his landmark work “On the Origin of Species by Means of Natural Selection” will also take place. A total of 295 abstracts are included in the book, consisting of 6 invited lecturers, 10 oral presentations and 44 short oral presentations given in 3 parallel sessions, along with 4 slots for viewing poster presentations. All abstracts have been reviewed and we are grateful to the members of scientific and organizing committees for their evaluations. It was an intensive task since 328 submitted abstracts were received. It has been an honor for us to contribute to setting up MicroBiotec09 during an intensive period of 6 months. We wish to thank the authors who have contributed to yield a high scientific standard to the program. We are thankful to the sponsors who have contributed decisively to this event. We also extend our gratefulness to all those who, through their dedicated efforts, have assisted us in this task. On behalf of the Scientific and Organizing Committees we wish you that together with an interesting reading, the scientific program and the social moments organized will be memorable for all.Fundação para a Ciência e a Tecnologia (FCT

PROTECTING OUR CROPS - APPROACHES FOR PLANT PARASITIC NEMATODE CONTROL

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