OBML - Ontologies in Biomedicine and Life Sciences

The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2(nd) in a series of meetings organized by the Working Group “Ontologies in Biomedicine and Life Sciences” of the German Society of Computer Science (GI) and the German Society of Medical Informatics, Biometry and Epidemiology (GMDS). Integrating, processing and applying the rapidly expanding information generated in the life sciences — from public health to clinical care and molecular biology — is one of the most challenging problems that research in these fields is facing today. As the amounts of experimental data, clinical information and scientific knowledge increase, there is a growing need to promote interoperability of these resources, support formal analyses, and to pre-process knowledge for further use in problem solving and hypothesis formulation. The OBML workshop series pursues the aim of gathering scientists who research topics related to life science ontologies, to exchange ideas, discuss new results and establish relationships. The OBML group promotes the collaboration between ontologists, computer scientists, bio-informaticians and applied logicians, as well as the cooperation with physicians, biologists, biochemists and biometricians, and supports the establishment of this new discipline in research and teaching. Research topics of OBML 2010 included medical informatics, Semantic Web applications, formal ontology, bio-ontologies, knowledge representation as well as the wide range of applications of biomedical ontologies to science and medicine. A total of 14 papers were presented, and from these we selected four manuscripts for inclusion in this special issue. An interdisciplinary audience from all areas related to biomedical ontologies attended OBML 2010. In the future, OBML will continue as an annual meeting that aims to bridge the gap between theory and application of ontologies in the life sciences. The next event emphasizes the special topic of the ontology of phenotypes, in Berlin, Germany on October 6-7, 2011

On Classifying Material Entities in Basic Formal Ontology

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category objec

CELDA - an ontology for the comprehensive representation of cells in complex systems

BACKGROUND: The need for detailed description and modeling of cells drives the continuous generation of large and diverse datasets. Unfortunately, there exists no systematic and comprehensive way to organize these datasets and their information. CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms. RESULTS: CELDA is a structure that can help to categorize cell types based on species, anatomical localization, subcellular structures, developmental stages and origin. It targets cells in vitro as well as in vivo. Instead of developing a novel ontology from scratch, we carefully designed CELDA in such a way that existing ontologies were integrated as much as possible, and only minimal extensions were performed to cover those classes and areas not present in any existing model. Currently, ten existing ontologies and models are linked to CELDA through the top-level ontology BioTop. Together with 15.439 newly created classes, CELDA contains more than 196.000 classes and 233.670 relationship axioms. CELDA is primarily used as a representational framework for modeling, analyzing and comparing cells within and across species in CellFinder, a web based data repository on cells (http://cellfinder.org). CONCLUSIONS: CELDA can semantically link diverse types of information about cell types. It has been integrated within the research platform CellFinder, where it exemplarily relates cell types from liver and kidney during development on the one hand and anatomical locations in humans on the other, integrating information on all spatial and temporal stages. CELDA is available from the CellFinder website: http://cellfinder.org/about/ontology

Pluralities, Collectives, and Composites

Forests, cars and orchestras are very different ontological entities, and yet very similar in some aspects. The relationships they have with the elements they are composed of is often assumed to be reducible to standard ontological relations, like parthood and constitution, but how this could be done is still debated. This paper sheds light on the issue starting from a linguistic and philosophical analysis aimed at understanding notions like plurality, collective and composite, and propos- ing a formal approach to characterise them. We conclude the presentation with a discussion and analysis of social groups within this framework

Disinfectants in food

Cílem bakalářské práce je popsat chemickou desinfekci používanou v potravinářství za účelem eliminování mikrobiální kontaminace potravin a potravinářských surovin a popsání možných alimentárních nákaz z potravin při nesprávném dodržení hygienické praxe. Experimentální část bakalářské práce obsahuje popis použité metody určené ke stanovení desinfekčního účinku a její následné praktické provedení pro dva typy desinfekčních přípravků s odlišným charakterem aktivní složky. Na základě získaných výsledků bylo provedeno jejich zhodnocení a vzájemné porovnání.The aim the of bachelor thesis is description of chemical disinfection, which is used in food industry to eliminate microbial contaminations of food, food intermediates and foodborne diseases, which can occur if hygienic regulations are not observed correctly. The experimental part of the bachelor thesis characterizes the method which was used to specify the disinfecting effect. This method was used to determine two types of disinfectants which contain two different active ingredients. Based on the results, two disinfectants were evaluated and compared.