SEMEDA (Semantic Meta-Database) : ontology based semantic integration of biological databases

Köhler J. SEMEDA (Semantic Meta-Database) : ontology based semantic integration of biological databases. Bielefeld (Germany): Bielefeld University; 2003.The work presented in this thesis is outlined in the following. The state of the art in the relevant disciplines is introduced and reviewed in chapter 2. This includes on the one hand the current state of molecular biological databases, their heterogeneity and the integration of molecular biological databases. On the other hand the current usage of ontologies in general and with special regard to database integration is described. The principles of semantic database integration as introduced in this thesis are new and suitable to be used also in other database integration systems, which have to deal with a high number of semantically heterogeneous databases. Therefore in Chapter 3 the newly introduced principles for ontology based semantic database integration are presented independent of their implementation. Chapter 4 introduces the requirements for the implementation of a semantic database integration system (SEMEDA). Several general requirements for the integration of molecular biological systems from the scientific literature are discussed with regard to the feasibility of their implementation in general and in SEMEDA. In addition, the requirements specific to semantic database integration are introduced. In addition how the BioDataServer is used to overcome "technical" heterogeneity, so that SEMEDA only has to deal with semantic heterogeneity is analysed. In chapter 5, an appropriate data structure for storing ontologies, database metadata and the semantic definitions as described in Chapter 3 is developed. Subsequently, it is discussed how this data structure can be edited and queried. In Chapter 6, SEMEDAs software design, implementation and system architecture is given. Chapter 7 describes the use of SEMEDA and its interfaces. The user interface SEMEDA-edit is used to collaboratively edit ontologies and to semantically define databases using ontologies. SEMEDA-query is the query interface that provides uniform access to heterogeneous databases. In addition, a set of procedures exists which can be used by external applications. In order to use SEMEDA to semantically define databases, an appropriate ontology is needed. Although SEMEDA allows building ontologies from the scratch, due to the fact that generating ontologies is a labour intensive time-consuming task, it would be preferable to use an existing ontology. Therefore, in chapter 8 several ontologies were evaluated for their usability in SEMEDA. The intention was to find out if a suitable ontology can be found and imported or whether it is more appropriate to build a custom ontology for SEMEDA. It turned out that the existing ontologies were not well suited for semantic database integration. In chapter 9 general and SEMEDA specific ontology design principles are introduced which were then followed to build a custom ontology for database integration. The structure of this custom ontology and some issues concerning its use for semantic database integration are explained. In chapter 10, the practical use of SEMEDA is described by two examples. The first section of this chapter shows how SEMEDA supports the building of user schemata for the BioDataServer. The second section describes how the clone database of the RZPD Berlin (Deutsches Ressourcenzentrum für Genomforschung GmbH) is connected to SEMEDA and thus linked to the other databases. In the discussion (chapter 11) SEMEDA is compared to existing database integration systems, especially other ontology based integration systems. It is further discussed how principles for semantic database integration apply to other database integration systems and how they might be implemented there. A database mirror is proposed to improve the overall performance of SEMEDA and the BioDataServer

Bert Vallee—A 20th Century Adventure(r) in Zincology

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Quality control for terms and definitions in ontologies and taxonomies

BACKGROUND: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. RESULTS: We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. CONCLUSION: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation

PHI-base: a new database for pathogen host interactions

To utilize effectively the growing number of verified genes that mediate an organism's ability to cause disease and/or to trigger host responses, we have developed PHI-base. This is a web-accessible database that currently catalogs 405 experimentally verified pathogenicity, virulence and effector genes from 54 fungal and Oomycete pathogens, of which 176 are from animal pathogens, 227 from plant pathogens and 3 from pathogens with a fungal host. PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions. As such, PHI-base is a valuable resource for the discovery of candidate targets in medically and agronomically important fungal and Oomycete pathogens for intervention with synthetic chemistries and natural products. Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene/transcript disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies (Gene Ontology terms, Enzyme Commission Numbers and so on), and provide links to other external data sources (e.g. NCBI taxonomy and EMBL). We welcome new data for inclusion in PHI-base, which is freely accessed at

Relations in biomedical ontologies

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena

Does the antidiabetic drug metformin affect embryo development and the health of brown trout (Salmo trutta f. fario)?

Abstract Background Due to the rising number of type 2 diabetes patients, the antidiabetic drug, metformin is currently among those pharmaceuticals with the highest consumption rates worldwide. Via sewage-treatment plants, metformin enters surface waters where it is frequently detected in low concentrations (µg/L). Since possible adverse effects of this substance in aquatic organisms have been insufficiently explored to date, the aim of this study was to investigate the impact of metformin on health and development in brown trout (Salmo trutta f. fario) and its microbiome. Results Brown trout embryos were exposed to 0, 1, 10, 100 and 1000 µg/L metformin over a period from 48 days post fertilisation (dpf) until 8 weeks post-yolk sac consumption at 7 °C (156 dpf) and 11 °C (143 dpf). Chemical analyses in tissues of exposed fish showed the concentration-dependent presence of metformin in the larvae. Mortality, embryonic development, body length, liver tissue integrity, stress protein levels and swimming behaviour were not influenced. However, compared to the controls, the amount of hepatic glycogen was higher in larvae exposed to metformin, especially in fish exposed to the lowest metformin concentration of 1 µg/L, which is environmentally relevant. At higher metformin concentrations, the glycogen content in the liver showed a high variability, especially for larvae exposed to 1000 µg/L metformin. Furthermore, the body weight of fish exposed to 10 and 100 µg/L metformin at 7 °C and to 1 µg/L metformin at 11 °C was decreased compared with the respective controls. The results of the microbiome analyses indicated a shift in the bacteria distribution in fish exposed to 1 and 10 µg/L metformin at 7 °C and to 100 µg/L metformin at 11 °C, leading to an increase of Proteobacteria and a reduction of Firmicutes and Actinobacteria. Conclusions Overall, weight reduction and the increased glycogen content belong to the described pharmaceutical effects of the drug in humans, but this study showed that they also occur in brown trout larvae. The impact of a shift in the intestinal microbiome caused by metformin on the immune system and vitality of the host organism should be the subject of further research before assessing the environmental relevance of the pharmaceutical

Impact of the Antidiabetic Drug Metformin and Its Transformation Product Guanylurea on the Health of the Big Ramshorn Snail (Planorbarius corneus)

Pharmaceuticals can enter surface waters via sewage treatment plants. In the environment, the substances and their transformation products, formed by the degradation of the parent compounds, can affect aquatic wildlife, including freshwater invertebrates. However, research on pharmaceutical-induced effects in wild freshwater organisms other than fish is still scarce. In our study, we investigated the impact of the highly consumed antidiabetic drug metformin and its main transformation product, guanylurea, on the health of a freshwater gastropod—the big ramshorn snail (Planorbarius corneus) by analysing its biochemical and cellular stress responses and apical parameters. The snails were exposed to different concentrations of the drug (0, 0.01, 0.1, 1, and 10 mg/L) and its transformation product (0, 0.1, 10, and 100 mg/L). The examined parameters were mortality, weight, tissue integrity of the hepatopancreas, and the levels of stress proteins and lipid peroxides. Mortality and the levels of stress proteins and lipid peroxides were not influenced by the two substances. In response to the highest concentrations of both chemicals, the weight of the snails was slightly but not significantly reduced. The histopathological investigation of the hepatopancreas revealed a significant effect of guanylurea at a concentration of 100 mg/L with an increased number of symptoms of cellular responses in the tissue (e.g., dilated lumen, disturbed compartmentation of the digestive cells, nucleus deformation, hyperplasia, and hypertrophy of crypt cells). For the parent compound, a similar trend was also observed for the highest concentration. Overall, the observed effects did not occur at environmentally relevant concentrations, but at concentrations which were 10,000 times higher than these. Thus, the results did not give rise to a major concern that metformin and guanylurea could pose a risk to the big ramshorn snail in the environment

The mid-infrared diameter of W Hydrae

Mid-infrared (8-13 microns) interferometric data of W Hya were obtained with MIDI/VLTI between April 2007 and September 2009, covering nearly three pulsation cycles. The spectrally dispersed visibility data of all 75 observations were analyzed by fitting a circular fully limb-darkened disk (FDD) model to all data and individual pulsation phases. Asymmetries were studied with an elliptical FDD. Modeling results in an apparent angular FDD diameter of W Hya of about (80 +/- 1.2) mas (7.8 AU) between 8 and 10 microns, which corresponds to an about 1.9 times larger diameter than the photospheric one. The diameter gradually increases up to (105 +/- 1.2) mas (10.3 AU) at 12 microns. In contrast, the FDD relative flux fraction decreases from (0.85 +/- 0.02) to (0.77 +/- 0.02), reflecting the increased flux contribution from a fully resolved surrounding silicate dust shell. The asymmetric character of the extended structure could be confirmed. An elliptical FDD yields a position angle of (11 +/- 20) deg and an axis ratio of (0.87 +/- 0.07). A weak pulsation dependency is revealed with a diameter increase of (5.4 +/- 1.8) mas between visual minimum and maximum, while detected cycle-to-cycle variations are smaller. W Hya's diameter shows a behavior that is very similar to the Mira stars RR Sco and S Ori and can be described by an analogous model. The constant diameter part results from a partially resolved stellar disk, including a close molecular layer of H2O, while the increase beyond 10 microns can most likely be attributed to the contribution of a spatially resolved nearby Al2O3 dust shell.Comment: 18 pages, 16 figure

Entangled Stories: The Red Jews in Premodern Yiddish and German Apocalyptic Lore

“Far, far away from our areas, somewhere beyond the Mountains of Darkness, on the other side of the Sambatyon River…there lives a nation known as the Red Jews.” The Red Jews are best known from classic Yiddish writing, most notably from Mendele's Kitser masoes Binyomin hashlishi (The Brief Travels of Benjamin the Third). This novel, first published in 1878, represents the initial appearance of the Red Jews in modern Yiddish literature. This comical travelogue describes the adventures of Benjamin, who sets off in search of the legendary Red Jews. But who are these Red Jews or, in Yiddish, di royte yidelekh? The term denotes the Ten Lost Tribes of Israel, the ten tribes that in biblical times had composed the Northern Kingdom of Israel until they were exiled by the Assyrians in the eighth century BCE. Over time, the myth of their return emerged, and they were said to live in an uncharted location beyond the mysterious Sambatyon River, where they would remain until the Messiah's arrival at the end of time, when they would rejoin the rest of the Jewish people. This article is part of a broader study of the Red Jews in Jewish popular culture from the Middle Ages through modernity. It is partially based on a chapter from my book, Umstrittene Erlöser: Politik, Ideologie und jüdisch-christlicher Messianismus in Deutschland, 1500–1600 (Göttingen: Vandenhoeck & Ruprecht, 2011). Several postdoctoral fellowships have generously supported my research on the Red Jews: a Dr. Meyer-Struckmann-Fellowship of the German Academic Foundation, a Harry Starr Fellowship in Judaica/Alan M. Stroock Fellowship for Advanced Research in Judaica at Harvard University, a research fellowship from the Heinrich Hertz-Foundation, and a YIVO Dina Abramowicz Emerging Scholar Fellowship. I thank the organizers of and participants in the colloquia and conferences where I have presented this material in various forms as well as the editors and anonymous reviewers of AJS Review for their valuable comments and suggestions. I am especially grateful to Jeremy Dauber and Elisheva Carlebach of the Institute for Israel and Jewish Studies at Columbia University, where I was a Visiting Scholar in the fall of 2009, for their generous encouragement to write this article. Sue Oren considerably improved my English. The style employed for Romanization of Yiddish follows YIVO's transliteration standards. Unless otherwise noted, translations from the Yiddish, Hebrew, German, and Latin are my own. Quotations from the Bible follow the JPS translation, and those from the Babylonian Talmud are according to the Hebrew-English edition of the Soncino Talmud by Isidore Epstein