Normalization And Matching Of Chemical Compound Names

We have developed ChemHits (http://sabio.h-its.org/chemHits/), an application which detects and matches synonymic names of chemical compounds. The tool is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Subsequently, matching of synonymous names is achieved by comparison of the normalized name forms. The tool is capable of normalizing a given name of a chemical compound and matching it against names in (bio-)chemical databases, like SABIO-RK, PubChem, ChEBI or KEGG, even when there is no exact name-to-name-match

Planetary Gearbox Prototype Development and Manufacturing

Goal of this research was to develop and manufacture planetary gearbox prototype using rapid prototyping technology (additive manufacturing). Developed prototype was used to visually analyse the design of the planetary gearbox. Also, it was used to improve and innovate education of students on several courses at Mechanical Design study program at Faculty of Mechanical Engineering. It is shown that low cost rapid prototyping technology can be used to manufacture prototypes of complex machines and machine elements. Prototypes manufactured using this technology have same functionality like the real one. Main limitation is the fact that they cannot sustain real world loads and stresses. This paper shows opportunities which low cost rapid prototyping technology is offering in improvement and innovation of education process at engineering schools and faculties. All complex and heavy machines can be manufactured using this type of technology and on that way more precisely presented to the students

Interoception in anxiety and depression

We review the literature on interoception as it relates to depression and anxiety, with a focus on belief, and alliesthesia. The connection between increased but noisy afferent interoceptive input, self-referential and belief-based states, and top-down modulation of poorly predictive signals is integrated into a neuroanatomical and processing model for depression and anxiety. The advantage of this conceptualization is the ability to specifically examine the interface between basic interoception, self-referential belief-based states, and enhanced top-down modulation to attenuate poor predictability. We conclude that depression and anxiety are not simply interoceptive disorders but are altered interoceptive states as a consequence of noisily amplified self-referential interoceptive predictive belief states

Extraktion von Information für die Biologie

High-throughput methods like the large scale sequencing of the human genome dramatically increase our knowledge of genetics and related biological processes. As a consequence these results accelerate the pace of research and development in the field of biomedicine. The overall goal of these research efforts is to obtain new findings about diseases in order to improve human health. However, these advances are responsible for an increase in complexity and a need for understanding when applying biomedical research and data. Meanwhile there is a strong agreement within life-science related academic laboratories and industry that addressing the complexity of biological data and knowledge entails intense interdisciplinary efforts. A major requirement for interdisciplinary research within life sciences is to correlate the data that is derived from text with data from experiments in biomedical laboratories (and with patient records). The main contribution of this work is to describe how natural language processing (NLP) methods and systems can fulfill this requirement by categorising, structuring and exploiting the massive amount of textual data available and in integrating the results with data derived from biomedical experiments. The present work is thematically divided into three parts. The first part is about text mining in the life sciences and is subdivided in two subsections. Subsection I presents an introduction to effective natural language processing techniques for identifying and retrieving information from large text collections. Furthermore it presents the characteristic features of biomedical terminology, which comprise synonymic, homonymic, orthographical, paragrammatical as well as other types of variance. This illustrates that the crucial difference between everyday language and the language used within biomedical scientific literature is mainly based on the difference of the terminology used. This subsection concludes with a description of basic criteria that an information extraction system has to meet. The implementation of such an information extraction system is described in the second subsection. This section documents a pilot study that was carried out in close collaboration with both the SDBV (Scientific DataBases and Visualisation) group of EML Research gGmbH and Peer Bork's group at the EMBL (European Molecular Biology Laboratory) both located in Heidelberg. The system implemented is used for the extraction of information on gene expression relations from biomedical scientific publications. The second part III focuses on the transfer of a computational linguistic tool (TIGERSearch), which was originally developed for the querying of hierarchical structures, to querying knowledge on protein domains from a protein database. It is demonstrated that TIGERSearch offers the possibility to make implicit knowledge about protein domains explicit by transforming the database entries to TIGERSearch-XML. In addition, TIGERSearch makes this implicit knowledge graphically visible. In fact, TigerSearch was initially developed for the querying and transparent representation of syntactically annotated corpora, so-called treebanks. This part also points out the problem that mapping the wide range of natural language annotations to precisely defined concepts presupposed by the search engine requires an ontological modelling of the domain. The third part addresses the problem of ontological modelling in a more general and more comprehensive way. It consists of two chapters. The first chapter introduces basic notions of ontologies as well as an overview of guidelines to be considered when building an ontology. In addition some examples of implemented (both general and biomedical) ontologies are presented. The second chapter presents an axiomatisation of a sub-domain of molecular biology (i.e. gene expression) that comprises the domain of proteins and their domains. The thesis demonstrates a highly interdisciplinary approach for text mining in the life sciences. Methods and knowledge from the fields of natural language processing, bioinformatics and biology have been successfully combined with knowledge from cell-biology and the problem of extracting knowledge from unstructured or partially structured data.Im Rahmen der vorliegenden Arbeit habe ich Methoden der Computerlinguistik diskutiert, erarbeitet und eingesetzt, um eine maschinelle Extraktion biomedizinischer Daten aus wissenschaftlichen Publikationen und Datenbanken zu ermöglichen. Im wesentlichen habe ich dabei drei Themengebiete bearbeitet. Im ersten Teil der Arbeit stelle ich eine Pilotstudie vor, die die Methoden der Informationsextraktion anwendet, um für eine vordefinierte Fragestellung Antworten aus großen Mengen biomedizinischer Texte zu extrahieren. Diese Arbeit ist von unmittelbarer biologischer Relevanz. Denn nachdem diese Arbeit in enger Kollaboration zwischen der SDBV (Scientific DataBases and Visualisation) Gruppe der EML Research gGmbH und der Gruppe um Peer Bork des EMBL (Europäisches Molekularbiologie Labor) entstanden ist, wird das System zur Extraktion von Genexpressionsdaten am EMBL eingesetzt. Im zweiten Teil der Arbeit stelle ich Einsatzmöglichkeiten der TigerSearch Suchmaschine im molekularbiologischen Kontext vor. TigerSearch wurde für die Suche auf syntaktisch annotierten Sätzen entwickelt. Ich habe sie ausgewählt, um strukturierte Information über Proteindomänen transparent darzustellen und komplexe Anfragen bearbeiten zu können. Der letzte Teil der Arbeit beschäftigt sich mit der Modellierung biologischen Wissens. Dabei steht die formale Repräsentation biologisch relevanter Konzepte im Vordergrund. Als wesentliches Merkmal der vorliegenden Arbeit möchte ich den interdisziplinären Charakter betonen, vor allem, weil interdisziplinäre Forschung nicht nur in der Bioinformatik, sondern auch in anderen Forschungsfeldern zunehmend an Bedeutung gewinnt

Ontology-driven Discourse Analysis for Information Extraction

Cimiano P, Saric J, Reyle U. Ontology-driven Discourse Analysis for Information Extraction. Data & Knowledge Engineering (DKE). 2005;55(1):59-83

SABIO-RK: A data warehouse for biochemical reactions and their kinetics.

Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways- Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use a

SABIO-RK: A data warehouse for biochemical reactions and their kinetics

Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/