An object-oriented database for the compilation of signal transduction pathways

Transpath ist ein Informationssystem fuer Signaltransduktionsnetze. Der Fokus liegt auf Signalpfaden und -kaskaden, die an der Regulation von Transkriptionsfaktoren beteiligt sind. Molekuele und Reaktionenen werden als Knoten in einem Signalgraphen aufgefasst und, zusammen mit Informationen ueber ihre Lokalisation, Qualitaet, Familienhierarchien und Signalmotive, in einer objekt-orientierten Databank gespeichert. Weiterhin werden Verweise zu anderen Datenbanken und der Originalliteratur gespeichert. Transpath unterscheidet zwischen den Zuständen eines Signalmoleküles und kann die Reaktionsmechanismen der Signalinteraktionen angemessen beschreiben. Transpath is über das World Wide Web (http://transpath.gbf.de) verfügbar durch ein Servlet-basiertes Interface, das dynamische Sichten direkt aus dem Inhalt der Datenbank erzeugt. Signalpfad-Abfragen und verschiedene Arten der Visualisierung werden zusammen mit textbasierenden Abfragen und Detailinformationen zu einzelnen Eintraegen unterstuetzt. Es wird gezeigt dass die Datenbank zur Analyse des Signalnetzes von Nutzen ist und die Grundlage fuer Simulationen liefern kann.Transpath is an information system on signal-transduction networks. It focuses on pathways involved in the regulation of transcription factors. Molecules and reactions are the nodes in a signaling graph. They are stored in an object-oriented database, together with information about their location, quality, family relationships and signaling motifs. Also stored are links to other databases and references to the original literature. Transpath differentiates between the states of a signal molecule, and can adequately describe the reaction mechanisms of signaling interactions. It is available over the web (http://transpath.gbf.de) through a Servlet-based interface, that creates dynamic content directly from the contents of the database. Pathway query mechanisms and several kinds of display are provided for the database in addition to text-based queries and information on single entries. We show that the database is useful for analysis of the signaling network and can provide the basis for simulations

In-silico-Systemanalyse von Biopathways

Chen M. In silico systems analysis of biopathways. Bielefeld (Germany): Bielefeld University; 2004.In the past decade with the advent of high-throughput technologies, biology has migrated from a descriptive science to a predictive one. A vast amount of information on the metabolism have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis with an easy-to-use computational system. One major task is to implement molecular information systems that will allow to integrate different molecular database systems, and to design analysis tools (e.g. simulators of complex metabolic reactions). Three key problems are involved: 1) Modeling and simulation of biological processes; 2) Reconstruction of metabolic pathways, leading to predictions about the integrated function of the network; and 3) Comparison of metabolism, providing an important way to reveal the functional relationship between a set of metabolic pathways. This dissertation addresses these problems of in silico systems analysis of biopathways. We developed a software system to integrate the access to different databases, and exploited the Petri net methodology to model and simulate metabolic networks in cells. It develops a computer modeling and simulation technique based on Petri net methodology; investigates metabolic networks at a system level; proposes a markup language for biological data interchange among diverse biological simulators and Petri net tools; establishes a web-based information retrieval system for metabolic pathway prediction; presents an algorithm for metabolic pathway alignment; recommends a nomenclature of cellular signal transduction; and attempts to standardize the representation of biological pathways. Hybrid Petri net methodology is exploited to model metabolic networks. Kinetic modeling strategy and Petri net modeling algorithm are applied to perform the processes of elements functioning and model analysis. The proposed methodology can be used for all other metabolic networks or the virtual cell metabolism. Moreover, perspectives of Petri net modeling and simulation of metabolic networks are outlined. A proposal for the Biology Petri Net Markup Language (BioPNML) is presented. The concepts and terminology of the interchange format, as well as its syntax (which is based on XML) are introduced. BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets. The language makes it possible to exchange biology Petri net diagrams between all supported hardware platforms and versions. It is also designed to associate Petri net models and other known metabolic simulators. A web-based metabolic information retrieval system, PathAligner, is developed in order to predict metabolic pathways from rudimentary elements of pathways. It extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. The system also provides a navigation platform to investigate metabolic related information, and transforms the output data into XML files for further modeling and simulation of the reconstructed pathway. An alignment algorithm to compare the similarity between metabolic pathways is presented. A new definition of the metabolic pathway is proposed. The pathway defined as a linear event sequence is practical for our alignment algorithm. The algorithm is based on strip scoring the similarity of 4-hierarchical EC numbers involved in the pathways. The algorithm described has been implemented and is in current use in the context of the PathAligner system. Furthermore, new methods for the classification and nomenclature of cellular signal transductions are recommended. For each type of characterized signal transduction, a unique ST number is provided. The Signal Transduction Classification Database (STCDB), based on the proposed classification and nomenclature, has been established. By merging the ST numbers with EC numbers, alignments of biopathways are possible. Finally, a detailed model of urea cycle that includes gene regulatory networks, metabolic pathways and signal transduction is demonstrated by using our approaches. A system biological interpretation of the observed behavior of the urea cycle and its related transcriptomics information is proposed to provide new insights for metabolic engineering and medical care

Physical Object Representation and Generation: A Survey of Programs For Semantic-Based Natural Language Processing

This article surveys a portion of the field of natural language processing. The main areas considered are those dealing with representation schemes, particularly work on physical object representation, and generalization processes driven by natural language understanding. The emphasis of this article is on conceptual representation of objects based on the semantic interpretation of natural language input. Six programs serve as case studies for guiding the course of the article. Within the framework of describing each of these programs, several other programs, ideas, and theories that are relevant to the program in focus are presented

A Semantic Framework for Declarative and Procedural Knowledge

In any scientic domain, the full set of data and programs has reached an-ome status, i.e. it has grown massively. The original article on the Semantic Web describes the evolution of a Web of actionable information, i.e.\ud information derived from data through a semantic theory for interpreting the symbols. In a Semantic Web, methodologies are studied for describing, managing and analyzing both resources (domain knowledge) and applications (operational knowledge) - without any restriction on what and where they\ud are respectively suitable and available in the Web - as well as for realizing automatic and semantic-driven work\ud ows of Web applications elaborating Web resources.\ud This thesis attempts to provide a synthesis among Semantic Web technologies, Ontology Research, Knowledge and Work\ud ow Management. Such a synthesis is represented by Resourceome, a Web-based framework consisting of two components which strictly interact with each other: an ontology-based and domain-independent knowledge manager system (Resourceome KMS) - relying on a knowledge model where resource and operational knowledge are contextualized in any domain - and a semantic-driven work ow editor, manager and agent-based execution system (Resourceome WMS).\ud The Resourceome KMS and the Resourceome WMS are exploited in order to realize semantic-driven formulations of work\ud ows, where activities are semantically linked to any involved resource. In the whole, combining the use of domain ontologies and work ow techniques, Resourceome provides a exible domain and operational knowledge organization, a powerful engine for semantic-driven work\ud ow composition, and a distributed, automatic and\ud transparent environment for work ow execution

Work flows in life science

The introduction of computer science technology in the life science domain has resulted in a new life science discipline called bioinformatics. Bioinformaticians are biologists who know how to apply computer science technology to perform computer based experiments, also known as in-silico or dry lab experiments. Various tools, such as databases, web applications and scripting languages, are used to design and run in-silico experiments. As the size and complexity of these experiments grow, new types of tools are required to design and execute the experiments and to analyse the results. Workflow systems promise to fulfill this role. The bioinformatician composes an experiment by using tools and web services as building blocks, and connecting them, often through a graphical user interface. Workflow systems, such as Taverna, provide access to up to a few thousand resources in a uniform way. Although workflow systems are intended to make the bioinformaticians' work easier, bioinformaticians experience difficulties in using them. This thesis is devoted to find out which problems bioinformaticians experience using workflow systems and to provide solutions for these problems.\u

Using conceptual graphs for clinical guidelines representation and knowledge visualization

The intrinsic complexity of the medical domain requires the building of some tools to assist the clinician and improve the patient’s health care. Clinical practice guidelines and protocols (CGPs) are documents with the aim of guiding decisions and criteria in specific areas of healthcare and they have been represented using several languages, but these are difficult to understand without a formal background. This paper uses conceptual graph formalism to represent CGPs. The originality here is the use of a graph-based approach in which reasoning is based on graph-theory operations to support sound logical reasoning in a visual manner. It allows users to have a maximal understanding and control over each step of the knowledge reasoning process in the CGPs exploitation. The application example concentrates on a protocol for the management of adult patients with hyperosmolar hyperglycemic state in the Intensive Care Unit

Office automation

Bibliography: p. 100-104.Office automation systems have become an essential tool for the operation of the modern office. With the emphasis of a modern office being placed on efficiency and ease of communication, office automation systems have become the backbone of successful businesses. COSNET is a prototype office automation system designed and implemented at the Department of the University of Cape Town and runs on Personal Computers that are linked to a NCR UNIX TOWER, which acts as the host. This dissertation investigates the different facilities supported by some of the office automation systems compared in this thesis, and describes the COSNET features. This prototype office automation system supports many of the facilities that are supported by large office automation systems. COSNET allows the user to define any MS-DOS based editor or word processor, and uses a simple editor for the creation of mail. The electronic filing facility allows documents to be created, filed, retrieved and deleted, and thus provides the users with the necessary features for document exchange. A user may set access permissions to each of his documents and may grant other users either read or write access to a specific document. The mail facility lets the user read, file, forward, delete and print a message, and supports classification of mail. A calendar facility is used as an electronic diary and stores all the user's schedules. These schedules may be viewed in either daily, weekly and monthly display modes. Read and write access to the calendar can be set by the user, in order to allow other users to manipulate his schedules. Any MS-DOS based application software can be added to COSNET. This facility allows the COSNET user to configure the office automation system to simulate the office environment. COSNET thus supports most of the necessary features required by an office automation system