Browsing by Subject "SBGN"

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    Efficient querying of SBGN maps stored in a graph database
    (2019-02) Karaca, Mustafa Enes
    Graph visualization is an important research area that endeavors to make graphs more understandable and easier to analyze. In various domains, graph visualization techniques and standards are developed to effectively analyze underlying graph based data. Systems Biology Graphical Notation (SBGN) is a standard language for modeling biological processes and pathways through graph visualization. Information about SBGN maps can be stored in XML based SBGNML files. libSBGN is a Java/C++ library for reading, writing SBGN-ML and manipulating SBGN maps in an object-oriented manner. Graph databases store data in terms of a graph structure consisting nodes and their relationships. Performing a computation on graph data stored in a graph database by traversals is more e cient than accessing tabled data in relational databases through costly join operations. Neo4j is a prominent graph database that provides a proprietary language named Cypher for querying stored graph data. Neo4j allows writing user defined procedures in Java as plugins to improve capabilities of Neo4j with third party Java libraries. With this thesis, we enable modeling SBGN maps in Neo4j graph database with support for compound structures. Using this SBGN data model in Neo4j, we developed graph based user defined procedures in Java using libSBGN as a plugin to Neo4j. These procedures were used to implement graph query algorithms, such as neighborhood, common stream, and paths between, along with helper functions such as populating a database from an SBGN map and loading an SBGN map from a graph database. These user defined procedures are designed to produce or consume SBGN-ML; hence, they can be used by any visualization tool which can import/export SBGN-ML text. Newt, a web based editor for viewing and diting SBGN maps, is such a tool making use of these procedures and hosting a local Neo4j instance by providing a web service to execute Cypher statements.
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    Libraries and tools for viewing and editing biological maps in SBGN
    (2017-07) Siper, Metin Can
    Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats including Systems Biology Graphical Notation (SBGN). E ective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewing and editing tools that support these platforms and other use cases. We propose to develop a modular software architecture to meet this need. This proposed architecture includes reusable web based libraries and easily customizable and embeddable tools developed using these libraries. Our libraries include SBGNViz.js, a Cytoscape.js based library providing a renderer and an API to develop tools visualizing pathway models represented by SBGN Diagrams, and ChiSE.js, an SBGNViz.js based library to visualize and construct pathway models represented in SBGN Diagrams, and miscellaneous Cytoscape.js extensions. Our tools are built using these libraries and include SBGNViz Viewer and Newt, which are sample applications for SBGNViz.js and ChiSE.js, respectively. Newt is being developed to become a rst web based, open source SBGN editor with full support for compound structures such as molecular complexes and compartment, advanced diagramming facilities including grid and alignment guidelines, static and incremental layout, and complexity management of large maps.
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    Methods and tools for visualization and management of SBGN process description maps
    (2014) Sarı, Mecit
    Graphs are commonly used to model relational information in many areas such as relational databases, software engineering, biological and social networks. In visualization of graphs, automatic layout, interactive editing and complexity management of crowded graphs are essential for effective utilization of underlying information. Advances in graphical user interfaces have given rise and value to interactive editing and diagramming techniques in graph visualization. As the size of the information to be visualized vastly increased, it became harder to analyze such networks, making use of relational information needed to be acquired. To overcome this problem, sophisticated and domain-specific complexity management techniques should be provided. The Systems Biology Graphical Notation (SBGN) has been developed over a number of years by biochemists and computer scientists to standardize visual representation of biochemical and cellular processes. SBGN introduces a concrete, detailed set of symbols for scientists to represent network of interactions, in a way that is not open to more than one interpretation. It also describes the manner, in which such graphical information should be interpreted. The SBGN Process Description (PD) language shows how entities are influenced by processes, which are represented by several reaction types in a biological pathway. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. We developed methods and tools to effectively visualize and manage SBGNPD diagrams. Specifically, we introduced new algorithms for proper management of complexity of large SBGN-PD diagrams. These algorithms strive to keep SBGN-PD diagrams intact as complexity management takes places. In addition, we provided software components and web-based tools that implement these methods. These tools use state-of-the-art web technologies and libraries.
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    Semantic validation of biological maps in SBGN
    (2019-09) Çalış, Umut Utku
    Graph visualization is a research field where relational information is graphically represented in the form of graphs or networks. It is applicable in numerous areas from computer network systems, to biology, to software engineering. In such areas, graph visualization techniques provide effective visual analysis of graph based data. Systems Biology Graphical Notation (SBGN) facilitates a standard model for representing biological entities and their interactions by using graph visualization. SBGN-ML is an XML based format for keeping information about SBGN maps. libSBGN enables writing and reading SBGN-ML files in an easy manner and is meant to bring syntactic and semantic validation to SBGN maps. It is currently available in Java/C++ (libSBGN) and JavaScript (libSBGN.js) programming languages with varying support for aforementioned. libSBGN enables important syntactic and semantic correctness concepts for manipulating SBGN maps and converting SBGN-ML files into several other formats. Syntactic validation of SBGN-ML files involves using a simple XML Schema Definition (XSD) file. This validation checks whether files are in correct form or not. However, this XSD file does not enable checking against semantic rules. For semantic validation of such files, the Schematron language was developed providing higher level semantic rule controls. With this thesis, we first enabled high level semantic validation (schematron validation) of SBGN maps in libSBGN.js, which uses XSLT and transformation of process description maps in SBGN-ML files. By using Schematron rules which are written in XPath syntax and enabling human-readable messages of validation errors and source of errors, we developed an XSLT stylesheet. We obtained validation result report by transforming SBGN-ML files using this XSLT stylesheet. In the JavaScript version of libSBGN library, we used a web based XSLT processor for transformation; hence, this library is now available for providing schematron validation in any SBGN related software. Furthermore, we added schematron validation checks to Newt, a web based SBGN pathway editor, using the updated libSBGN.js library. With this addition, Newt is now able to show validation results not only in a human-readable message text for the current map but also highlights the invalid map objects graphically, and, where appropriate, suggests a way to fix the problem automatically.
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    Systems biology graphical notation markup language (SBGNML) version 0.3
    (De Gruyter, 2020) Luna, A.; Bergmann, F. T.; Czauderna, T.; Doğrusöz, Uğur; Rougny, A.; Dräger, A.; Touré, V.; Mazein, A.; Mazein, M. L.
    This document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, modelers, and computer scientists. SBGN aims at representing networks of biochemical interactions in a standard, unambiguous way to foster efficient and accurate representation, visualization, storage, exchange, and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. SBGN is defined neutrally to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language. The notable changes from the previous version include the addition of attributes for better specify metadata about maps, as well as support for multiple maps, sub-maps, colors, and annotations. These changes enable a more efficient exchange of data to other commonly used systems biology formats (e. g., BioPAX and SBML) and between tools supporting SBGN (e. g., CellDesigner, Newt, Krayon, SBGN-ED, STON, cd2sbgnml, and MINERVA). More details on SBGN and related software are available at http://sbgn.org. With this effort, we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.
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    Systems biology graphical notation: process description language Level 1 Version 2.0
    (De Gruyter, 2019) Rougny, A.; Touré, V.; Moodie, S.; Balaur, I.; Czauderna, T.; Borlinghaus, H.; Doğrusöz, Uğur; Mazein, A.; Dräger, A.; Blinov, M. L.; Villéger, A.; Haw, R.; Demir, E.; Mi, H.; Sorokin, A.; Schreiber, F.; Luna, A.
    The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).