Browsing by Subject "Pathways"
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Item Unknown Collaborative workspaces for pathway curation(CEUR-WS, 2016-08) Durupınar-Babur, F.; Siper, Metin Can; Doğrusöz, Uğur; Bahceci, İstemi; Babur, O.; Demir, E.We present a web based visual biocuration workspace, focusing on curating detailed mechanistic pathways. It was designed as a flexible platform where multiple humans, NLP and AI agents can collaborate in real-time on a common model using an event driven API. We will use this platform for exploring disruptive technologies that can scale up biocuration such as NLP, human-computer collaboration, crowd-sourcing, alternative publishing and gamification. As a first step, we are designing a pilot to include an author-curation step into the scientific publishing, where the authors of an article create formal pathway fragments representing their discovery- heavily assisted by computer agents. We envision that this "microcuration" use-case will create an excellent opportunity to integrate multiple NLP approaches and semi-automated curation. © 2016, CEUR-WS. All rights reserved.Item Open Access Libraries and tools for viewing and editing biological maps in SBGN(Bilkent University, 2017-07) Siper, Metin CanInformation 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.Item Open Access Methods and tools for visualization and management of SBGN process description maps(Bilkent University, 2014) Sarı, MecitGraphs 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.Item Open Access PATIKAmad: putting microarray data into pathway context(Wiley - V C H Verlag GmbH & Co. KGaA, 2008-06) Babur, Özgün; Colak, Recep; Demir, Emek; Doğrusöz, UğurHigh-throughput experiments, most significantly DNA microarrays, provide us with system-scale profiles. Connecting these data with existing biological networks poses a formidable challenge to uncover facts about a cell's proteome. Studies and tools with this purpose are limited to networks with simple structure, such as protein-protein interaction graphs, or do not go much beyond than simply displaying values on the network. We have built a microarray data analysis tool, named PATIKAmad, which can be used to associate microarray data with the pathway models in mechanistic detail, and provides facilities for visualization, clustering, querying, and navigation of biological graphs related with loaded microarray experiments. PATIKAmad is freely available to noncommercial users as a new module of PATIKAweb at http://web.patika.org. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.