Browsing by Subject "Database"
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Item Open Access The BioPAX community standard for pathway data sharing(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.Item Open Access Content-based retrieval of historical Ottoman documents stored as textual images(IEEE, 2004) Şaykol, E.; Sinop, A. K.; Güdükbay, Uğur; Ulusoy, Özgür; Çetin, A. EnisThere is an accelerating demand to access the visual content of documents stored in historical and cultural archives. Availability of electronic imaging tools and effective image processing techniques makes it feasible to process the multimedia data in large databases. In this paper, a framework for content-based retrieval of historical documents in the Ottoman Empire archives is presented. The documents are stored as textual images, which are compressed by constructing a library of symbols occurring in a document, and the symbols in the original image are then replaced with pointers into the codebook to obtain a compressed representation of the image. The features in wavelet and spatial domain based on angular and distance span of shapes are used to extract the symbols. In order to make content-based retrieval in historical archives, a query is specified as a rectangular region in an input image and the same symbol-extraction process is applied to the query region. The queries are processed on the codebook of documents and the query images are identified in the resulting documents using the pointers in textual images. The querying process does not require decompression of images. The new content-based retrieval framework is also applicable to many other document archives using different scripts.Item Open Access Development of a specialized zebrafish xenotransplantation database and establishment of ALU-based tumor DNA quantification method in zebrafish: focus on models of overexpression and microenvironment(2020-09) Targen, SeniyeSuccessful xenotransplantation of human cancer cells into zebrafish host marked a new era in cancer research enabling high throughput in vivo screens. Zebrafish xenotransplantation literature continues to rapidly accumulate, and this necessitates the development of an interactive database for accommodating the collective data for fined-tune search, visualization and statistical representation purposes. Herein, I have introduced an interactive database, ZenoFishDb v1.1 (https://konulab.shinyapps.io/zenofishdb), housing manually curated details on molecularly-modified cell transplantations, PDXs, stem cell and cancer stem cell transplantation studies as well as transplantation studies bearing modified host details. The database projects collected data in a table format via various attributes and provides graphical representation of the curated details as well as statistical analyses yielding information on incorporated numbers and frequencies of selected attributes; hence can be used for reviews and designing new experiments. Zebrafish PDX studies are separately conceptualized and displayed through ZenoFishDb v1.1. Development of the ZenoFishDb v1.1 leads to a better understanding of tumor analysis methods such as assessment of proliferation and/or tumor growth in xenotransplantation studies and further marks the need for development of novel methods for precise quantification of tumor size. In the light of these findings, I have helped establish a novel qRT-PCRbased proliferation assessment method for xenografts in zebrafish, adapted from previous mouse xenotransplantation studies. Herein, the use and precision of ALU repeat-based quantification of transplanted liver cancer cells in genotyped zebrafish ache mutants and wildtype siblings was shown exemplifying microenvironment as an important factor for tumor growth. I further demonstrated the power of ALU repeatbased quantification in Mineralocorticoid Receptor (MR) overexpressing breast cancer cells (MCF7) injected to the transparent casper zebrafish as a case study. First, I demonstrated that MR expression and signaling was important in breast cancer biology and prognosis based on in silico TCGA and custom RNA sequencing as well as other in vitro and ex vivo assays. I further showed that results obtained from ALU repeatbased quantification of tumor growth in MR-overexpressing MCF7 cells paralleled fluorescent image-based intensity measurements while the former being relatively less time-consuming and more high-throughput. In this study, accurate quantification of MR overexpression in xenografts was also successfully performed by a cDNA-specific primer pair; and the rate of tumor growth based on image analysis, did not correlate with the amount of MR DNA in casper fish xenografts. However, MCF7 cells overexpressing MR exhibited lower cell viability in vitro although some of these effects were due to empty vector (EV) integration. Accordingly, tumor size in xenografts of naïve, EV- and MR-transfected MCF7 cells injected into pigmented AB larvae were quantified for ALU-repeats yet no significant difference was observed due to high within-group variability in vivo. Future studies are needed to assess the role of varying the volume and placement of injected cells along with the amount of MR gene transfected on tumor growth in vivo.Item Open Access An index structure for moving objects in video databases(1999) Yavuz, TubaModeling moving objects and Iiandling various types of motion queries are interesting topics to investigate in the area of video databases. In one type of motion queries, motion of multiple objects is specified by the changes in relative spatial positions of objects. Answering such kind of queries, that involve motion of multiple objects whose identifications cire not specified, requires some type of indexing because the time complexity of processing such a query in the absence of an index structure is 0{N \l{N — n)!), where N is the number of objects in the database and n is the number of objects in the query. In this work, we propose a spatio-temporal index structure, which we call ,S'M/A7-index, and compare its performance against a similar scheme proposed in [18]. The scheme presented in [18] consists of a constraint satisfaction algorithm, which is called Join Window Reduction (JW R ), combined with a spatial index structure (R*- tree). Experimental results indicate thcit SMIST-'mdex outperforms the JW R algorithm. Also, SMIST-'mdex is shown to be scalable to increasing number of frames and objects.Item Open Access “Interface: the actual story”(Inter-Disciplinary Press, 2014) Şenova Tunalı, Funda; Dun, S.; Moser, D.Technological enhancements and the integration of digital media into our daily lives have brought us many possibilities to form new associations and interact with the content that we are confronted with. Digital storytelling is such a field, which by using the characteristics of new media tries to form new semantic and syntactic relations between the authors/producers/designers/creators, the stories told and the users. Interface appears as the gateway through which the user accesses the content. The physical and digital interfaces (graphical user interfaces) and how the user interacts with them set the rules of the process by which the data is accessed. New media places the interface and the user at the heart of this interaction. The possibility of customising the user experience is an exciting one, which can bring dynamism to any story that is being told. The graphical user interface not only provides access to the content being represented but also gives freedom to the user to a degree on how to experience the story and provides visual information about the look and feel of the story. This chapter probes into the idea that an interface beyond being an undetachable part of the story being told, also acts as a part of the story with which it unfolds. Whether it is an online book, a hyperlinked story, a new media documentary, a computer game, or any other form of transmedia storytelling, interface becomes an important element of the story that gives visual hints and designates the look and feel of the story being told. This study intends to put forward interface as the element that is the gateway to the story, a part of the story and the reflection of the user who access the content through interacting with the interface.Item Open Access NEON-A script-based software framework for querying cellular pathways(2003) Nişancı, GürkanA cellular pathway can be defined briefly as a readable abstraction of events by human happening in the cell. With the PATIKA project, our aim was to model and store vast amount of cellular pathway data in a centralized database. A common problem of every scientific database is the risk of losing highly valuable hidden relations in the data. If appropriate query tools can not be provided to users for analyzing pathway data, these hidden relations can not be detected, which may infer new information. For that reason form-based visual query tools are built to provide querying facility that will be needed by PATIKA users. However, queries made with visual tools are not flexible enough to let users modify the existing queries or define new queries to execute on the PATIKA database. Also lack of powerful expression with these tools restricts the users while defining queries. In this thesis we propose an advanced query framework, NEON, which is developed for the PATIKA project for querying cellular pathways by using and extending a scripting language. It utilises a novel integration of the well-known Jython scripting language with the PATIKA project to provide a software environment where systems can be developed in a seamless mixture of Java and Jython. The framework is designed flexible enough to enable users analyze any part of the PATIKA database by writing their own query scripts. According to the tests done on the PATIKA system, querying through scripting methodology works fine on our pathway database and more effective analysis of cellular pathways through PATIKA seems to be facilitatedItem Open Access Remediating the data : a study on the interactive dimensions in new media(2005) Şenova, FundaThis thesis analyses the role of interface in altering perception and customizing interaction in new media. It comprehends the correlation of theory and practice while probing into the current debate by means of examples and case studies. The general structure of this research is based on the objectives of interactivity in cultural and social levels. In each level, interactivity is analyzed through function, operation oriented and design-wise aspects of new media. This study focuses on the interactive dimensions in new media and their affects on the user’s perception and engagement within a digitally framed work.Item Open Access ZenoFishDb v1.1: a database for xenotransplantation studies in zebrafish(Mary Ann Liebert, 2020) Targen, Seniye; Kaya, Tuğberk; Avcı, M. E.; Güneş, Damla; Keşküş, Ayşe Gökçe; Konu, ÖzlenRapidly accumulating literature has proven feasibility of the zebrafish xenograft models in cancer research. Nevertheless, online databases for searching the current zebrafish xenograft literature are in great demand. Herein, we have developed a manually curated database, called ZenoFishDb v1.1 (https://konulab.shinyapps.io/zenofishdb), based on R Shiny platform aiming to provide searchable information on ever increasing collection of zebrafish studies for cancer cell line transplantation and patient-derived xenografts (PDXs). ZenoFishDb v1.1 user interface contains four modules: DataTable, Visualization, PDX Details, and PDX Charts. The DataTable and Visualization pages represent xenograft study details, including injected cell lines, PDX injections, molecular modifications of cell lines, zebrafish strains, as well as technical aspects of the xenotransplantation procedures in table, bar, and/or pie chart formats. The PDX Details module provides comprehensive information on the patient details in table format and can be searched and visualized. Overall, ZenoFishDb v1.1 enables researchers to effectively search, list, and visualize different technical and biological attributes of zebrafish xenotransplantation studies particularly focusing on the new trends that make use of reporters, RNA interference, overexpression, or mutant gene constructs of transplanted cancer cells, stem cells, and PDXs, as well as distinguished host modifications.