chapter{Introduction}
The System Biology Graph Extender(SBGE) ~cite{eckman} extends the relational database management system with graph objects and operations to support SQL queries over biological networks. It uses SQL to manage graph nodes and edge property data and uses functional extensions to SQL via extit{user defined functions(UDF)} to manage graph operations. UDFs can be used anywhere in an SQL query that an expression of their return type can be used. It defines a graph as a first--class SQL data type, permitting graph instances using SQL in the same way with strings and numbers. Graph operations such as compare, combine, find components, compute shortest paths are implemented as UDFs. A SBGE query is still text--based SQL--like query. It is not as intuitive as a visual query diagram and hard to adapt to. A exploring neighborhood in function space example query would result in a lengthy SQL script.
The Pathway Query Language(PQL) ~cite{UlfLeser} is similar to the SBGE in that it is built on top of an RDBMS and address the same use case as biological networks. PQL has a similar syntax to SQL though the semantics of queries is quite different. Only node variables can appear in the FROM clause. Query evaluation considers each node variable in the FROM clause, for each of these all possible assignment of a variable to nodes of the graph are determined with the conditions of WHERE clause evaluate to true. PQL has a special syntax to allow path expression in both SELECT and WHERE clauses. Unlike SBGE, a PQL query is compiled into a PL/SQL stored procedure. The PQL is limited to its graph data model: nodes are molecules and interactions. It can only answer queries about the properties of a node or a path finding quer...
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...ivalent translation to SQL3. The algebra hence provides a semantics for a query language and facilitate a query language implementation based on this algebra. A unifying database architecture using a visual query language based on this algebra is proposed.
end{itemize}
section{Thesis Organization}
The rest of this thesis is organized as follows. Chapter 2 illustrates the background knowledge that is related to this thesis work. Chapter 3 describes the implemented visual graph database system. A query benchmark in genomics domain that is used to test the performance of the system are described in Chapter 4. The query optimization experiment and results are presented and analyzed in Chapter 5. An algebra of a visual query language for gene feature topological relationship is introduced in Chapter 6. Chapter 7 discusses final conclusion and future work.
Smith, W., & Jewett, D. (2009). Tableau software and teradata database the visual approach to the active data warehouse. In Retrieved from http://www.tableausoftware.com/learn/whitepapers
These are covered briefly in appendices in the text. The relational model was first proposed by E.F. Codd in 1970 and the first such systems were developed in 1970s. The relational model is now the dominant model for commercial data processing applications. The relational model can be used in both conceptual and logical database design. The basic structure in the model is a table .Tables consists of rows and columns. Relationships in the relational model are represented implicitly through common attributes between different relations.
As defined by Kroenke Database is an integrated, self-describing collection of related data. Data is stored in a uniform way, typically all in one place- for example, a single physical computer. A database maintains a description of the data it contains and the data has some relationship to other data in the databa...
Nevertheless, functional genomics is an area of research which has been widely developed due to microarray technology; providing a wide-scale platform for the analysis of genes.
In 1977, Larry Ellison, Bob Miner, and Ed Oates founded System Development Laboratories. After being inspired by a research paper written in 1970 by an IBM researcher titled “A Relational Model of Data for Large Shared Data Banks” they decided to build a new type of database called a relational database system. The original project on the relational database system was for the government (Central Intelligence Agency) and was dubbed ‘Oracle.’ They thought this would be appropriate because the meaning of Oracle is source of wisdom.
The relational model, as implemented in most RDBMSs, can represent a lot of different models, but has difficulty representing inheritance hierarchies, and complex relationships (many many-to-many's) are costly to process
The Revolution in Database Architecture, by Jim Gray, describes the path that Gray thought that the evolution of the Database Architecture would take after 2004. He considers that databases had been stagnated for several years and that, beginning in 2004, the development of several technologies would pave the way into a revolution in the database world.
[7] Elmasri & Navathe. Fundamentals of database systems, 4th edition. Addison-Wesley, Redwood City, CA. 2004.
Bioinformatics is a discipline which is a mixture of molecular biology and computer sciences. In this field the computers are utilized to assemble, accumulate, analyse and incorporate biological and the genetic information of living organisms. The necessity for bioinformatics came during the project to find out the sequence of the whole genome of the human was started (Chris S., 2003). This project was known to be as “Human Genome Project”. This subject is considered to be as very significant for the utilization of genetic information to know about the human diseases and to recognize a novel approaches f...
Numerous parts of bioinformatics are applicable for pharmacology. Pill focuses in irresistible organic entities might be uncovered by entire genome correlations of irresistible and non–infectious creatures. The examination of single nucleotide polymorphisms uncovers genes conceivably answerable for hereditary sicknesses. Forecast and investigation of protein 3d structure is utilized to create pills and comprehend drug safety.
In the previous chapter we generally mentioned Graph databases together with other types of NoSQL database; however, since one of the main goals of this thesis is giving a simple analysis for two systems, it is necessary to understand what main features and what these systems have. Consequently, in this chapter we will find what are the most Databases that have the best availability and scalability. First of all, we will choose a simplest type of the relational database and describe it which is MySQL. Secondly, will choose one type of the NoSQL database and try to analyze it and we will choose Neo4j which it is a graph database.
The scope of this article is narrowed to LINQ to SQL. This is the use of LINQ to access data from database particularly Microsft SQL Server.
Bioinformatics is very update with the information about the gene structure and function. It can locate a gene within a sequence as well as predict the structure and or function of a particular gene. By applying bioinformatics to understand different biological processes, it allows a more global perspective in design, to test hypotheses about a gene or a protein and as well as allowing us the ability to take advantage of upcoming technology.
Oracle's relational databases represent a new and exciting database technology and philosophy on campus. As the Oracle development projects continue to impact on University applications, more and more users will realize the power and capabilities of relational database technology.
In database system, main data structure used in relational tables with well define values for each row and column.