Data Models in Enhancement Information Based Systems - Coursework Example

Name : xxxxxxxxxxx Institution : xxxxxxxxxxx Tutor : xxxxxxxxxxx Title : Survey on reactome Course : xxxxxxxxxxx @2009 Introduction Data Models Data models do describe the arrangement and the flow of information and data within a given organization structure and how the information or data is a accessed. The figure below demonstrates a good example ok data model diagram (Jay, 2005). . SAMPLE DATA MODEL DIAGRAM The data models helps in the process of enhancement information based systems, they do define how the information is to be done, and the manner and the outline the information should take during processing period. The models appears in different form for instance l (uml,er diagram,xml dtd/schema orsimilar), But in our case we will elaborate on XML. Xml Data models Extensible Mark-up language (XML) is progressively gaining recognition in most cases as a data format tool in the information technology community. According to (Jay, 2005).Its features which are considerably powerful have made it the real data image as well as swap over the web. As a result of its recognition and widespread use, XML data has started to expand considerably. For that reason, an effective statistics management scheme for storing and querying large repositories is needed. Among the most widely acknowledged procedures for managing a large number of XML repositories include the storage and querying XML data set by use of indigenous XML databases RDBMS. Within this approach, XML data are mapped to relations. On the other hand, queries are converted into RDBMS-based or ORDB SQL. The storage of XML data to RDMBS may result into a reduced level of performance because recording XML data to relational databases is likely to take a considerable amount of time mainly on processing a database schema with a number of relations. Researchers like Kentarou and his group proposed XML data to be stored in a relational database and use PC-clusters to process XML data [21]. The strategy was to map XML schema into relational databases tables and segregate these tables relative to the complexity or workload of the query. The partitions are then distributed to each available cluster nodes. The partitions in this approach are being managed by a relational database system. OOXP layer 1: Semantics layer In this section, semantics partitioning layer will be discussed along with its various components and algorithms for XTree and Objects based partitioning rules. The semantic model of XML is very important particularly for object identification, establishing logical relationship, associations, aggregations, and generalization before a partitioning begins. Similarly, XTree will be used to represent these semantic features of XML data based on XML schema. 4.3.1 Semantic XML Tree (XTree) The proposed method for XML partitioning that will be discussed in this chapter is based on the principles of logical and semantic partitioning for XML documents. The concept of semantics relies on the consideration of an object-oriented concept that may include relationships. Since there should be a technique that would determine the logical description of objects in XML documents and the relation between them, an XTree will be used to represent the XML database on XML schema.. In creating XTree, one would need to identify the input that will result to XTree as being the output. In this thesis, the input is the XML document and schema that is generally ‘XML Entry’ in this study’s term.The important criteria that will be used to partition an XML data and represent XTree will be selected based on chosen XML Entry Steven, (2003) 2.3.5 Sibling Partitioning Algorithm BioCyc BioBioCyc refes to accumulation of 506 is a collection of 506 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. BioCyc Tools The BioCyc Web site contains many tools for navigating and analyzing these databases, and for analyzing omics data, including the following. Genome browser Display of individual metabolic pathways, and of full metabolic maps Visual analysis of user-supplied omics datasets by painting onto metabolic map, regulatory map, and genome map Comparative analysis tools The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site [more]. Multiple database configurations are available for installation with the software including multiple E. coli and Shigella genomes, multiple Bacillus genomes, multiple Mycobacterium genomes, and multiple mammalian genomes. BioCyc Pathway/Genome Databases The BioCyc databases are divided into three tiers, based on their quality. Tier 1 databases have received person-decades of literature-based curation, and are the most accurate. Tier 2 and Tier 3 databases contain computationally predicted metabolic pathways, predictions as to which genes code for missing enzymes in metabolic pathways, and predicted operands. PGDBs for many other organisms are available outside the BioCyc collection, created by other users of Pathway Tools. Some of these PGDBs are highly curated, and exist for important model organisms including Mouse, Arabidopsis, and Yeast. For more information on accessing these PGDBs, click here. BioCyc Tier 1: Intensively Curated Databases Database Scope Highlights EcoCyc Escherichia coli K-12 MG1655 Model-Organism Database Literature curation of complete genome Information from 17,000 publications Transcriptional regulatory network Protein complexes Enzyme and transporter functions Gene Ontology assignments MetaCyc Multiorganism Metabolic Pathway and Enzyme Database 1,200 metabolic pathways Pathways elucidated from 1,500 organisms Extensive commentary Information from 19,000 publications BioCyc Tier 2: Computationally-Derived Databases Subject to Moderate Curation Reactome is a free site that is enabled for every one to access and view information or path ways that are grouped in data bases and structure mostly in the field of Biology. Data that is incorporated in these databases is only allowed to be viewed with the researchers who are based in the field of genetic sciences. the information is manned by the authenticated biological experts for instance they are referenced in regards to the HapMap, Ensembi, Most of the time the data are used in the process of infer orthologous which do incorporated mouse, chicken Tools that are designed for the process of data collection includes Sbml,BioPAX and Biomart. Conclusion Most of the research work has credited database partitioning claiming that it is a very important and ideal method in the process of data and information manipulation. Majority of the XML applications documents and projects normally utilize the tool Most applications that deal with XML documents utilized a technique that divides or split partition particularly large XML into smaller documents. (Paul,2007).This is because to retrieve data in a very large XML document often accompanies shortage of memory space. Consequently, applications manipulate resulting XML documents by retrieving and combining their XML Tree. In this thesis, numerous areas of XML partitioning were examined through various literatures and found that semantic structure of XML data were not included in the resulting XML documents. Since this is an important part of XML, this thesis decided to explore this issue and develop a new concept on semantic and optimization to contribute and overcome the difficulties encountered by previous XML data partitioning concepts. Analysis of different literature was performed in Chapters 2 and 3 to clarify the issues involved in XML data partitioning. Knowledge gained from this study enable the author to develop and propose a fresh concept regarding XML partitioning and address its existing problems. Bibliography Steven, M., 2003, Information. Upper Saddle River, New Jersey. Roger, B., 2001, Data’s Process Management: Profiting From Process, Prentice Hall, Chicago. James, F., 2006, Business Process Management Systems, Harper Macmillan, New York. Jay, R., 2005, Designing the Customer-Centric Organization: A Guide to Strategy, Structure and Process, Belknap Press of Harvard University, London. Jean, G., 2008, The complete guide to Business Process Management, Felix Alcan, Paris. Paul, H., 2007, Business Process Change: A Guide for Business Managers and BPM and Six Sigma Professionals, Sage, London. Read More