DISEASE GENE PREDICTION BY INTEGRATING PPI

NETWORK, CLINICAL RNA-SEQ DATA AND OMIM

DATA

A PROJECT REPORT

Submitted by

HARISH R (710616205005)
MOHAMED ASARUDEEN J (710616205014)
KEERTHI T (710616205013)

In partial fulfillment for the award of the degree

of

BACHELOR OF TECHNOLOGY

In

INFORMATION TECHNOLOGY

CSI COLLEGE OF ENGINEERING, THE NILGIRIS

ANNA UNIVERSITY: CHENNAI 600 025

APRIL 2020
DISEASE GENE PREDICTION BY INTEGRATING PPI
NETWORK, CLINICAL RNA-SEQ DATA AND OMIM
DATA

A PROJECT REPORT

Submitted by

HARISH R (710616205005)
MOHAMED ASARUDEEN J (710616205014)
KEERTHI T (710616205013)

In partial fulfillment for the award of the degree

of

BACHELOR OF TECHNOLOGY

In

INFORMATION TECHNOLOGY

CSI COLLEGE OF ENGINEERING, THE NILGIRIS

ANNA UNIVERSITY:: CHENNAI 600 025

APRIL 2020
 ANNA UNIVERSITY: CHENNAI 600 025

BONAFIDE CERTIFICATE
Certified that this project report “DISEASE GENE PREDICTION BY

INTEGRATING PPI NETWORKS,CLINICAL RNA-SEQ DATA AND

OMIM DATA” is the bona fide work of “HARISH R, MOHAMED

ASARUDEEN J, KEERTHI T” who carried out the project work under my

supervision.

Prof.G.THIAGARAJAN M.TECH., Prof.G.THIAGARAJAN M.TECH.,

HEAD OF THE DEPARTMENT SUPERVISOR
Department of Information Technology Department of Information Technology
CSI College Of Engineering CSI College Of Engineering
Ketti(Near Ooty) Ketti(Near Ooty)
The Nilgiris-643215 The Nilgiris-643215

SUBMITTED FOR THE ANNA UNIVERSITY PROJECT VIVO-VOCE

EXAMINATION HELD ON…………………

INTERNAL EXAMINER EXTERNAL EXAMINER

 ACKNOWLEDGEMENT

First of all, we thank the almighty god for his grace and mercy, which
made us to complete our project successfully.

We express our sincere gratitude to our dear parents who have been the
major contributor of inspiration and encouragement to us throughout our
career.

We would like to express our sincere gratitude to our Bishop

Rt. Rev. Timothy Ravinder B.Sc., B.D., ZD.

We wish to convey our earnest greatfulness to our cherished principal

Dr. J. Joshua Gnana Sekaran B.E., M.S., Ph.d., MISTE, MSCI, MCSI.,
who have been a source of inspiration throughout the project.

We articulate our genious thanks to our dear head of the department

Prof. G. Thiagarajan M.Tech., who have been the key spring of motivation to
us throughout the completion of our course and our project work.

We wish to extend our sincere obligation to our Project Coordinator

Prof. M. Mohan M.E., Department of Information Technology for their
consistent encouragement, immense help and guidance.

We owe a deeper sense of gratitude and our heartfelt thanks to our Project
Guide Prof. G. Thiagarajan M.Tech., Department of Information
Technology, for his remarkable guidance and Valuable suggestions direction
for completion of the project.

We are also thankful to all our faculty members of information technology

department for their help.

Most of all we thank our parents for their blessings and to our friends for
extending their support and encouragement.

ABSTRACT
 Multiple genomic and proteomic semantic annotations scattered in many
distributed and heterogeneous data sources; such heterogeneity and dispersion
hamper the biologists’ ability of asking global queries and performing global
evaluations. To overcome this problem, we developed a software architecture to
create and maintain a Genomic and Proteomic Knowledge Base (GPKB), which
integrates several of the most relevant sources.

Gene Ontology (GO) is a structured repository of concepts that are

associated to one or more gene products through a process referred to as
annotation. There are different approaches of analysis to get bio information.
One of the analysis is the use of Association Rules (AR) which discovers
biologically relevant associations between terms of GO. In existing work we
used GO-WAR (Gene Ontology-based Weighted Association Rules) for
extracting Weighted Association Rules from ontology-based annotated datasets.
We here adapt the MOAL algorithm to mine cross-ontology association rules,
i.e. rules that involve GO terms present in the three sub-ontologies of GO. We
are proposing cross ontology to manipulate the Protein values from three sub
ontologies for identifying the gene attacked disease. Also our proposed system,
focus on intrinsic and extrinsic. Based on cellular component, molecular
function and biological process values intrinsic and extrinsic calculation would
be manipulated.

For each proteomic analysis for every gene disease, we analyze OMIM
id, disease caused by, associated genes, medicine if available, and images of
that particular gene disorder. Thus a common man also would be able to
understand the membranes and enzymes associated for his / her gene disorder
and able to identify intrinsic and extrinsic factors.
 In this Project, We done the Co-Regulatory modules between miRNA
(microRNA), TF (Transcription Factor) and gene on function level with
multiple genomic data.. We compare the regulations between miRNA-TF
interaction, TF-gene interactions and gene-miRNA interaction with the help of
integration technique. These interaction could be taken the genetic disease like
breast cancer, etc., Iterative Multiplicative Updating Algorithm is used in our
project to solve the optimization module function for the above interactions.
After that interactions, we compare the regulatory modules and protein value for
gene and generate Bayesian rose tree for efficiency of our result.

TABLE OF CONTENTS

CHAPTER NO. TITLE PAGE NO

 ABSTRACT iii
LIST OF TABLE xvi
LIST OF FIGURES xviii
LIST OF SYMBOLS xxvii

1. INTRODUCTION 1

1.1 Overview of the project

1.2 Existing system
1.3 Proposed system
1.4 Methods and Materials
1.4.1. General Model
1.4.2. Differential Network Construction
1.4.3. Non-disease Genes
1.4.4. Feature Extraction
1.4.5. Validation Methods and Evaluation Criteria
1.4.6. Data source
2. LITERATURE REVIEW
2.1 Literature survey

3.

CHAPTER 1
INTRODUCTION
1.1 OVERVIEW OF THE PROJECT
 Ontologies are specifications of a relational vocabulary. Gene
ontology (GO) is a major bioinformatics initiative to unify the
representation of gene and gene product attributes across all species. The
GO project has developed three structured controlled vocabularies
(ontologies) that describe gene products in terms of their associated
biological processes, cellular components and molecular functions in a
species-independent manner. The ontology covers three domains:

i. CELLULAR COMPONENT, the parts of a cell or its extracellular

environment;
ii. MOLECULAR FUNCTION, the elemental activities of a gene
product at the molecular level, such as binding or catalysis; and 
iii. BIOLOGICAL PROCESS, operations or sets of molecular events
with a defined beginning and end, pertinent to the functioning of
integrated living units: cells, tissues, organs, and organisms.

The introduction of high-throughput technologies in molecular biology has

produced the accumulation of a large set of experimental data. Such amount of
experimental data has been integrated with additional information able to
explain such data. For instance, genes and proteins have been accompanied by
the storing of additional information used for the elucidation of the role of the
investigated molecules. In order to systematize such knowledge, formal
instruments such as controlled vocabularies and ontologies have been used to
manage the used terms. Different ontologies have been proposed to elucidate
different fields. For instance, the Gene Ontology (GO) is one of the frameworks
that are largely used. Gene Ontology includes three main sub-ontologies:
Biological Process (BP), Molecular Function (MF), and Cellular Component
(CC). Each ontology stores and organizes biological concepts, called GO
Terms, used for describing functions, processes and localization of biological
molecules. Each GO term is uniquely identified by a code, it belongs to only
one ontology, and for each GO Term a textual description is also available. For
instance GO: 0006915 represents the apoptosis process.

Increasingly large amounts of valuable, but heterogeneous and sparse,

biomolecular data and information are characterizing life sciences. In particular,
semantic controlled annotations of biomolecular entities, i.e. the associations
between biomolecular entities (mainly genes and their protein products) and
controlled terms that describe the biomolecular entity features or functions, are
of great value; they support scientists with several terminologies and ontologies
describing structural, functional and phenotypic biological features of such
entities.

Data Mining, also popularly known as Knowledge Discovery in

Databases (KDD), refers to the nontrivial extraction of implicit, previously
unknown and potentially useful information from data in databases. While data
mining and knowledge discovery in databases (or KDD) are frequently treated
as synonyms, data mining is actually part of the knowledge discovery process.

The Knowledge Discovery in Databases process comprises of a few steps

leading from raw data collections to some form of new knowledge. The iterative
process consists of the following steps:

 Data cleaning: also known as data cleansing, it is a phase in which noise

data and irrelevant data are removed from the collection.
 Data integration: at this stage, multiple data sources, often
heterogeneous, may be combined in a common source.
 Data selection: at this step, the data relevant to the analysis is decided on
and retrieved from the data collection.
  Data transformation: also known as data consolidation, it is a phase in
which the selected data is transformed into forms appropriate for the
mining procedure.
 Data mining: it is the crucial step in which clever techniques are applied
to extract patterns potentially useful.
 Pattern evaluation: in this step, strictly interesting patterns representing
knowledge are identified based on given measures.
 Knowledge representation: is the final phase in which the discovered
knowledge is visually represented to the user. This essential step uses
visualization techniques to help users understand and interpret the data
mining results.

1.2 EXISTING SYSTEM

The existing system proposed association rules to support GO

curators. It evaluates the annotation consistency in order to avoid possible
inconsistent or redundant annotations. It uses the method called Classical
association rules mining algorithms. Understanding complex biological
phenomena involves answering complex biomedical questions on multiple
biomolecular information simultaneously, which are expressed through multiple
genomic and proteomic semantic annotations scattered in many distributed and
heterogeneous data sources; such heterogeneity and dispersion hamper the
biologists’ ability of asking global queries and performing global evaluations.
There is no common knowledge base for gene analysis.

DRAWBACKS:
  The disadvantage of this method is that Classical association rules mining
algorithms are not able to deal with different sources of production of GO
annotations.
 Consequently, when used on annotated data they produce candidate rules
with low Information Content.
 Consequently, a large amount of information is usually missed.

1.3 PROPOSED SYSTEM:

In our Project, we proposed co-regulatory modules between
Transcription Factor, gene and MiRNA on functional level with genomic data.
The integration technique is implemented between miRNA, Transcription
Factor (TF) and gene. After integration, Iterative Multiplicating update
algorithm is used to check the optimization function between the regulatory
modules. We get the expression or some value from this algorithm then
compare to protein values. The protein value get from Biological Process (BP),
Molecular Function (MF) and Cellular Component (CC) with the help of cross
ontology technique. At last we generate a bayseian rose tree structure for the
relation between regulatory modules and protein values of our gene. By this
structure we know our disease which was affected in our chromosome and also
know how to cure. Also we can identify the symptoms applicable for our gene
by our proposed system.

ADVANTAGES:

1. First initiative to create a common knowledge base for gene, protein,

transcription factors and MiRNA factors.
2. It would create a greater impact as scientist across world can update their
inventions in the medical fields and cure for dangerous diseases.
3. The patient can able to understand which particular enzyme is been
produced less or above the normal level and figure out the diagnosis, thus
eliminating medical errors.
4. Flexible and low cost application for identifying particular disease in the
early stage and detect the diagnosis.
 CHAPTER 2
LITERATURE SURVEY

2.1 INTEGRATION AND QUERYING OF GENOMIC AND

PROTEOMIC SEMANTIC ANNOTATIONS FOR BIOMEDICAL
KNOWLEDGE EXTRACTION
Problem: This research article states that the gene and protein research results
are been scattered. Multiple genomic and proteomic semantic annotations
scattered in many distributed and heterogeneous data sources; such
heterogeneity and dispersion hamper the biologists’ ability of asking global
queries and performing global evaluations.
Solution and Benefit: We developed a software architecture to create and
maintain a Genomic and Proteomic Knowledge Base (GPKB), which integrates
several of the most relevant sources of such dispersed information (including
Entrez Gene, UniProt, IntAct, Expasy Enzyme, GO, GOA, BioCyc, KEGG,
Reactome and OMIM).
Thus the proposed system assures consistency, quality and provenance tracking
of all integrated data and hierarchical relationships

2.2 SPATIAL GENE EXPRESSION DATA FOR ASSOCIATION RULES

Gene Expression Database (EMAGE) which is a high quality data source
for spatio-temporal gene expression patterns.
The research article describes two processes to form association rules based
on spatial configurations, one that associates spatial regions, the other associates
genes.
Thus this paper provides good knowledge about the gene association based on
association rules.
2.3 IMPROVING ANNOTATION QUALITY IN GENE ONTOLOGY BY
MINING CROSS-ONTOLOGY WEIGHTED ASSOCIATION RULES
We designed a novel algorithm, (GO-WAR), Mining Weighted Association
Rules from GO, that is based on the extraction of weighted association rules
considering the IC of terms.
This paper aims to provide a novel algorithm for mining annotations based on
weighted association rule mining.

2.4 OPTIMIZING GENOME FEATURES USING T-TEST TO

CLASSIFY THE GENE EXPRESSIONS AS CORONARY ARTERY
DISEASE PRONE AND SALUBRIOUS
In regard to this a substantial requirement is feature optimization, which is
since the overall genes observed in human body are closely 25000 and among
them 636 genes are cardio vascular related. Hence, it complexes the process of
training the machine learning models using these entire cardio vascular gene
features. Hence, this manuscript proposed the usage of ANOVA standard called
t-test to select optimal features.
The proposed model pools the values observed for a specific genome from the
records labelled as disease prone as a vector. Also pools the values observed for
same genome in set of records labelled as salubrious and estimates the t-score
between these two vectors using the test.

2.5 MINING SPATIAL GENE EXPRESSION DATA FOR

ASSOCIATION RULES
Description: This research article have used association rule mining to identify
relationships among up and down regulated genes in gene expression studies.
These studies do not make use of the GO and its hierarchical structure. Previous
research applying association rule mining to the GO includes studies mining
single level, multi-level and cross-ontology association rules.
2.6 INTEGRATED ANALYSIS OF GENE EXPRESSION BY
ASSOCIATION RULES DISCOVERY.
Description: This paper describes mine single level associations between GO
annotations and expressed genes from microarray data integrated with GO
annotation information. The approach does not utilize the inherent information
provided by the GO structure thereby limiting the knowledge discovered.
 CHAPTER 3
SYSTEM REQUIREMENTS
3.1 SOFTWARE REQUIREMENTS SPECIFICATION

• Operating System :Windows95/98/2000/XP

• Front End : HTML, Java, JSP,AJAX
• Scripts: JavaScript.
• Server side Script : Java Server Pages
• Database Connectivity: Mysql.

3.2 HARDWARE REQUIREMENTS SPECIFICATION

•      System: Pentium IV & above

•      Hard disk: 40GB or above
•      RAM: 1GB or above

CHAPTER 4
 FEASABILITY STUDY

 A Feasibility Study is the analysis of a problem to determine if it can be

solved effectively.

 The results determine whether the solution should be implemented.

 This activity takes place during the project initiation phase and is made
before significant expenses are engaged.

DEFINITION OF FEASIBILITY STUDY:

 A feasibility study is an evaluation of a proposal designed to determine

the difficulty in carrying out a designated task. Generally, a feasibility
study precedes technical development and project implementation.

 A feasibility study looks at the viability of an idea with an emphasis on

identifying potential problems and attempts to answer one main question:
Will the idea work and should you proceed with it?

OBJECTIVE:

 The feasibility study answers the basic questions: is it realistic to address

the problem or the opportunity under consideration?

 And it produce a final proposal for the management, this final report
might include.

FEASIBILITY INCLUDES:

 Project name

 Problem or opportunity definition

 Project description

 Expected benefit

 Consequence of rejection
  Resource requirements

 Alternatives

 Other consideration

 Theorization

FIVE COMMON FACTORS (TELOS)

1. Technology and system feasibility

2. Economic feasibility

3. Legal feasibility

4. Operational feasibility

5. Schedule feasibility

4.1 TECHNOLOGY AND SYSTEM FEASIBILITY

The assessment is based on an outline design of system requirements in

terms of Input, Processes, Output, Fields, Programs, and Procedures. This can
be quantified in terms of volumes of data, trends, frequency of updating, etc. in
order to estimate whether the new system will perform adequately or not this
means that feasibility is the study of the based in outline.

4.2 ECONOMIC FEASIBILITY

Economic analysis is the most frequently used method for evaluating the
effectiveness of a new system. More commonly known as cost/benefit analysis,
the procedure is to determine the benefits and savings that are expected from a
candidate system and compare them with costs. If benefits outweigh costs, then
the decision is made to design and implement the system. An entrepreneur must
accurately weigh the cost versus benefits before taking an action. Time Based.

4.3 LEGAL FEASIBILITY

 Determines whether the proposed system conflicts with legal
requirements, e.g. a data processing system must comply with the local Data
Protection Acts.

4.4 OPERATIONAL FEASIBILITY

Is a measure of how well a proposed system solves the problems, and

takes advantages of the opportunities identified during scope definition and how
it satisfies the requirements identified in the requirements analysis phase of
system development.

4.5 SCHEDULE FEASIBILITY

A project will fail if it takes too long to be completed before it is useful.

Typically this means estimating how long the system will take to develop, and if
it can be completed in a given time period using some methods like payback
period. Schedule feasibility is a measure of how reasonable the project timetable
is. Given our technical expertise, are the project deadlines reasonable? Some
projects are initiated with specific deadlines. You need to determine whether the
deadlines are mandatory or desirable.

CHAPTER 5
 SYSTEM ARCHITECTURE

CHAPTER 6
MODULE DESCRIPTION
Modules:
 1. Collaborative Filtering
2. Depth First Search
3. Multiplicative Update Algorithm
4. Tree Representation

6.1 COLLABORATIVE FILTERING

In our Project we used semantic mining for logical analysis. User get the
details from Ontology base with help of Collaborative filtering, also the gene
disease and symptoms with the help of logical calculation for protein value of
human and normal value for particular gene id, then cross ontology process we
get the BP,CC&MF value for gene to identify the gene have Intrinsic or
extrinsic.
I) Intrinsic:

If the normal protein value of human is compare to lower than that of

calculating cross ontology value (comparing BP&CC or MF&CC or MF&BP)
is said to be Intrinsic.

II) Extrinsic:

If the normal protein value of human is compare to higher than that of

calculating cross ontology value (comparing BP&CC or MF&CC or MF&BP)
is said to be extrinsic.
MOAL (Multi ontology data mining at all levels) algorithm for mines
the cross ontology relationship between the ontologies. MOAL algorithm to
mine cross-ontology association rules, i.e. rules that involve GO terms present
in the three sub-ontologies of GO.
By using collaborative filtering, user get the details about the gene id for
cross ontology technique we have to compare the protein value and getting BP&
MF value, or MF&CC value or CC&BP value getting the gene disease and
symptoms for user requirements.

6.2 DEPTH FIRST SEARCH

Depth first search in relation to specific domains such as searching for

solutions in artificial intelligence. The graph to be traversed is often either too
large to visit in its entirety or infinite. In this cases search is performed to
a depth due to limited resources. Such as memory or disk space one typically
does not use data structures to keep track the set of all previous visited vertices.
When DF search is performed to a limited depth the time is still linear in
terms to number of expanded vertices. Edges although this number is not the
same as the capacity of the entire graph because some vertices may be searched
more than once and others not at all but the space complexity of this variant of
DFS is only proportional to the depth limit. As a result is much smaller than
the space needed for searching to the same depth using BFS. DF search also
lends itself much better to heuristic methods for choosing a likely-looking
branch.

DFS is an iterative approach. the DFS implementation are as follows:

DFS(G, u)

u.visited = true

for each v ∈ G.Adj[u]

if v.visited == false

DFS(G,v)

init () {
 For each u ∈ G

u.visited = false

For each u ∈ G

DFS(G, u)

6.3 MULTIPLICATIVE UPDATE ALGORITHM

A novel approach to identify miRNAs and transcription factors co-
regulatory modules (miRNA-TF-gene) is essential. To this end, an objective
function is constructed by integrating the miRNA/TF/gene expression
profiles, target site information (miRNA-gene and TF-gene regulations) as
well as the protein-protein interactions. In order to obtain the optimal
solution of the objective function, we solve the optimization model function
effectively by iterative multiplicative updating algorithm.

6.4 TREE REPRESENTATION:

In this section, we briefly introduce the BRT algorithm. Bayesian

hierarchical clustering algorithm that can produce trees with arbitrary branching
structure at each node known as rose trees. We interpret these trees as mixtures
over partitions of a data set and use a computationally efficient greedy
agglomerative algorithm to find the rose trees which have high marginal
likelihood given the data.
CHAPTER 7
SOFTWARE DESCRIPTION

7.1 JAVA:
 Initially the language was called as “oak” but it was renamed as “java” in
1995.The primary motivation of this language was the need for a platform-
independent(i.e. architecture neutral)language that could be used to create
software to be embedded in various consumer electronic devices.

Java is a programmer’s language

Java is cohesive and consistent
Except for those constraint imposed by the Internet environment.
Java gives the programmer, full control

Finally Java is to Internet Programming where c was to System

Programming.
Importance of Java to the Internet
Java has had a profound effect on the Internet. This is because; java expands
the Universe of objects that can move about freely in Cyberspace. In a
network, two categories of objects are transmitted between the server and the
personal computer. They are passive information and Dynamic active
programs. in the areas of Security and probability. But Java addresses these
concerns and by doing so, has opened the door to an exciting new form of
program called the Applet.

Applications and applets. An application is a program that runs on our

Computer under the operating system of that computer. It is more or less like
one creating using C or C++ .Java’s ability to create Applets makes it important.
An Applet I san application, designed to be transmitted over the Internet and
executed by a Java-compatible web browser. An applet I actually a tiny Java
program, dynamically downloaded across the network, just like an image. But
the difference is, it is an intelligent program, not just a media file. It can be react
to the user input and dynamically change.
Java Architecture
Java architecture provides a portable, robust, high performing
environment for development. Java provides portability by compiling the
byte codes for the Java Virtual Machine, which is then interpreted on each
platform by the run-time environment. Java is a dynamic system, able to load
code when needed from a machine in the same room or across the planet.
Compilation of code
When you compile the code, the Java compiler creates machine code (called
byte code)for a hypothetical machine called Java Virtual Machine(JVM).
The JVM is supposed t executed the byte code. The JVM is created for the
overcoming the issue of probability. The code is written and compiled for
one machine and interpreted on all machines .This machine is called Java
Virtual Machine.

Java
Pc Java interpreter
compiler Byte
code
Java
Source Macintosh interpreter
code compiler Platform
macintosh
independ
ent
SPARC Java
Compiler interpreter(
SPARC)

)))

During run-time the Java interpreter tricks the byte code file into
thinking that it is running on a Java Virtual Machine. In reality this
could be an Intel Pentium windows 95 or sun SPARCstation running
 Solaris or Apple Macintosh running system and all could receive code
from any computer through internet and run the Applets.

7.2 JVM:
The Java Virtual Machine is the cornerstone of the Java platform. It is
the component of the technology responsible for its hardware- and operating
system independence, the small size of its compiled code, and its ability to
protect users from malicious programs. The Java Virtual Machine is an abstract
computing machine. Like a real computing machine, it has an instruction set
and manipulates various memory areas at run time. It is reasonably common to
implement a programming language using a virtual machine; the best-known
virtual machine may be the P-Code machine of UCSD Pascal. The first
prototype implementation of the Java Virtual Machine, done at Sun
Microsystems, Inc., emulated the Java Virtual Machine instruction set in
software
Hosted by a handheld device that resembled a contemporary Personal Digital
Assistant (PDA). Oracle's current implementations emulate the Java Virtual
Machine on mobile, desktop and server devices, but the Java Virtual Machine
does not assume any particular implementation technology, host hardware, or
host operating system. It is not inherently interpreted, but can just as well be
implemented by compiling its instruction set to that of a silicon CPU. It may
also be implemented in microcode or directly in silicon. The Java Virtual
Machine knows nothing of the Java programming language, only of a particular
binary format, the class file format. A class file contains Java Virtual Machine
instructions (or byte codes) and a symbol table, as well as other Ancillary
information. For the sake of security, the Java Virtual Machine imposes strong
syntactic and structural constraints on the code in a class file. However, any
language with Functionality that can be expressed in terms of a valid class file
can be hosted by the Java Virtual Machine. Attracted by a generally available,
machine-independent platform, implementers of other languages can turn to the
Java Virtual Machine as a delivery vehicle for their languages. The Java Virtual
Machine specified here is compatible with the Java SE 7 platform, and supports
the Java programming language specified in The Java Language Specification,
Java SE 7 Edition.
Object oriented
Java was not designed to be source-code compatible with any other
language. This allowed the Java team the freedom to design with a blank
state. One outcome of this was a clean usable, pragmatic approach to objects.
The object model in Java is simple and easy to extend, while simple types,
such as integers, are kept as high-performance non-objects.
Robust
The multi-platform environment of the web places extraordinary demands on
a program, because the program must execute reliably in a variety of
systems. The ability to create robust programs. Was given a high priority in
the design of Java. Java is strictly typed language; it checks your code at
compile time and runtime.
Java virtually eliminates the problems of memory management and deal
location, which is completely automatic. In a well-written Java program, all
run-time errors can and should be managed by your program.

7.3 JSP
The most significant of the many good reasons for this is that it is
amazingly easy to develop sophisticated Web sites with JSPs. Anyone who can
write HTML can quickly create rich, dynamic, and responsive Web sites that
enable users to get the most out of their online time. Through a mechanism
called JavaBeans, JSPs have made it possible for large teams or individuals
working on complex projects to divide the work in such a way as to make each
piece simple and manageable, without sacrificing any power. JSPs also provide
a great deal of flexibility when generating HTML, through the ability to create
HTML-like custom tags.
In addition to this fundamental ease of development, high-quality JSP
tools are readily available and easy to use. Developers do not need to buy
expensive software or commit to a particular operating system in order to use
JSPs. The CD-ROM accompanying this book contains everything a JSP author
needs to get started, and the tools are powerful enough to serve even a midsized
Web site without problems. These free, open-source tools are stable and secure
and run on nearly every platform. Of course, high-quality commercial JSP tools
are available as well, suitable for serving even the most complex and high-
traffic Web sites. Although JSPs have been useful and powerful since the
beginning, this is an especially exciting time to be a JSP developer. The recently
released version 2.0 of the JSP
Specification provides even more features that simplify the process of creating
Web sites. In addition, a standard tag library that provides many JSP tags that
solve a wide range of common problems has been released. Finally, in the time
since they were released, a number of best practices for using JSPs have
emerged. This book covers all the topics: the basic powerful features of the JSP
specification, the improvements introduced with version 2.0, as well as the new
standard tag library and all the things it does. In addition, this book discusses
how best to use these tools, based on real-world experiences. However, before
we get into all the fun, let's take a look back at how the Web has evolved. This
will highlight the kinds of problems that Web authors have faced since the 12
beginning. Once this is understood, it will be clear how JSPs solve these
problems and make page creation so easy.

SERVLETS:
Java Servlets are programs that run on a Web or Application server and act as a
middle layer between a requests coming from a Web browser or other HTTP
client and databases or applications on the HTTP server.

Using Servlets, you can collect input from users through web page forms,
present records from a database or another source, and create web pages
dynamically.

Java Servlets often serve the same purpose as programs implemented using the
Common Gateway Interface (CGI). But Servlets offer several advantages in
comparison with the CGI. Performance is significantly better. Servlets execute
within the address space of a Web server. It is not necessary to create a separate
process to handle each client request. Servlets are platform-independent because
they are written in Java. Java security manager on the server enforces a set of
restrictions to protect the resources on a server machine. So servlets are trusted.
The full functionality of the Java class libraries is available to a servlet. It can
communicate with applets, databases, or other software via the sockets and RMI
mechanisms that you have seen already.

SERVLET ARCHITECTURE:
 Servlets Perform The Following Major Tasks:

 Read the explicit data sent by the clients (browsers). This includes an HTML
form on a Web page or it could also come from an applet or a custom HTTP
client program.
 Read the implicit HTTP request data sent by the clients (browsers). This
includes cookies, media types and compression schemes the browser
understands, and so forth.
 Process the data and generate the results. This process may require talking to a
database, executing an RMI or CORBA call, invoking a Web service, or
computing the response directly.
 Send the explicit data (i.e., the document) to the clients (browsers). This
document can be sent in a variety of formats, including text (HTML or XML),
binary (GIF images), Excel, etc.
 Send the implicit HTTP response to the clients (browsers). This includes telling
the browsers or other clients what type of document is being returned (e.g.,
HTML), setting cookies and caching parameters, and other such tasks.
7.4 CSS

While (X)HTML is used to describe the content in a web page, it is

Cascading Style Sheets (CSS) that describe how you want that content to look.
In the web design biz, the way the page looks is known as its presentation. CSS
is now the official and standard mechanism for formatting text and page
layouts. CSS also provides methods for controlling how documents will be
presented in media other than the traditional browser on a screen, such as in
print and on handheld devices. It also has rules for specifying the non-visual
presentation of documents, such as how they will sound when read by a screen
reader. Style sheets are also a great tool for automating production, because you
can make changes to all the pages in your site by editing a single style sheet
document. Style sheets are supported to some degree by all modern browsers.

Although it is possible to publish web pages using (X)HTML alone, you’ll

probably want to take on style sheets so you’re not stuck with the browser’s
default styles. If you’re looking into designing web sites professionally,
proficiency at style sheets is mandatory.

7.5 XML

XML stands for Extensible Markup Language. It is a text-based markup

language derived from Standard Generalized Markup Language (SGML).

XML tags identify the data and are used to store and organize the data,
rather than specifying how to display it like HTML tags, which are used to
display the data. XML is not going to replace HTML in the near future, but it
introduces new possibilities by adopting many successful features of HTML.

There are three important characteristics of XML that make it useful in a

variety of systems and solutions:
  XML is extensible: XML allows you to create your own self-descriptive
tags, or language, that suits your application.
 XML carries the data, does not present it: XML allows you to store
the data irrespective of how it will be presented.
 XML is a public standard: XML was developed by an organization
called the World Wide Web Consortium (W3C) and is available as an
open standard.

A short list of XML usage says it all:

 XML can work behind the scene to simplify the creation of HTML
documents for large web sites.
 XML can be used to exchange the information between organizations
and systems.
 XML can be used for offloading and reloading of databases.
 XML can be used to store and arrange the data, which can customize
your data handling needs.
 XML can easily be merged with style sheets to create almost any desired
output.
 Virtually, any type of data can be expressed as an XML document.

7.6 NET BEANS

Net Beans IDE is the official IDE for Java 8. With its editors, code
analyzers, and converters, you can quickly and smoothly upgrade your
applications to use new Java 8 language constructs, such as lambdas, functional
operations, and method references. Batch analyzers and converters are provided
to search through multiple applications at the same time, matching patterns for
conversion to new Java 8 language constructs. With its constantly improving
Java Editor, many rich features and an extensive range of tools, templates and
samples, Net Beans IDE sets the standard for developing with cutting edge
technologies out of the box.

7.7 APACHE TOMCAT SERVER

Tomcat is a Java servlet container and web server from the Jakarta project
of the Apache Software Foundation (http://jakarta.apache.org). A web server is,
of course, the program that dishes out web pages in response to requests from a
user sitting at a web browser. But web servers aren’t limited to serving up static
HTML pages; they can also run programs in response to user requests and
return the dynamic results to the user’s browser. This is an aspect of the web
that Apache’s Tomcat is very good at because Tomcat provides both Java
servlet and Java Server Pages (JSP) technologies (in addition to traditional static
pages and external CGI programming). The result is that Tomcat is a good
choice for use as a web server for many applications. And it’s a very good
choice if you want a free, open source (http://opensource.org/) servlet and JSP
engine. Tomcat can be used stand-alone, but it is often used “behind” traditional
web servers such as Apache http, with the traditional server serving static pages
and Tomcat serving dynamic Servlet and JSP requests. No matter what we call
Tomcat, a Java servlet container or servlet and JSP engine, we mean Tomcat
provides an environment in which servlets can run and JSP can be processed.
Similarly, we can absolutely say a CGI-enabled Web server is a CGI program
container or engine since the server can accommodate CGI programs and
communicate with them according to CGI specification. Between Tomcat and
the servlets and JSP code residing on it, there is also a standard regulating their
interaction, servlet and JSP specification, which is in turn a part of Sun’s J2EE
(Java 2 Enterprise Edition).
7.8 MY SQL

MySQL is (as of March 2014) the world's second most widely

used open-source relational database management system (RDBMS). It is
named after co-founder Michael Widenius's daughter, My. The SQL phrase
stands for Structured Query Language.The MySQL development project have
made its source code available under the terms of the GNU General Public
License, as well as under a variety of proprietary agreements. MySQL was
owned and sponsored by a single for-profit firm, the Swedish company MySQL
AB, now owned by Oracle Corporation. MySQL is a popular choice of database
for use in web applications, and is a central component of the widely
used LAMP open source web application software stack (and
other 'AMP' stacks). LAMP is an acronym for "Linux, Apache, MySQL, and
Perl/PHP/Python." Free-software-open source projects that require a full-
featured database management system often use MySQL. Applications which
use MySQL databases include: TYPO3, MODx, Joomla, Word
Press, phpBB, MyBB, Drupal and other software. MySQL is also used in many
high-profile, large-scale websites, including Google (though not for
searches), Face book, Twitter, Flickr, and YouTube.

7.9 SQL YOG:

SQLyog is a GUI tool for the RDBMS MySQL. It is developed by

Webyog, Inc. based out of Bangalore, India and Santa Clara, California.
SQLyog is being used by more than 30,000 customers worldwide and has been
downloaded more than 2,000,000 times.

CHAPTER 8
SYSTEM TESTING

Testing is an important step in software development life cycle. The

process of testing takes place at various stages of development in programming.
This is a vital step in development life cycle because the process of testing helps
to identify the mistakes and sends the program for correction.
This process gets repeated at various stages until the final unit or program
is found to be complete thus giving a total quality to the development process.
The various levels and types of testing found in a software development life
cycle are as follows:
1. White Box Testing
2. Black Box Testing
3. Unit Testing
4. Regression Testing
5. Integration Testing
6. Smoke Testing
7. Alpha Testing
8. Beta Testing
After getting an idea of what all to be tested by communicating with
developers and others in the design phase of the software development life cycle
the testing stage carries on parallel. Test plan is made ready during the planning
stage of testing. This test plan has details like environment of setting like
software, hardware, operating system used, the scope and limitation of testing,
test type and so on. In the next phase the test case is prepared which has details
of each step for module to be checked, input which can be used for each action
are described and recorded for testing. It also has details about what is the
expected outcome or expected result of each action.
The next phase is the actual testing phase. In this phase the testers make
testing based on the test plan and test case made ready and record the output or
result resulting from each module. Thus the actual output is recorded. Then a
report is made to find the error or defect between expected outcome and actual
output in each module in each step. This is sent for rework for developers and
testing cycle again continues as above.
8.1 White Box Testing
For doing this testing process the person have to acess to the source code
of the product to be tested. So it is essential that the person doing this white box
testing have some knowledge of the program being tested. Though not
necessary it would be more worth if the programmer itself does this white box
testing process since this testing process requires the handling of source code.

8.2 Black Box Testing (Functional Testing)

This is otherwise called as functional testing. In contrary to white box
testing here the person who is doing the black box testing need not have the
programming knowledge. This is because the person doing the black box testing
would access the output or outcomes as the end user would access and would
perform thorough functionality testing to check whether the developed module
or product behaves in functionality in the way it has to be.
8.3 Unit Testing
This testing is done for each module of the program to ensure the validity
of each module. This type of testing is done usually by developers by writing
test cases for each scenarios of the module and writing the results occurring in
each step for each module.
8.4 Regression Testing
We all know that development life cycle is subjected to continuous
changes as per the requirements of user. Suppose if there is a change in the
existing system which has already been tested it is essential that one has to
make sure that this new changes made to the existing system do not affect the
existing functionality. For ensuring this regression testing is done.
8.5 Integration Testing
By making unit testing for each module as explained above the process of
integrated testing as a whole becomes simpler. This is because by correcting
mistakes or bugs in each module the integration of all units as a system and
testing process becomes easier. So one might think why the integration is
testing needed. The answer is simple. It is needed because unit testing ad
explained test and assures correctness of only each module. But it does not
cover the aspects of how the system would behave or what error would be
reported when modules are integrated. This is done in the level of integration
Testing.
8.6 Smoke Testing
This is also called as sanity testing. This is mainly used to identify
environmental related problems and is performed mostly by test manager. For
any application it is always necessary to have the environment first checked for
smooth running of the application. So in this testing process the application is
run in the environment technically called as dry run and checked to find that the
application could run without any problem or abend in between.
8.7 Alpha Testing
The above different testing process described takes place in different
stages of development as per the requirement and needs. But a final testing is
always made after a full finished product that is before it released to end users
and this is called as alpha testing. The alpha testing involves both the white box
testing and black box testing thus making alpha testing to be carried out in two
phases.
8.8 Beta Testing
This process of testing is carried out to have more validity of the software
developed. This takes place after the alpha testing. After the alpha phase also
the generally the release is not made fully to all end users. The product is
released to a set of people and feedback is got from them to ensure the valididy
of the product. So here normally the testing is being done by group of end users
and therefore this beta testing phase covers black box testing or functionality
testing only.
 Having seen about testing levels and types it does not mean that the
system released is bug free or error free hundred percent. This is because no real
system could have null percentage error. But an important point to bear in mind
is that a system developed is a quality system only if the system could run for a
period of time after its release without error and after this time period only
minimal errors are reported. For achieving this testing phase plays an essential
role in software development life cycle.

8.9 TESTING METHODOLOGIES

All testes should be traceable to customer requirements. The focus of
testing will shift progressively from programs, to individual modules and finally
to the entire project. To be more effective, testing should be one, which has
highest probability of finding errors. The testing procedure that has been used is
as follows:
Source Code Testing
This examines the logic of the system. If we are getting the output that is
required by the user, then we can say that the logic is perfect.
Specification Testing
We can set with, what program should do and how it should perform
under various condition. This testing is a comparative study of evolution of
system performance and system requirements.

Module Level Testing

In this the error will be found at each individual module, It encourages
the programmer to find and rectify the errors without affecting the other
modules.
Unit Testing
 Unit testing focuses on verifying the effort on the smallest unit of
software module. The local data structure is examined to ensure that the data
stored temporarily maintains its integrity during all steps in the algorithm’s
execution. Boundary conditions are tested to ensure that the module operates
properly at boundaries established to limit.
Output Testing
After performing the validation testing, the next step is output testing of
the proposed system since no system would be termed as useful until it does
produce the required output in the specified format. Output format is considered
in two ways, the screen format and the printer format.
User Acceptance Testing
User acceptance testing is the key factor for the success of any system.
The system under consideration is tested for user acceptance by constantly
keeping in touch with prospective system users at the time of developing and
making changes whenever required. Acceptance testing involves planning and
execution of functional tests. Performance tests and stress tests in order to
demonstrate that the implemented system satisfied its requirements. When
custom software its bulid for one customer, a series of acceptance tests are
conducted to enable the customer to validate all requirements. In fact
acceptance cumulative errors that might degrade the system over time will
incorporate test cases developed during integration testing, Additional testing
cases are added to achieve the desired level functional, performance and stress
testing of the entire system.
Integration Testing
Integration Testing is the phase of software testing in which individual
software modules are combined and tested as a group. It follows unit testing and
precedes system testing.
Integration testing takes as its input modules that have been checked out by unit
testing groups them in larger aggregates, applies tests, and delivers as its output
the integrated system ready for system testing.

CHAPTER 9
CONCLUSION
Relevant progresses in biotechnology and system biology are creating a 
remarkable amount of biomolecular data and semantic annotations; they increas
e in number and quality, but are dispersed and only partially connected. Integrat
ion and mining of these distributed and evolving data and information have the 
high potential of discovering hidden biomedical knowledge useful in understand
ing complex biological phenomena, normal or pathological, and ultimately of en
hancing diagnosis, prognosis and treatment; but such integration poses huge cha
llenges. Our work has tackled them by developing a novel and generalized way 
to define and easily maintain updated and extend an integration of many evolvin
g and heterogeneous data sources; our approach proved useful to extract biomed
ical knowledge about  complex biological processes and diseases. 

CHAPTER 10
APPENDICES
10.1 CODING
REG

import java.io.IOException;
import java.io.PrintWriter;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;
import javax.swing.JOptionPane;
public class register extends HttpServlet
{
protected void processRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException, ClassNotFoundException, SQLException
{
response.setContentType("text/html;charset=UTF-8");
try (PrintWriter out = response.getWriter()) {
String name=request.getParameter("name");
String gender=request.getParameter("gender");

String dob=request.getParameter("dob");
String phone=request.getParameter("phone");
String email=request.getParameter("email");
String city=request.getParameter("city");
String uname=request.getParameter("uname");
String psw=request.getParameter("psw");
HttpSession session=request.getSession();
session.setAttribute("un",uname);
session.setAttribute("na",name);
try {
Class.forName("com.mysql.jdbc.Driver");
Connection
con=DriverManager.getConnection("jdbc:mysql://localhost:3306/gene","root","root");
Statement st=con.createStatement();

String sql="insert into reg

values('"+name+"','"+psw+"','"+email+"','"+phone+"','"+gender+"','"+city+"')";
st.executeUpdate(sql);
out.println("<script type=\"text/javascript\">");
out.println("alert('Registered Successfully')");
out.println("location='login.jsp'");
out.println("</script>");
}
catch(Exception e)
 {
JOptionPane.showMessageDialog(null, e);
}
}
}
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
try {
processRequest(request, response);
} catch (ClassNotFoundException ex) {
Logger.getLogger(register.class.getName()).log(Level.SEVERE, null, ex);
} catch (SQLException ex) {
Logger.getLogger(register.class.getName()).log(Level.SEVERE, null, ex);
}
}

protected void doPost(HttpServletRequest request, HttpServletResponse response)

throws ServletException, IOException {
try {
processRequest(request, response);
} catch (ClassNotFoundException ex) {
Logger.getLogger(register.class.getName()).log(Level.SEVERE, null, ex);
} catch (SQLException ex) {
Logger.getLogger(register.class.getName()).log(Level.SEVERE, null, ex);
}
}

public String getServletInfo() {

return "Short description";
}// </editor-fold>

LOGIN

import java.io.IOException;
import java.io.PrintWriter;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;
import javax.swing.JOptionPane;

public class login extends HttpServlet

{
protected void processRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException, ClassNotFoundException, SQLException {
response.setContentType("text/html;charset=UTF-8");
try (PrintWriter out = response.getWriter()) {
/* TODO output your page here. You may use following sample code. */
String un=request.getParameter("uname");
String pw=request.getParameter("psw");
String pos=request.getParameter("pos");
HttpSession session=request.getSession();
session.setAttribute("uname",un);
try {
if(!un.equals("admin"))
{
Class.forName("com.mysql.jdbc.Driver");
Connection
con=DriverManager.getConnection("jdbc:mysql://localhost:3306/gene","root","root");
Statement st=con.createStatement();

String username="Select * from reg where username= '"+un+"' and

password='"+pw+"' ";
ResultSet rs=st.executeQuery(username);
if(rs.next())
{
out.println("<script type=\"text/javascript\">");
out.println("alert('Login Success');");
out.println("location='home.jsp'");
out.println("</script>");
}
else
{
out.println("<script type=\"text/javascript\">");
out.println("alert('Wrong Username or Password');");
out.println("location='login.jsp'");
out.println("</script>");
}
}
else
{
if(un.equals("admin")&&pw.equals("admin123"))
{
out.println("<script type=\"text/javascript\">");
out.println("alert('Login Success');");
out.println("location='admin.jsp'");
out.println("</script>");
}
else
 {
out.println("<script type=\"text/javascript\">");
out.println("alert('Login Failed');");
out.println("location='admin.jsp'");
out.println("</script>");
}
}
}
catch(Exception e)
{
JOptionPane.showMessageDialog(null, e);
}
}
}

protected void doGet(HttpServletRequest request, HttpServletResponse response)

throws ServletException, IOException {
try {
processRequest(request, response);
} catch (ClassNotFoundException ex) {
Logger.getLogger(login.class.getName()).log(Level.SEVERE, null, ex);
} catch (SQLException ex) {
Logger.getLogger(login.class.getName()).log(Level.SEVERE, null, ex);
}
}

protected void doPost(HttpServletRequest request, HttpServletResponse response)

throws ServletException, IOException {
try {
processRequest(request, response);
} catch (ClassNotFoundException ex) {
Logger.getLogger(login.class.getName()).log(Level.SEVERE, null, ex);
} catch (SQLException ex) {
Logger.getLogger(login.class.getName()).log(Level.SEVERE, null, ex);
}
}

public String getServletInfo() {

return "Short description";
}// </editor-fold>

UPLOAD
import Cloudme.CloudmeUser;
import java.io.IOException;
import java.io.PrintWriter;
import javax.servlet.RequestDispatcher;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.swing.JOptionPane;

public class upload extends HttpServlet {

protected void processRequest(HttpServletRequest request, HttpServletResponse response)

throws ServletException, IOException {
response.setContentType("text/html;charset=UTF-8");
try (PrintWriter out = response.getWriter()) {
try
{
String fnam=request.getParameter("id");
String path = "D:\\file\\gene\\ori\\"+fnam;

CloudmeUser user=new CloudmeUser("ccaf","ccaf123");

user.getFileManager().uploadFile(path,"/Personaldetails/");
user.killUser();
JOptionPane.showMessageDialog(null, "upload Success");
RequestDispatcher rd = request.getRequestDispatcher("history.jsp");
rd.forward(request, response);
}
catch(Exception e)
{
JOptionPane.showMessageDialog(null, e);
RequestDispatcher rd = request.getRequestDispatcher("history.jsp");
rd.forward(request, response);
}
}
}
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
processRequest(request, response);
}

protected void doPost(HttpServletRequest request, HttpServletResponse response)

throws ServletException, IOException {
processRequest(request, response);
}

public String getServletInfo() {

return "Short description";
}// </editor-fold>

ADMIN
<%@page import="org.apache.poi.ss.usermodel.Cell"%>
<%@page import="org.apache.poi.ss.usermodel.Row"%>
<%@page import="java.util.Iterator"%>
<%@page import="org.apache.poi.xssf.usermodel.XSSFSheet"%>
<%@page import="org.apache.poi.xssf.usermodel.XSSFWorkbook"%>
<%@page import="java.io.FileInputStream"%>
<%@page import="java.io.File"%>
<%@page import="javax.swing.JOptionPane"%>
<%@page import="java.sql.ResultSet"%>
<%@page import="java.sql.DriverManager"%>
<%@page import="java.sql.Statement"%>
<%@page import="java.sql.Connection"%>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Ontology</title>
<meta property="og:url" content="http://www.valeron.net/index.html" />
<meta property="og:type" content="website" />
<meta property="og:title" content="Free responsive web template Istria" />
<meta property="og:description" content="Free responsive web template Istria 1 by Valeron
design studio" />
<meta property="og:image" content="http://www.valeron.net/img/valeron-artist.jpg" />
<meta name="description" content="Free responsive web template Istria 1 by Valeron design
studio" />
<meta name="msapplication-tap-highlight" content="no" />
<meta name="robots" content="index,follow,all" />
<meta name="keywords" content="Izrada web stranica, web studio Istra" />
<meta name="author" content="Valeron design studio" />
<link rel="apple-touch-icon" sizes="57x57" href="img/apple-touch-icon-57x57.png">
<link rel="apple-touch-icon" sizes="60x60" href="img/apple-touch-icon-60x60.png">
<link rel="apple-touch-icon" sizes="72x72" href="img/apple-touch-icon-72x72.png">
<link rel="apple-touch-icon" sizes="76x76" href="img/apple-touch-icon-76x76.png">
<link rel="apple-touch-icon" sizes="114x114" href="img/apple-touch-icon-114x114.png">
<link rel="apple-touch-icon" sizes="120x120" href="img/apple-touch-icon-120x120.png">
<link rel="apple-touch-icon" sizes="144x144" href="img/apple-touch-icon-144x144.png">
<link rel="apple-touch-icon" sizes="152x152" href="img/apple-touch-icon-152x152.png">
<link rel="apple-touch-icon" sizes="180x180" href="img/apple-touch-icon-180x180.png">
<link rel="icon" type="image/png" href="img/favicon-32x32.png" sizes="32x32">
<link rel="icon" type="image/png" href="img/android-chrome-192x192.png"
sizes="192x192">
<link rel="icon" type="image/png" href="img/favicon-96x96.png" sizes="96x96">
<link rel="icon" type="image/png" href="img/favicon-16x16.png" sizes="16x16">
<link rel="manifest" href="img/manifest.json">
<meta name="msapplication-TileColor" content="#da532c">
<meta name="msapplication-TileImage" content="img/mstile-144x144.png">
<meta name="theme-color" content="#ffffff">
<link rel="stylesheet" href="css/animsition.min.css">
<link rel="stylesheet" type="text/css" href="css/grid.min.css" />
<link rel="stylesheet" type="text/css" href="css/style.css" />
<link rel="stylesheet" type="text/css" href="css/menu.css" />
<link rel="stylesheet" type="text/css" href="css/overlay.css" />
<link rel="stylesheet" type="text/css" href="css/owl.carousel.css">
<link rel="stylesheet"
href="https://cdnjs.cloudflare.com/ajax/libs/animate.css/3.5.1/animate.min.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.5.0/css/
font-awesome.min.css">
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.8.3/modernizr.min.js"></
script>
</head>
<body>
<%
String uname=(String)session.getAttribute("uname");

%>
<div class="animsition-overlay">
<div id="section-1">
<header class="main_h">
<div class="menufix"> <a class="logo" href="index.html"><img src="images/logo-
sample.png" alt="Hello"></a>
<div class="mobile-toggle"> <span></span> <span></span> <span></span> </div>
<nav>
<ul>
<li><a class="out active animsition-link" href="admin.jsp">HOME</a></li>
<!--<li class="line"><a class="out animsition-link" href="asso.jsp"></a>Gene
List</li>-->
<li class="line"><a class="out animsition-link" href="asso1.jsp">Gene Disease
List</a></li>
<li class="line"><a class="out animsition-link" href="adminupload.jsp">Update
Gene</a></li>
<!--<li class="line"><a class="out animsition-link"
href="genelist.jsp">History</a></li>-->
<li class="line"><a class="out animsition-link" href="login.jsp">LOGOUT</a></li>

</ul>
</nav>
</div>
<!-- / row -->

</header>
<div class="hero">
<h1 id="title-1">WELCOME<em><%=uname%></em></h1>

<!-- /.social-btn-container -->

<div class="fixbottarro"> <a class="scroll" href="#section-2">Scroll for more</a>

</div>
</div>
 <!-- /.hero -->
</div>
<center>
<h1 style="margin-left: 50px">GENE lIST</h1>
<!--<h2 style="margin-left: 500px">list of genes and their id</h2>-->
<table style="margin-left: 100px;width: 700px;background-color:
darkgray;padding: 20px">
<tr><td><strong>Serial No</strong></td><td><strong>Gene
Name</strong></td><td><strong>Gene ID</strong></td></tr>
<%
try
{
int j=0;
File myFile = new File("D://as//geneid.xlsx");
FileInputStream fis = new FileInputStream(myFile);
XSSFWorkbook myWorkBook = new XSSFWorkbook(fis);
XSSFSheet mySheet = myWorkBook.getSheetAt(0);
Iterator<Row> rowIterator = mySheet.iterator();
while (rowIterator.hasNext()) {
String th="";
Row row = rowIterator.next();
Iterator<Cell> cellIterator = row.cellIterator();
int i=0;

while (cellIterator.hasNext()) {
i++;

Cell cell = cellIterator.next();

switch (cell.getCellType())
{
case Cell.CELL_TYPE_STRING:
th=(String)cell.getStringCellValue();
// System.out.print(one);
// th=th+"zzz"+one;
break;

case Cell.CELL_TYPE_NUMERIC:
double d=cell.getNumericCellValue();
th=""+d;
break;
// case Cell.CELL_TYPE_BOOLEAN:
// System.out.print(cell.getBooleanCellValue() + "\t");
// break;
default :
}
if(j!=0)
{
%>

<%
 if(i==1)
{
%>
<tr><td><%=j%></td><td><%=th%></td>
<%
}
else if(i==2)
{
%>
<td><%=th.replace(".0","")%></td></tr>
<%
}
}

}
j++;
}
}
catch(Exception e)
{
JOptionPane.showMessageDialog(null, e);
}
%>
</table></center>

<div class="colw_6 paddbott100 spec-r">

</div>
<!-- END col_6 -->

</div>
<!-- END row -->

<!-- End GRID FLEX -->

<!-- END .animsition-overla -->

<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
<script type="text/javascript" src="js/jquery.matchHeight-min.js"></script>
<script src="js/wow.min.js"></script>
<script src="js/animsition.min.js"></script>
<script src="http://cdnjs.cloudflare.com/ajax/libs/jquery-easing/1.3/jquery.easing.min.js"></
script>
<script src="js/jquery.parallax-scroll.js"></script>
<script src="js/owl.carousel.min.js"></script>
<script src="js/jquery.cbpQTRotator.min.js"></script>
<script>
$(document).ready(function() {
 $("#owl-partners").owlCarousel({

autoPlay: 4000,
stopOnHover : true,
pagination : false,
items : 5,
itemsDesktop : [1199,4],
itemsDesktopSmall : [959,3]
});
});
</script>
<script>
$( function() {
$( '#cbp-qtrotator' ).cbpQTRotator();
});
</script>
<script src="js/functions.js"></script>
<script src="js/particle.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-15815880-3']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-
analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</body>
</html>

USER
<%@page import="java.sql.ResultSet"%>
<%@page import="java.sql.DriverManager"%>
<%@page import="java.sql.Statement"%>
<%@page import="java.sql.Connection"%>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Ontology</title>
<meta property="og:url" content="http://www.valeron.net/index.html" />
<meta property="og:type" content="website" />
<meta property="og:title" content="Free responsive web template Istria" />
<meta property="og:description" content="Free responsive web template Istria 1 by Valeron
design studio" />
<meta property="og:image" content="http://www.valeron.net/img/valeron-artist.jpg" />
<meta name="description" content="Free responsive web template Istria 1 by Valeron design
studio" />
<meta name="msapplication-tap-highlight" content="no" />
<meta name="robots" content="index,follow,all" />
<meta name="keywords" content="Izrada web stranica, web studio Istra" />
<meta name="author" content="Valeron design studio" />
<link rel="apple-touch-icon" sizes="57x57" href="img/apple-touch-icon-57x57.png">
<link rel="apple-touch-icon" sizes="60x60" href="img/apple-touch-icon-60x60.png">
<link rel="apple-touch-icon" sizes="72x72" href="img/apple-touch-icon-72x72.png">
<link rel="apple-touch-icon" sizes="76x76" href="img/apple-touch-icon-76x76.png">
<link rel="apple-touch-icon" sizes="114x114" href="img/apple-touch-icon-114x114.png">
<link rel="apple-touch-icon" sizes="120x120" href="img/apple-touch-icon-120x120.png">
<link rel="apple-touch-icon" sizes="144x144" href="img/apple-touch-icon-144x144.png">
<link rel="apple-touch-icon" sizes="152x152" href="img/apple-touch-icon-152x152.png">
<link rel="apple-touch-icon" sizes="180x180" href="img/apple-touch-icon-180x180.png">
<link rel="icon" type="image/png" href="img/favicon-32x32.png" sizes="32x32">
<link rel="icon" type="image/png" href="img/android-chrome-192x192.png"
sizes="192x192">
<link rel="icon" type="image/png" href="img/favicon-96x96.png" sizes="96x96">
<link rel="icon" type="image/png" href="img/favicon-16x16.png" sizes="16x16">
<link rel="manifest" href="img/manifest.json">
<meta name="msapplication-TileColor" content="#da532c">
<meta name="msapplication-TileImage" content="img/mstile-144x144.png">
<meta name="theme-color" content="#ffffff">
<link rel="stylesheet" href="css/animsition.min.css">
<link rel="stylesheet" type="text/css" href="css/grid.min.css" />
<link rel="stylesheet" type="text/css" href="css/style.css" />
<link rel="stylesheet" type="text/css" href="css/menu.css" />
<link rel="stylesheet" type="text/css" href="css/overlay.css" />
<link rel="stylesheet" type="text/css" href="css/owl.carousel.css">
<link rel="stylesheet"
href="https://cdnjs.cloudflare.com/ajax/libs/animate.css/3.5.1/animate.min.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.5.0/css/
font-awesome.min.css">
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.8.3/modernizr.min.js"></
script>
</head>
<body>
<%
String uname=(String)session.getAttribute("uname");

%>
<div class="animsition-overlay">
<div id="section-1">
<header class="main_h">
<div class="menufix"> <a class="logo" href="index.html"><img src="images/logo-
sample.png" alt="Hello"></a>
<div class="mobile-toggle"> <span></span> <span></span> <span></span> </div>
<nav>
<ul>
 <li><a class="out active animsition-link" href="home.jsp">HOME</a></li>
<!--<li class="line"><a class="out animsition-link" href="asso.jsp"></a>Gene
List</li>-->
<li class="line"><a class="out animsition-link" href="asso.jsp">Gene List</a></li>
<li class="line"><a class="out animsition-link" href="go.jsp">Search Gene</a></li>
<li class="line"><a class="out animsition-link" href="history.jsp">History</a></li>
<li class="line"><a class="out animsition-link" href="login.jsp">LOGOUT</a></li>

</ul>
</nav>
</div>
<!-- / row -->

</header>
<div class="hero">
<h1 id="title-1">WELCOME<em><%=uname%></em></h1>

<!-- /.social-btn-container -->

<div class="fixbottarro"> <a class="scroll" href="#section-2">Scroll for more</a>

</div>
</div>

<!-- /.hero -->

</div>
<center>
<table border="4" style="border: #080808;size:40px ">
<%
try
{
Class.forName("com.mysql.jdbc.Driver");
Connection
con=DriverManager.getConnection("jdbc:mysql://localhost:3306/gene","root","root");
Statement st=con.createStatement();
String username="Select * from reg where username='"+uname+"' ";
ResultSet rs=st.executeQuery(username);
while(rs.next()){
String name=rs.getString(1);
String ge=rs.getString(5);
String email=rs.getString(3);
String mbl=rs.getString(4);
// String dob=rs.getString(3);
String add=rs.getString(6);
%>
<tr><td>NAME</td><td><%=name%></td></tr>
<tr><td>GENDER</td><td><%=ge%></td></tr>
<tr><td>MOBILE</td><td><%=mbl%></td></tr>
<tr> <td>EMAIL</td><td><%=email%></td></tr>
<tr><td>CITY</td><td><%=add%></td></tr>
 <%
} } finally {

}%>
</table></center>

<div class="colw_6 paddbott100 spec-r">

</div>
<!-- END col_6 -->

</div>
<!-- END row -->

<!-- End GRID FLEX -->

<!-- END .animsition-overla -->

<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
<script type="text/javascript" src="js/jquery.matchHeight-min.js"></script>
<script src="js/wow.min.js"></script>
<script src="js/animsition.min.js"></script>
<script src="http://cdnjs.cloudflare.com/ajax/libs/jquery-easing/1.3/jquery.easing.min.js"></
script>
<script src="js/jquery.parallax-scroll.js"></script>
<script src="js/owl.carousel.min.js"></script>
<script src="js/jquery.cbpQTRotator.min.js"></script>
<script>
$(document).ready(function() {

$("#owl-partners").owlCarousel({

autoPlay: 4000,
stopOnHover : true,
pagination : false,
items : 5,
itemsDesktop : [1199,4],
itemsDesktopSmall : [959,3]
});
});
</script>
<script>
$( function() {
$( '#cbp-qtrotator' ).cbpQTRotator();
});
</script>
<script src="js/functions.js"></script>
<script src="js/particle.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-15815880-3']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-
analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</body>
</html>

10.2 SCREENSHOTS
10.3 REFERENCES
[1] M. Cannataro, P. H. Guzzi, and A. Sarica, “Data mining and-life sciences
applications on the grid,” Wiley Interdisc. Rew.: Data Mining and Knowledge
Discovery, vol. 3, no. 3, pp. 216–238, 2013. [Online]. Available:
http://dx.doi.org/10.1002/widm.1090

[2] P. Guzzi, M. Mina, C. Guerra, and M. Cannataro, “Semantic similarity

analysis of protein data: assessment with biological features and issues,”
Briefings in bioinformatics, vol. 13, no. 5, pp.569–585, 2012.
[Online].Available:
http://bib.oxfordjournals.org/content/early/2011/12/02/bib.bbr066.short

[3] M. A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, and et al, “The

gene ontology (go) database and informatics resource.” Nucleic Acids Res
Nucleic Acids Res, vol. 32, no. Database issue, pp.258–61, January 2004.

[4] E. Camon, M. Magrane, D. Barrell, V. Lee, E. Dimmer, J. Maslen, D. Binns,

N. Harte, R. Lopez, and R. Apweiler, “The gene ontology annotation (goa)
database: sharing knowledge in uniprot with gene ontology,” Nucl. Acids Res.,
vol. 32, no. suppl 1, pp. D262–266, January 2004. [Online]. Available:
http://dx.doi.org/10.1093/nar/gkh021

[5]M. Masseroli, O. Galati, and F. Pinciroli, “GFINDer: Genetic disease and ph
enotype location statistical analysis and mining of dynamically annotated gene l
ists”, Nucleic Acids Res., vol.  33, pp. W717‐W723, 2005.  

[6]M. Masseroli, “Management and analysis of genomic functional and phenoty
pic controlled annotations to support biomedical investigation and practice”, IE
EE Trans. Inf. Technol. Biomed., vol. 11, 4, pp. 376‐385, 2007.  
[7]T. Etzold, A. Ulyanov, and P. Argos, “SRS: Information Retrieval System fo
r molecular biology data banks”, Methods Enzymol., vol. 266, pp. 114‐128, 199
6. 

[8]T.A. Tatusova, I. KarschMizrachi, and J.A. Ostell, “Complete genomes in W
WW Entrez: data representation and analysis”, Bioinformatics, vol. 15, pp. 536‐
543, 1999.