Hawassa University

INSTITUTION OF TECHNOLOGY FACULITY OF INFORMATICS

DEPARTMENT OF COMPUTER SCIENCE

FINAL PROJECT I

WEB BASED BIOLOGICAL DATA MANAGEMENT SYSTEM FOR

ETHIOPIAN INSTITUTE OF BIODIVERSITY

Name ID No signature

1.ZEMENU MANAMNO Evcs/195/09 __________

2. HAILE JENBERIE Evcs/0198/09 __________

3. SEWNET ASRES Evcs/136/09 __________

Advisors:

Name Signature

1. GEZAHAGN ----------------------------------------------
Submitted to department of computer science Hawassa University in partial fulfillment for
the requirement of the degree of bachelor Science in computer science

Hawassa Sidama, Ethiopia

May 19,2021 G.C

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 Acknowledgement
First of all we heartily thanks our advisor Mr Gezahagn G. for their continuous support in every
phase of the project and who continuously provided us with their valuable advice to work on the
project and this document. He also help us show his loyalty. Secondly we would like to
acknowledge all our friends for their morals, idea and materials support during the preparation of

Table of content

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Contents page
CHAPTER ONE..........................................................................................................................................3
1. INTRODUCTION...........................................................................................................................3
1.1. BACKGROUND..............................................................................................................................3
1.2. STATEMENT OF THE PROBLEM................................................................................................4
1.3. OBJECTIVES OF THE PROJECT..................................................................................................5
1.3.1. GENERAL OBJECTIVES............................................................................................................5
1.3.2. SPECIFIC OBJECTIVES..............................................................................................................5
1.4 SCOPE OF THE PROJECT..............................................................................................................5
1.5 LIMITATIONS OF THE PROJECT.................................................................................................6
1.6. METHODOLOGY...........................................................................................................................6
1.6.1 DATA GATHERING TECHNIQUES....................................................................................6
1.6.2 SYSTEM ANALYSIS AND DESIGN METHDOLOGY.......................................................6
1.6.3 SYSTEM IMPLEMENTATION.............................................................................................7
1.6.3.1. HARDWARE AND SOFTWARE REQUIREMENTS..............................................................7
1.7. FEASIBILITY STUDY....................................................................................................................7
1.7.1. ECONOMICAL FEASLIITY........................................................................................................7
1.7.2. TIME FEASIBILITY....................................................................................................................8
1.8. SIGNIFICANCE OF THE PROJECT..............................................................................................8
CHAPTER TWO.......................................................................................................................................10
DESCRIPTION OF EXSTING SYSTEM.................................................................................................10
2.1 INTRODUCTION...........................................................................................................................10
2.2 EXISTING SYSTEM................................................................................................................10
2.3. STRENGTH OF EXISTING SYSTEM.....................................................................................12
2.4 WEAKNES OF EXISTING SYSTEM............................................................................................12
CHAPTER THREE...................................................................................................................................13
SYSTEM REQUIREMENTS....................................................................................................................13
3.2 FUNCTIONAL REQUIREMENTS..........................................................................................13
3.3 NONFUNCTIONAL REQUIREMENTS AND CONSTRAINTS............................................14
3.3.1 Security Consideration...........................................................................................................15
3.3.2 User Friendly Interface..........................................................................................................15
3.3.3 . Good Performance..............................................................................................................15

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 3.3.4 . System Modification and Maintainability...........................................................................15
3.3.5 . Availability..........................................................................................................................15
3.3.6 . Scalability............................................................................................................................15
3.3.7 Reliability..............................................................................................................................16
3.4.2 SEQUENCE DIAGRAM..........................................................................................................18
3.4.3 ACTIVITY DIAGRAM.........................................................................................................23
3.4.4. CLASS DIAGRAM...................................................................................................................28
3.4.5 USER INTERFACE PROTOTYPING.....................................................................................29
Create user home page.......................................................................................................................30
CHAPTER FOUR...............................................................................................................................31
SYSTEM DESIGN..............................................................................................................................31
4.2 PURPOSE OF THE SYSTEM DESIGN DOCUMENT.......................................................31
4.3 Scope...................................................................................................................................................31
4.4 Software Architecture Design..............................................................................................................31
Performance:....................................................................................................................................31
Reusability:......................................................................................................................................32
Portability:.......................................................................................................................................32
4.4.1 Logical view of the Architecture................................................................................................32
4.4.2 Process view..........................................................................................................................33
4.4.3 DEPLOYMENT DIAGRAM.......................................................................................................37
4.5 Database Design..................................................................................................................................37
CHAPTER FIVE.......................................................................................................................................39
CONCLUSION AND RECOMMENDATION.........................................................................................39
5.1 Conclusion...........................................................................................................................................39
5.2 Recommendation.................................................................................................................................39

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 Abstract
Ethiopia is one of the mega biodiversity centers and is also known for its traditional knowledge
of conservation. The varied regions of the country with unique floral and faunal richness, their
vastness, endemism, heterogeneity and inaccessibility of large area have necessitated creation of
authenticated baseline on biodiversity. This information system is essential to monitor, analyze
and plan action oriented programs for conserving and preserving our biological wealth.

Biological inventory and monitoring data should be stored and managed in computer database to
facilitate its effective analysis and use with regard to biological data management. Biological
data are data commonly stored in files or databases.

Biological data management system (BDMS) is a software solution for storage, management,
analysis and publication of biological data and it can be the best choice for any relevant research
or industrial laboratory, culture collections and management. Service that Biological Data
Management System provides are registering biological entities including plant and animal
species with their specific behavior, identify the species whose status is threatened and endemic
in Ethiopian ecosystem.. BDMS has a site to visit flora and fauna, scientific research permit
returns, comprehensive biological survey program, and lists of endemic and threatened species,
vector borne diseases and their traditional medicines.
Our system contains the data of taxonomical differentiation of plants and animals exist in
Ethiopia ecology. Our database contains animal and plant species including Endemic and
threatened species that exist in Ethiopian climax. We will design database for plants, animals and
database for endemic, endanger species of Ethiopia.

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 CHAPTER ONE

1. INTRODUCTION
Ethiopia is one of the richest countries in biological diversity which have different species of
plant and animal. Biological inventory and monitoring data should be stored and managed in
computer database to facilitate its effective analysis and use with regard to biological data
management. Biological data management systems in academic settings were originally confined
to relatively small individual scientific groups or laboratories these systems were often limited to
specialized data sets and analysis operations and were developed by analyzing workflows,
heterogeneity, evolution, and scalability issues. Addressing such problems requires a systematic
process for analyzing the data structure and operations for application domain. This process
entails substantial digitization which is especially difficult to maintain biological data whose
semantics are complex and tend to evolve. These data are generated via processes that involve
multiple transformations between different levels of data granularity and are based on evolving
technology platforms and computational methods. In spite of this complexity a systematic
application domain analysis process and comprehensive documentation are essential for
providing effective data analysis support and to address this frustration scientists often encounter
in dealing with public biological data management systems.

Our aim is to assist biologists, biological laboratory industries, researchers, biodiversity institutes
managers, and governmental or public organizations in their research through the development
of the web site for the integration of biological data distributed over the web, and we placed in
very particular context that is the study of different species of biodiversity in Ethiopia ecosystem.

1.1. BACKGROUND
Ethiopia institute of biodiversity is a national organization for the collection, collection
management, analysis and dissemination of Ethiopian biological diversity. Biological data are
key requirement for understanding our natural surroundings, for tracking change in our
environment and for gaining a greater insight on how we benefit from, impact upon the
ecosystem goods and services provided by the biological diversity. Biological data management
includes the traditional areas of data generation, acquisition, modeling, integration, and analysis.
Web based biological data management system for Ethiopia institute of biodiversity is a web
based application for collection of species, vector bound diseases and traditional medicines data,
store, and manage of those data that are exist in Ethiopian ecosystem. Biological data
management system (BDMS) is web based system that enables researchers, biologists,
laboratory experiment workers to access the biological data and record specific properties of
species, diseases and traditional medicines. Ethiopia is one of the richest country in plant and
animal species in the different parts of the country. But those plenty of diverse life is not
digitized in one system to share and manage the biological data online through internet. In order
to resolve this problem we will develop Biological data management system for Ethiopian
institute of Biodiversity.

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The system will have the components of species (includes flora/plant biodiversity, Fauna/animals
biodiversity, which includes endemic and endanger species of Ethiopia), traditional medicines
that Ethiopian society use, vector Born diseases, microbial land insect biodiversity.

1.2. STATEMENT OF THE PROBLEM

It is not secret that Ethiopia is country of many diverse fauna and flora species, bacteria, lichens
and mosses in the wild ecosystem. And also Ethiopia is known with its traditional medicines in
the rural society with different areas of the country. But many of those species are not identified
for use and management under one system. This makes hard to proof the traditional medicines
scientifically and to get information of those species easily. So as to develop this system we
identify the following problems;

 Ethiopia is country of biodiversity in all parts of the country and those biological diversity
data are not registered in database, and are not accessible through internet.
 Ethiopia has not an organized system that manage its biological data of its biodiversity
wealth exist in different ecosystem.
 High rate loss of genes, species, ecosystem and human knowledge by lack of well-defined
system for scientists and biological data initiative groups to conserve the gene of species.
 There is no system that helps to indicate species whose status is vulnerable to extinct,
endanger, normal and abundant and where it is.
 There is no web based system that guides investors, bio researchers, nongovernmental and
governmental organizations to distinguish species and their latitude and longitude locations.
 No system which provides mechanism to assess the biological diversity of Ethiopian
ecosystem.
 There is no automated system for scientists that display the species information and to prove
traditional medicines.
 No database is exists in Ethiopia for plants species, animals, vectors, diseases, traditional
medicines which accessed through web applications.
 There is no automated database for endemic and endanger plants and animals (species) exist
only in Ethiopian ecosystem.
 There is no database of vectors, diseases and their traditional medicines for (human, plants
and animals).

1.3. OBJECTIVES OF THE PROJECT

1.3.1. GENERAL OBJECTIVES

The objective of the project is to develop a secured web based biological data management
system for Ethiopian Institute of biodiversity.

To develop a secured system which will help to manage the biological data for conservation,
promotion and sustainable utilization of the country’s biological diversity wealth?
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1.3.2. SPECIFIC OBJECTIVES
To develop a secured web based biological data management system has the following specific
objectives:
 To develop user friendly system that is easily accessible by biologist, researchers, botanists,
and zoologists.
 Develop system that will register, manage, access, and share biological data online through
internet.
 To keep track of biological data information in structural database and develop national site
for those data and make accessible online.
 To document digitally local knowledge of the society on uses of traditional medicines over
vector borne diseases and adaptive traits species.
 Develop system which is easy to assess periodically countries biota and capacity, identify an
evolving set of priorities and actions for responding to new opportunities and prepare
different reports to government, society and to make convention on their findings and
conclusions.

1.4 SCOPE OF THE PROJECT

The scope of system is intended to support the collection and registration, arrangement,
management of the biological data exists in Ethiopian ecosystem. BDMS intended to be usable
by all levels of government and the nongovernmental private sectors. The system will have
capability in the storage, manipulation of the species data, and effective search of the information
of specific species and their available data. In this component data will be returned from the field
which may be most useful. This includes kingdom, phylum, class, order, family, genera, and
species taxonomy information on the morphological behavior likes stems, roots, leaves of flora,
breeding system of fauna and flora. Plants, animals including endemic and threatened species of
Ethiopia have automated database to make accessible through internet.
BDMS will be develop by defining information required by a prospective user to determine the
availability of biological data includes plants, animals, vectors, diseases exist in Ethiopian
biodiversity ecosystem

1.5 LIMITATIONS OF THE PROJECT

When we develop this system the following limitations are identified. The major difficulty in
biological data is wide area, lack of information that helps the prospective user to determine that
data exist in the ecosystem. Challenges of biological words, overlapping of species property and
functional rolls are dynamic to differentiate. Biological data is broad and diverse to arrange and
register in database. Scalability of the system with the growing technology is another limitation.

1.6. METHODOLOGY
The project is aimed to develop web based biological data management system for Ethiopian
institute of biodiversity. Because of the heterogeneity of biological data in the Ethiopian
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ecosystem we must use different software development tools, data gathering techniques,
programming languages, design and analysis techniques.

1.6.1 DATA GATHERING TECHNIQUES

To collect data about the problem and the requirement of the existing system we use the
following methodologies;

Written document: in this method of requirements elicitation technique, we tried to read different
papers that states about Ethiopian biodiversity and their management.

We go to southern agricultural research institution and we interview biodiversity experts.

1.6.2 SYSTEM ANALYSIS AND DESIGN METHDOLOGY

After the requirements are fully elicited, the next step to be done is analysis model. This model
is a bridge to design model. Analysis model focus on the requirement that is visible within the
problem. Each element we analyze will add to an overall understanding of the software
requirements and provide insight into the information domain, function and behavior of the
system.
To develop our system we use Object-Oriented Modeling Approach because object oriented
modeling approach gives the following benefits;
 The ability to tackle more challenging problem domains.
 Reusability of analysis, design, and programming results
 Increased consistency among the models developed during object-oriented analysis, design,
and programming.
 The Object-Oriented modeling use Unified Modeling Language (UML) to allow the modeler
to specify, visualize and construct the artifacts of software systems, as well as business
models by the use of:
 Use cases Diagram
 Class diagrams
 Sequence diagrams
 Subsystems diagrams
 ER Diagram for database schema

1.6.3 SYSTEM IMPLEMENTATION

To develop this system we need different hardware requirements and software requirements. The
system requires to a minimum, a computer with the following description:

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 1.6.3.1. HARDWARE AND SOFTWARE REQUIREMENTS
We use the following hardware tools in order to accomplish our project.
 Processor: Intel, Corei5
 RAM: 128 MB (In order the system to run faster)
 Internal NIC (Network Interface Card)
 computer
 Flash
 Programming Environment (Front End): PHP, JavaScript, CSS
 Database (Back End): MySQL Server
 Operating system: Any operating systems have no effect on the proposed system
 VERTRIGO with PHP and MYSQL, apache server
 Notepad++ used as an editor.
 Microsoft word: used for documentation.
 WhiteStar UML to draw use case diagram, sequence diagram, and class diagram
 Micro Soft Access database relation used for draw persistent database schema diagram
 Web browser and latest antivirus with internet connection: Firefox, chrome
 Visual paradigm UML use to draw activity diagram and user interface
 Star UML used to draw ER diagram

1.7. FEASIBILITY STUDY

BDMS is web applications that used to manage Ethiopian biological data online. Because the
system is online so it used for managing, registering, searching of the species of plants, animals,
microorganism, with its specific characteristic is easy. Collecting traditional medicinal species
and vector borne diseases in one digital system are another use.

1.7.1. ECONOMICAL FEASLIITY

We assess the economic feasibility of our project implementation alternative the basic question
we will answer is does the project make a financial sense? And we do this by performing a
cost/benefit analysis, by comparing the full/ real costs of the application to its full financial
benefit. By considering this we include both qualitative and quantitative factors of costs or
benefits for which monetary values can easily identify as follow:
The system reduce the hardware/software upgrade costs, requires minimum labor cost by
reducing the personal cost for biological data collection, management and storage. BDMS
supports cost for application to increase the organization revenue. BDMS provides accurate and
secured information about the species to maximize improved decision. It will avoid employee
dissatisfaction from fear change and negative public perception from layoffs as automated.

1.7.2. TIME FEASIBILITY

We accomplished the document of our project based on the time table as we indicate by the
department schedule. we will finish all the attribute of the document with in specified time. We
start April 5, 2021 GC and continue on our project until the submission date on the first of may
15, 2021 GC by spending different time duration on different stages of our project.

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1.8. SIGNIFICANCE OF THE PROJECT
Our web facilitates the collection of biological diversity, diseases and traditional medicines data
for biologists to search among heterogeneous and distributed data in public or private data
sources on the web. BDMS particularly helps them to analyze specific characteristics of species,
by building a platform for integrating biological data. The system provides the following
significance;

Store biodiversity data: The proposed system provides mechanism to save, manage, and secure
biological data easily. Restrict access to data by giving rights to given tables, fields and records.
Perform identification clustering of new discovered strains or specimen.

In museums: Store any kind of biological data such as yeast, plants, insects, and animals. The
integrated biological data is easy to use and can help us to keep track of all the steps performed
in the laboratory.

In industries: Industries can create their own tables, fields, records and store and manage their
data easily. Industries can get information about the species that used for traditional medicines
and other source that are available for their factory easily. Analyze the data and use the results
for the prediction of new products or the development and improvement of current products.

In hospitals: Hospitals can be used the system to identify new vector cause pathogens by
analyzing the microorganism’s morphology and the results could be used for the prediction of
new medicine. Hospitals can easily get the list of medicinal plants exist in Ethiopian biodiversity
climax.

In universities: Biological data in educational institutions is one of the tools to train students in
medical, environmental, biological and other fields of study. The system reduces the load of
work for finding the specific biological and morphological characteristics of organisms by
digitally documenting the organism’s unique behavior, habitat, latitudinal and longitudinal
existence, nomenclature. So that students, teachers and biologist can access the information
easily through network.

In culture collections: Store all kinds of strains or specimen information in one system. Enter
new data or import large amount of data in the database. Share data online and make it possible
to order new culture online or deposit new information through the web. Keep track of the
number of stocks in the collection and manage easily. It is simple to identify new species based
on the data available in the database.

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 CHAPTER TWO

DESCRIPTION OF EXSTING SYSTEM

2.1 INTRODUCTION
The purpose of this document is to differentiate the functional and nonfunctional system
requirements that represent the characteristics of the biological data management system. Those
requirements are used by the developers and will use for validating the final delivered system. In
this section we deeply describe our system in terms of use case diagram, sequence diagram,
activity diagram, state chart, class diagram, database schema, class responsibility collaboration
diagram and user interface.

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 2.2 EXISTING SYSTEM
In Ethiopia biological data management is the responsibility of the institute of Ethiopia
biodiversity and the community as the whole. So that the institute follows its own rule and
regulations for management, collection recording, register new species, diseases and traditional
medicines, and making assessment on the diversity. The institution tracks the information of both
territorial and aquatic species of plant, animal, vectors and insects, vector borne disease and
traditional medicines of plants, animals and humans, and document it in proper way, then puts in
Herbarium, museum or any Gene banks. The information is recorded in system that cannot be
accessed at any time and everywhere through internet. This is the main difficulty of scientists,
biologists, environmental and conservation initiative groups, the public and others. When
someone wants the data of specific plants, animals or traditional medicine she/she cannot get it
without visiting the National herbarium of Ethiopia institution of biodiversity. This is very time
consuming, tiredness and not available at exact time and place. The current system has the
following features;

Registration of new Data: when new plants or new feature of Animals is discovered, the
discovery owners writes the information of the new biological data manually on paper and send
to the national institution of Ethiopian biodiversity or any regional gene museum. The institution
records and documents the necessary data of the species and put in the herbarium or in museums.

Access of information: The data of the biological diversity cannot be accessed from anywhere.
Because no automated national/central database are exist that stores the data of Ethiopia plants,
animals, vectors, vector borne diseases, traditional medicines and list of endemic and endanger
species. The accessing of this huge information needs getting printed document or walking to
national museum or national herbarium in Addis Ababa or near biological museum if exist. This
is upsetting and tiredness. Generally in Ethiopia there is no distinguished database of Ethiopian
species that can be accessed through internet. Searching and getting the species data is time
taking and boring. Endemic species that exist only Ethiopia is our heritage have no their
distinguish database, they cannot be advertised. Traditionally Ethiopian communities are used
plants and animals for preparations of traditional medicines unfortunately; the species that are
used for these applications are not collected in one system so this is difficult to prove medicinal
values of the species scientifically. No means are exist to adversities Ethiopian wealth in species
diversity for investors, because the species data are in the hands of the community living in the
different territory of the country.

BUSINESS RULES
A business rule is an operating principle or policy that our software satisfies. A rule can enforce
business policy, make a decision, or infer new data from existing data. This includes the rules and
regulations that the system users should abide by. This includes the cost of the project and the discount
offers provided. The users should avoid illegal rules and protocols. Neither administrator nor the users
should cross the rules and regulations. We try to embed the business rule of our system in structural

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requirement artifacts because those rules are uncovered during elicitation activities for the requirements.
We try to identify our system business rule during the normal course requirement gathering and object
oriented analysis. In our system we will identify business rules using use case model documents for
behavioral (functional) requirements, and domain model documents for the major business concepts and
their relationship pertinent to a system. The overall business rules of our system are described below in
the form of diagram

Figure 2.1 business rule

2.1. STRENGTH OF EXISTING SYSTEM

The system that we will develop gives the correct solutions for the challenges described above in
the existing system analysis. Our system records the data of plant species, animal species,
vectors, and traditional medicines in automated database to make accessible in anywhere through
internet. Our system holds information about classification of plants, Animals, traditional
medicines of human, animal, and plants. Also we design database for those plants and animals
used as a source of traditional medicines for making available for further scientific proofs. And
we also design a database for endemic and endanger species of Ethiopia for identifying them and
record on the web based system. We design query builder for advanced search mechanism. This
helps the users of our system to get full information of vector borne diseases with their causal
vector and traditional medicines that used to treat the diseases. Also it will used to display the
information of species in structural file format.

For developing this system we will identify the following functional and nonfunctional
requirements.

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2.4 WEAKNES OF EXISTING SYSTEM
The system that we will develop the correct solution for the challenges discussed above in the
strength of existing system. Our system does not include vector born diseases, animal and plant
diseases in the cases of time and resource.

CHAPTER THREE

SYSTEM REQUIREMENTS
3.1 INTRODUCTION
The software and hardware components of the computer system are required to install and use
the software efficiently. If the computer system does not meet the system requirements the
software may not work correctly.

3.2 FUNCTIONAL REQUIREMENTS

A functional requirement describes the relationship between the system and the user or the
environment. Here the relation means the direct and indirect interactions between users and the
system. The system has the information components needed for assessing Ethiopian species
biodiversity. The system gives different service based on the type of the user.

We have three actors in our system, those are

Administrator
Staff members and

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Client Users

The features that are available to the Administrator are:-

Query: used to search and build complex data from different related database tables. It is used
for searching in species, disease, vectors and traditional medicines data and lists. In this stage we
design query builder for searching data of related tables and those data are available by
appropriate queries.

Authentication: the administrator must use his/her user name and password to login the system.

Register New Data: The administrator can register list of species and information of the species
Update Data: The administrator has power to delete, modify, and edit the species (plants,
animals, diseases, traditional medicines) information/data.

Access Data: The administrator can search the list of the species and the information of the
species available in the database. And can view all the data of the species (flora, fauna, diseases,
vectors, traditional medicines) from the database.

Manage Profile: The administrator can manage the profile of the system and by editing, resizing
and uploading the profile of the system. He/she can edit the title of the system. The
administrators also create accounts for staffs and view all the staff member and Client users
profile.

Manage Calendar: He/she can date the availability of service of a specific activity or data for
members by managing the calendar of the system.

Manage Volunteers: The administrator of the system can grant volunteers participating in the
conservation, usage of the existing biological data.

Client Users: The features that are available to the client user are:-

Create User Account: The system will allow the user to create user account and register in the
system.
Query: used to search and build complex data from different related database tables. It is used
for searching in disease, vectors and traditional medicines data relation.
Register New Data: the client user can upload new species data, the occurrence of diseases of
plants, animals, and humans, discovery of traditional medicines.
Access Data: After the user creates account once they login in the system and can access the
information of the species from the national database of plants, animals, and vectors, diseases
and traditional medicines.
Manage Personal Profile: The client user and the can change their personal information.

Staff Members

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The staff of institute includes researchers, laboratory technicians, field assistants and finance
officers and other supportive staffs.
The features that are available to the staff members are:-

Query: used to search and build complex data from different related database tables. It is used
for searching in disease, vectors and traditional medicines data relation.

Access Data: The staffs of the institution will have the right to view members of the system.
And they also view the information of plants, vectors, disease and the traditional medicines
database.

Register New Data: The staff members can register data of plants and animals’ species,
diseases, traditional medicines and vectors species.

Change Password: The staff members have the right to change their account password created
by the administrator and manage their personal information created by the administrator.

Manage Volunteers: the staffs can check the members detail and can grant access privileges.

3.3 NONFUNCTIONAL REQUIREMENTS AND CONSTRAINTS

Non-functional requirements are requirement constraints and quality standards that the system
we are building will adhere to. We are finding out what these non-functional requirements
should be by reading documents and interviews. Also, we can use try and discover what non-
functional requirements will be. Here are some areas that we will have in our non-functional
requirements document. Our system will have the following nonfunctional requirements:

3.3.1 Security Consideration

The system allows its user to perform their task only after login process. The user will be
accompanied with the legible account and password otherwise they won’t be allowed. All users
have access only their own interface. Normal users can just read information but they cannot edit
or modify except their personal information.

3.3.2 User Friendly Interface

The system will have consistent user interface formats and button sets for all forms in the
application will have a form based interface for all data entry, viewing, search formats and will
generate reports that are formatted in table and that should look like the existing manual report
format for user friendliness. We will develop a query builder for advanced search mechanisms to
make user friendly for computer and non-computer science customers.

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3.3.3 . Good Performance
The system is capable of carrying huge amount of data with many related databases. The system
carries information sufficiently. In our system when user requests or want to operate some task,
the system responses what the user request quickly to satisfy the user need.

3.3.4 . System Modification and Maintainability

Maintainability of a system is the effort required to locate and fix an error in the operational
program. So that we will try to write comment when we write the code of the program to make it
easy to locate and fix error. The final software implementation of this project will be a flexible.
The software will be built in such a way that most of the major functionalities can be accessed
from any interface. We will make the coding of the software flexible, fault tolerant and easy to
diagnose.

3.3.5 . Availability
System availability is the time when the application must be available for use. Required system
availability is used in determining when maintenance may be performed. Definitely we think
about time zones, schedules, and user location. The system is available everywhere which have
internet access. The system will be operable.

3.3.6 . Scalability
The system will be scalable by modifying the source code when additional feature exists. Our
system will iteratively scalable because of the data of biological entities are huge and different.
Each biological entity will have specific component with huge database that contains those data.
In the current time we will implement some parts of the biological wealth of Ethiopia so the
system will scalable for future advancement of technology in satellite and internet.

3.3.7 Reliability
Reliability is the chance that the system processes work correctly without being aborted. The
system will fault tolerant and run on a machine to generate precise output.

3.4 ANALYSIS MODELS

The graphical user interface (GUI) supports English language. All users of the system will have
user name and password (for identification) to login and use the system. The database holds only
biological data of Ethiopian biological diversity.

3.4.1. USE CASE DIAGRAM

A system use case model describes the potential usage of the proposed system. It is part of the
analysis document which consists of use case describes sequence of actions that provide
measureable value to an actor and it’s drawn as horizontal eclipse.

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An actor is a person, system, or real object that plays a role in one or more interactions with the
system. Relationship between actors and classes are indicated within use case diagrams. A
relationship exists whenever an actor is involved with an interaction described by a use case. The
rectangle around the use case is called system boundary and the name suggests it indicates the
system and the use cases inside the rectangle represent the functionally that the system intended
to implement. Our system will have the following use cases and actors

Actors Use cases

 Administrator  Authentication
 Client Users  Manage Profile
 Staff Members
 Query
 Access Data
 Register New Data
 update Data
 Manage Calendar
 Create Account
 Change Password
 Manage Personal Profile
Table 2.1 Use Cases and Actors

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Figure 3.1 Use Case Diagram for Biological Data Management System
This is the broad level diagram of the project showing a basic overview. The users can either the
client users or the staff members. This system provide a search functionality to facilitate the
search of biological resources. This search will be based on various categories via name of data
being searched. Further the administrator can add, update resources and resource users in the
system. The users of the system can request th system to access data, also can upload new data of
plants, animals, vectors, Vector borne diseases and traditional medicines.

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 3.4.2 SEQUENCE DIAGRAM

FIGURE 3.2 sequence diagram for authentication login

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FIGURE 3.3 sequence diagram New Data

FIGURE 3.4 sequence diagram search Data

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FIGURE 3.5 Sequence diagram view Data

FIGURE 3.6 Sequence diagram Delete Data

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FIGURE 3.7 Sequence diagram for manage personal profile

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FIGURE 3.8 Sequence diagram for manage profile

FIGURE 3. 9 Sequence diagram for manage Calendar

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FIGURE 3.10 Sequence diagram for query

3.4.3 ACTIVITY DIAGRAM

Activity diagram is a diagram which used for modeling the logic captured by single use case
usage scenario. It also helps to model the internal logic of complex operations of the system. In
addition to this, it shows the work flow from start point to end point details and many decision
parts that exist in progression of event contain in activity. Based on this we design the following
activity diagrams for our system;

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FIGURE 3.11 Activity diagram for authentication

FIGURE 3.12 Activity diagram for Create Amount

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FIGURE 3.13 Activity diagram for Screech

FIGURE 3.14 Activity diagram for Delete

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 FIGURE 3.15 Activity diagram for Register New data

FIGURE 3.16 Activity diagram for Manage profile

FIGURE 3.17 Activity diagram for View Data

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FIGURE 3.18 Activity diagram for change password

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 FIGURE 3.19 Activity diagram for query

3.4.4. CLASS DIAGRAM

A class is an abstract, user-defined description of a type of data. It identifies the attributes of the
data and the operations that can be performed on instance of the data. A class of data has a name,
a set of attributes that describes its characteristics, and a set of operations that can be performed
on the objects of that class. There are different kinds of relationships between the classes as
shown in the diagram like normal association, aggregation, and generalization. Hence class
diagram provides an overview of the target system by describing the object and classes inside the
system and the relationship between them.

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Figure 3.20 Class Diagram of Biological Data Management System

3.4.5 USER INTERFACE PROTOTYPING

The user interface is the part of the system that users will always see, and interact with. So
having screen shots of the user interface in our documentation will allow us how the system
looks like. The following screen shoots show our system interface.

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Create user home page

Figure 3,21Create user home page

Create account user interface page

Figure 3.22 create account user interface

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 CHAPTER FOUR

SYSTEM DESIGN
4.1 Introduction:
This chapter provides a system design stage of the project in development. This chapter contains
and describes about the system architecture, database schema and deployment diagram of our
system.

4.2 PURPOSE OF THE SYSTEM DESIGN DOCUMENT

Software architecture is the fundamental framework for structuring the system we will develop.
We design our system by enhancing the attributes like performance, security, availability, and
maintainability.

Based on this our system we will adhere the following goals

 Developing reusable components that are easy to modify and maintain

 Developing efficient and reliable networked components.
 To increase user friendliness.

4.3 Scope
The scope of system is intended to support the collection and registration, arrangement,
management of the biological data exists in Ethiopian ecosystem. BDMS intended to be usable
by all levels of government and the nongovernmental private sectors. The system will have
capability in the storage, manipulation of the species data, and effective search of the information
of specific species and their available data. In this component data will be returned from the field
which may be most useful. This includes kingdom, phylum, class, order, family, genera, and
species taxonomy information on the morphological behavior likes stems, roots, leaves of flora,
breeding system of fauna and flora.

4.4 Software Architecture Design

There are different biological databases for storing and managing the biological data of
Ethiopian biodiversity. Those databases are not accessed through internet and it is impossible to
upload data of species on the client side. This software is used to access biological data
management purpose.

Performance:
The system is capable of carrying huge amount of data with many related databases.

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User Friendliness:

We will develop a system which is user friendly by designing interactive user interfaces for those
stakeholders to communicate with the system easily. This is valuable because end users know
their own context and needs better than anybody else and they often have real time awareness of
shifts in their respective domains.

Reusability:
The system that we will develop can reuse easily by modifying the source code for further
features of the system with rapid change in technology.

Portability:
The system can run on different platforms because it is platform independent

4.4.1 Logical view of the Architecture

Architecture determines the type of interactions that the components of the system are going to
have. The architecture we use for this work is three tiers client/server Architecture. It is mainly
based on the system analysis document.

The first tier is client side tier Users can interact directly with the applications through internet.
The client tier interacts with the system to make request and retrieve data from the database.
Then it displays to the client users the data retrieved from the server database. A client use
internet browsers to access the services provided by the system located anywhere having internet
access.

The second tier is web server

The web server is the program that runs on server computer to respond to the HTTP request of
the client. Web server used in this system is apache. HTTP is used to transfer data across
internet.

The third tier called the data tier which is database used to store any information

Figure 4.1 System Architecture Design Diagram of Biological Data Management System

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4.4.2 Process view
Subsystem process is the collection of classes, associations, operations, events and constraints
that are closely interrelated with each other.

Figure 4.2 Subsystem Decomposition for Biological Data Management System

Figure 4.2 shows the subsystem that our system mainly has as generally. The resource
management subsystem includes all the data of the species

Now we decompose each subsystem in to other related subsystems and components. This
decomposition activity helps us to identify cohesion and coupling property of each subsystem for
building one integrated system. Each subsystem gives service for doing certain operations in the
object interface of its layer.

Based on this we decompose the subsystem of our system as follow:

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Figure 4.3 Subsystem Decomposition for User Management subsystem.

In this figure 4.3 we sub decompose all the user related activities that are applicable in our
system. The account creation component includes the activities that our system users register in
our system themselves or the administrator can create user account for staff members, and the
members can change their password. The authentication component is used to secure our system
by requesting user name and password when you try to enter in the system. The subsystem user
type which has subcomponent of anonymous user, registered user, the staff member and the
administrator those are users in different access level in our system.

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Figure4.4 subsystem Decomposition for Resource Management subsystem
In the figure4.4 above subsystem Resource management is composed different subsystems and
components that interacts each other. We sub decompose the subsystem of the resource
management subsystem components as follow;

The plant subsystem has either the terrestrial plants or the aquatic plant component. Those
components build up the plant subsystem.

Figure4.5 subsystem Decomposition for Flora/Plants Data subsystem

The animal subsystem has either the terrestrial animal or the aquatic animal component. Those
components build up the animal subsystem.

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Figure 4.6 subsystems Decomposition for Fauna/Animals Data subsystem

Figure 4.7 subsystems Decomposition for Insects Data subsystem

Figure 4.8 Subsystem Decomposition for Query Builder subsystem

Figure 4.8 describes about the sub component of query builder subsystem which is advanced
search mechanism used to search efficient data of species, diseases and traditional medicines

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from different data tables. So the query builder has sub component query which is used to search
the available data from our system.

4.4.3 DEPLOYMENT DIAGRAM

Deployment diagram depicts how the deployable units of the system applications, components
and data stores are assigned to various nodes as well as how the nodes communicate with each
other and with devices. It is useful for mapping our system and as a means of studying the load
across our system.

Figure 4.9 Deployment Diagram for Biological Data Management system

4.5 Database Design

In order to store the information of species, we need tables to map objects and attributes in fields
based on the objects found on the system. Therefore we identified the major tables that will be
implemented on the selected Database and show the necessary relationships among the objects,
which are selected to store the data persistently in the system. Generally there are three types of
relationships database system. These are one-to-one, one-to-many and many-to-many. For this
reason, we map objects in tables as follow:

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 Fig
ure 4.10 ER Model of Biological Data Management System

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 CHAPTER FIVE

CONCLUSION AND RECOMMENDATION

5.1 Conclusion
Effective data analysis across biological data management systems involves providing support
for seamless composition of analysis operations, which in turn requires systematic process for
analyzing the data structure and operations of the application domain. The development process
of biological data management system involves detailed application domain analysis based on
use case scenarios subsequently used for defining abstract species, vector-borne diseases and
traditional medicines data model in terms of data types and operations. BDMS aims to increase
the accessibility of Ethiopian biological data for users of the biological diversity wealth in
different areas with various purposes.

5.2 Recommendation
We recommend that Ethiopian biodiversity institution use this systematic project, because it
simplifies the tasks performed in the biodiversity institution, makes the system fast registration
of plant and animal species, it is easy and accessible the reliability is that much better.

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Reference
1. Ensembl national biological database organization.
http://www.ensembl.org/info/about/species.html
2. http://www.ncbi.nlm.nih.gov/geoprofiles/
3. https://www.cbd.int/doc/world/et/et-nbsap-01-en
4. http://darwin.ansp.org/hosted/aes/membership.htm
5. object oriented business rule Dr.Dobbs
http://www.drdobbs.com/object-oriented-business-rule
6. V.M. Markowitz, J. Campbell, I.A. Chen, A. Kosky, K. Palaniappan, and T. Topaloglou,
Integration Challenges in Gene Expression Data Management.
7. Bioinformatics: Managing Scientific Data, Morgan Kauffman Publishers (Elsevier Science),
277-301,
8. Somerville software engineering (2011- 9th edition)
http://www.SoftwareEngineering-9.com/Web/History/
9. Asfaw, N., Demissew, S., 2009. Aromatic plants of Ethiopia. Shama Books, Addis Ababa.
http://botanicaethiopia.com/herbs/
10. National biodiversity strategy of Ethiopian ecosystem

Appendix

Biological Data – Any communication or representation of biologically related facts or

information collected for computation or analysis.
Class – The primary subdivision of a taxonomic division or phylum, usually consisting of one or
more orders.
Division-Phylum – The primary subdivision of a taxonomic kingdom consisting of one or more
classes of organisms.
Family – The major subdivision of a taxonomic order or suborder consisting of one or more
genera.
Genus – The major subdivision of a taxonomic family or subfamily usually consisting of one or
more species.
Kingdom – One of the taxonomic divisions of living organisms includes animal and plants.
Methodology – A set or system of methods, principles, and rules for a biological inquiry
procedure. This includes laboratory, field, data processing and statistical methodologies.
Order – The major subdivision of a taxonomic class or subclass consisting of one or more
taxonomic families.

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