BIOPEN: A PROPOSED WEB APPLICATION FOR

IMPLEMENTING THE BIOLOGICAL ELECTRONIC PROTOCOL

SYSTEM OF ENTEROPATHOGENS CHARACTERIZATION

Personalized Web Sites and Services

Terumi Paula Bonﬁm Kamada, Danielle Forbeci Suzuki, Maicon Silva Costa

Leonardo Magalhes Cruz and Luiz Ant

onio Pereira Neves

Bioinformatics Master Program, Federal University of Paran

a - UFPR, Curitiba, Brazil

Keywords:

Protocol electronic, Enteropathogens, Health care system, Information technology, Biological database.

Abstract:

In the present work, we have developed a Biological Electronic Protocol System for Enteropathogens Char-

acterization (BIOPEN) with a Web Application interface that allows users to query data for characterization

and analysis of pathogens through an integrated management of accurate collection, storage and retrieval of

data, which aids decisions in health actions to combat diseases caused by these microorganisms. The proposed

tool is an electronic protocol that aims to facilitate data sharing in health care, using a structured database to

store information concerning about clinical assays and molecular characterizations of pathogenic strains and

clinical isolates. BIOPEN was developed using open source facilities and is freely distributed, allowing a par-

ticular laboratory create a customized, reliable, and low cost database. Thus, the principal contribution of this

work is to provide a tool that store and integrate results of physiological, biochemical, and molecular clinical

tests that can help researchers in taxonomic identiﬁcation of clinical isolates and prospective epidemiological

studies.

1 INTRODUCTION

The objective of this research is the development

of a web application called BIOPEN which stand

for Biological Electronic Protocol System of En-

teropathogens Characterization as a research tool.

This project presents an integrated uniform interface

for sharing biological data among researchers in the

Internet about characterization of Enteropathgens or-

ganisms for medical evaluation. The development of

this system has been done through a shared electronic

protocol, by implementing a web platform for integra-

tion of researchers and professionals in various areas,

such as medicine, biology, technology and informa-

tion systems, biochemistry and bioinformatics. The

web resources allow the connection to multiple re-

mote locations and advanced research centers (Gorga

et al., 2002). And so, the use of technology is relevant

for providing the information to improve care for dis-

eases that have high priority in health systems.

And so, the use of technology is relevant for pro-

viding the information to improve care for diseases

that have high priority in health systems.

(Young et al., 2007) suggests the use of the soft-

ware for storage, communication, treatment and avail-

able of biological and medical information. The

strategies should be developed, for example, creating

electronic information or records of electronic proto-

col. The use of web technologies, integrating medical

information clinical and laboratory treatment allow a

fast distribution. Then, using information technology

is the key to success of health organizations.

Currently, the health sector is experiencing an

accelerated growth of implementations of computa-

tional systems, including software development, net-

work design and communication tools and so creating

the need for new strategies of information manage-

ment in health centers (Young et al., 2007). More-

over, (Doebbeling et al., 2006) comment that the tra-

ditional forms of information storage, retrieval and

analysis tools are inadequate in the health’s area be-

cause the majority of investments in information tech-

nology also have focused only on the administrative

part.

However, (Uslu and Stausberg, 2008) failed to

deﬁne the economic beneﬁts of cost-effectiveness of

438

Paula Bonﬁm Kamada T., Forbeci Suzuki D., Silva Costa M., Magalhaes Cruz L. and Antônio Pereira Neves L..

BIOPEN: A PROPOSED WEB APPLICATION FOR IMPLEMENTING THE BIOLOGICAL ELECTRONIC PROTOCOL SYSTEM OF ENTEROPATHO-

GENS CHARACTERIZATION - Personalized Web Sites and Services.

DOI: 10.5220/0003403404380441

In Proceedings of the 7th International Conference on Web Information Systems and Technologies (WEBIST-2011), pages 438-441

ISBN: 978-989-8425-51-5

 2011 SCITEPRESS (Science and Technology Publications, Lda.)

electronic protocol. The authors based on two basic

factors proposed by (Berg et al., 1998): First, proto-

cols should not be overly structured or have a degree

of complexity to not generate problems of usability

and second, the system must ensure immediate bene-

ﬁts for primary users. As these factors were insufﬁ-

cient for research, (Bean and Martin, 2001) proposed

a system whose data generated by health electronic

protocol provides a mechanism of action in the pub-

lic health system that can quickly identify problems

and take necessary measures to prevent the spread of

disease. Therefore, (Druszcz, 2006) declared that the

use of electronic protocols can provide greater credi-

bility to clinical data and, consequently, improve the

methods of scientiﬁc research.

(Aranha Junior et al., 2009) and (Pinto, 2006) and

(Doebbeling et al., 2006) deﬁne the protocol as an ap-

propriate resource of information technology used in

the medical ﬁeld for capturing, storing and searching

data effectively and becoming a high relevant tool for

clinical studies.

On the other hand, (Bean and Martin, 2001) alerts

that the implementation of health electronic protocols

can be effective if planned previously. The biggest

challenge for implementing these protocols is to im-

prove the electronic interface to facilitate communica-

tion among users of the practice of infectious diseases

in public health (Wurtz and Cameron, 2005).

The pathogens used in this project are the enter-

obacteria. These organisms have their importance in

disease infectious, especially in diarrhea which is a

major cause of death in developing countries as re-

ported by (UNICEF/WHO, 2009). Considering the

difﬁculty in identifying these pathogens and their im-

portance as a cause of diseases in humans, this re-

search aims to assist the map-reading of data, after

characterization of these species, sharing the contents

of these data to researchers and professionals through

the creation of an efﬁcient electronic protocol. This

project has been built based on the integration project

electronic protocols called SINPE (Integrated System

Protocols Electronics) proposed by (Aranha Junior

et al., 2009).

Such analysis will generate various types of

data for identiﬁcation and characterization of these

pathogens. Several biochemical and molecular tests

are used, such as tests of resistance to antibiotics and

characterization exams of species, for example RFLP

(Restriction Fragment Length Polymorphism) among

others (Aguilera-Arreola et al., 2007). Hence storing

in a systematic, objective and secure way, allowing

the user to recover the data and further analysis is im-

portant.

Therefore, the present research proposes the

BIOPEN. This project is a data management with

electronic protocol using data coming from laboratory

analysis and the characterization of pathogens by the

molecular tests for prospective epidemiological stud-

ies. For this reason, the protocol resources and inte-

gration of electronic databases are our main contribu-

tion of this research.

2 PROPOSED METHODOLOGY

Four steps were followed to achieve the objectives.

The ﬁrst step involved the architecture and deﬁnition

of data modeling; in the second step an interface for

the electronic protocol was designed; in the third step,

it illustrates the implementation of planned applica-

tion and in the fourth step tests were performed to

validate the proposed system.

2.1 Results of Step 1:

Architecture and Data Modeling

This step is the deﬁnition of the data modeling, us-

ing a tool to describe the input and output and rela-

tional modeling to identify all the system’s informa-

tion based on literature.

This data modeling is relational and has been built

using twenty-seven tables as illustrated in Figure 1.

Figure 1 shows the visualization and sequencing

of the tables used in the database. The sequencia table

and organism table are the main reference. The ﬁrst is

related to the taxonomies of bacteria (domain, king-

dom, phylum, class, order, family, genus, species, be-

sides the classiﬁcation of a more speciﬁc using the ni-

trogenous bases (adenine, cytosine, guanine, thymine

and uracil) as gene, isolated, read and sequence of a

gene. In the second table, which makes the base of the

database, will be stored tests and results of laboratory

analysis in addition to the registration administration.

The used tool for creating this data modeling is the

DBDesigner. This tool is freeware and has resources

for implementing of SQL codes.

For architecture modeling of electronic protocol,

we are used the (JUDE, 2010). This modeling tool

supports the software planning and speciﬁcation by

UML (Uniﬁed Modeling Language). This diagram

represents a use case that describes the feature set of

electronic protocol. The proposal of the electronic

protocol structure is based on user interactions with

the system, such as consultations accomplishment,

maintenance of records, information generation and

generation of statistical graphics.

The proposed system offers user registration, or-

ganism registration, records the test results, generates

BIOPEN: A PROPOSED WEB APPLICATION FOR IMPLEMENTING THE BIOLOGICAL ELECTRONIC

PROTOCOL SYSTEM OF ENTEROPATHOGENS CHARACTERIZATION - Personalized Web Sites and Services

439

Figure 1: Data modeling of BIOPEN Project.

graphics based on these results and information re-

trieval according to the requirements of researchers.

Analyzing the protocol modeling, we have divided

the information in six main groups that are: admin-

istrative data, operation control, history reports, and

epidemiological control and test results. Each one has

a detailed description in step 2.2 with its features. We

have created sub-items like a division of the principal

groups as illustrated in Figure 2.

Relating to its architecture, Figure 2 shows the

concept of the screens and its links. This way, the

user can easily navigate through several pages inter-

actively. For example, the Figure 2 shows that the

screens contain ﬁelds with selection logic and this be-

comes the user interface more friendly.

2.2 Results of Step 2:

Conception of Interface Design

During stage 2.2, an user friendly interface has been

implemented, similar to other reported web appli-

cations ((Aranha Junior et al., 2009) and (Porcides

et al., 2010). (Porcides et al., 2010) propose a web

application called SBIM (Shared Biological Image

Figure 2: Main Screen of BIOPEN Project.

Manager). This project presents an integrated uni-

form interface for sharing biological images among

researchers in the Internet.

(Aranha Junior et al., 2009) propose the use of sta-

tistical graphs in SINPE project, showing data objec-

tively and organized. This functionality is been im-

plemented in this project.

WEBIST 2011 - 7th International Conference on Web Information Systems and Technologies

440

2.3 Results of Step 3: Implementation

The third step consists in the computational imple-

mentation of the proposed system using the pro-

gramming language PHP and the DBMS (Data Base

Management System) PostgreSQL. Both are freeware

tools. Currently, this phase is being implemented

based on the proposed modeling in the previous steps.

2.4 Results of Step 4: Validation Tests

In the fourth step, tests were made to validate the pro-

posed system. In this phase, the validation protocol is

based on methods proposed by (Pressman, 1995), the

use of a checklist to evaluate the user perception of the

system and initial tests of database. As initial results

of validation, tests were used to evaluate the database

using the command truncate table and retrieval of re-

sults by the name of the exams, besides the positive

and negative conditioning. The recovery of examina-

tions and the names, and the names with the condi-

tioning of positive and negative shows the average of

7503.2 ms and 5222.75 ms.

3 CONCLUSIONS

This project is in implementation stage. The rele-

vance of BIOPEN project is to facilitate the availabil-

ity of data about diseases caused by enteropathogens

among laboratories of Bacteriology in web environ-

ment, becoming a public database of any research, re-

liable and secure information that could be used in

prospective epidemiological studies. This is the prin-

cipal contribution of this research. In future studies

we will implement some other functionalities, as al-

gorithms for data mining with pattern features for im-

proved researches.

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