A MEDICAL INFORMATION SYSTEM TO MANAGE A CANCER

DATABASE

André Cid Ferrizzi, Toni Jardini, Leandro Rincon Costa, Jucimara Colombo

Paula Rahal, Carlos Roberto Valêncio

UNESP, São José do Rio Preto, São Paulo, Brazil

Edmundo Carvalho Mauad, Lígia Maria Kerr, Geraldo Santiago Hidalgo

Hospital do Câncer de Barretos, Barretos, São Paulo, Brazil

Keywords: Medical Information System, Cancer Database, Bioinformatics.

Abstract: Cancer is the second main cause of death in Brazil, and according to statistics disclosed by INCA – National

Cancer Institute 466,730 new cases of the disease are forecast for 2008. The storage and analysis of tumour

tissues of various types and patients' clinical data, genetic profiles, characteristics of diseases and

epidemiological data may provide more precise diagnoses, providing more effective treatments with higher

chances for the cure of cancer. In this paper we present a Web system with a client-server architecture,

which manages a relational database containing all information relating to the tumour tissue and their

location in freezers, patients, medical forms, physicians, users, and others. Furthermore, it is also discussed

the software engineering used to developing the system.

1 INTRODUCTION

Cancer is a fairly diverse disease and the multiple

genetic and epigenetic changes peculiar to it make

its prevention, diagnosis and therapy difficult. Thus,

studies that are meant to establish the tumour’s

molecular genetic profile are essential so that one

can understand the disease's complexity, establish

the biological basis and provide means to identify

the best therapeutic strategies, since, in spite of the

developments in chemotherapy, in surgical

techniques and in drug combinations, there are types

of neoplasies in which there has been practically no

prognosis improvement within the last ten years, a

fact that underscores the need to know the tumour's

biology (O’Connor, 2007) (He et al., 2007).

Cancer is the second main cause of death in

Brazil, and according to statistics disclosed by INCA

– National Cancer Institute 466,730 new cases of the

disease are forecast for 2008. Out of these, 231,860

are expected to be new male patient cases, while

234,870 are expected to be new female patient cases

(Brazilian National Cancer Institute, 2008).

The Barretos Cancer Hospital - SP is showcase

for a cancer treatment hospital. It rates among the

largest cancer hospitals in Brazil. Over 400 thousand

consultations take place and over 6 thousand new

cases of cancer, from all Brazilian states, are

diagnosed at the facility, every year. Since the

Hospital treats patients from a number of states and

regions within Brazil, the Barretos Cancer Hospital’s

Information System to Manage the Tumour Bank

(SCGBT) will make it possible to develop studies in

the area of prognosis, diagnosis and therapeutic

markers in representative samples of the Brazilian

population.

This article is meant to describe the SCGBT, the

system that underpins the whole management

process of a tumour samples database, by showing

its architecture, construction processes,

functionalities, and presenting some extracted data.

2 METHODOLOGY

The software development process employed is the

Unified Process – UP (Larman, 2001); Modeling of

some aspects of the system was performed with the

Unified Modeling Language (UML) and for

configuration management, Subversion (SVN) is

used (Subversion, 2008).

268

Cid Ferrizzi A., Jardini T., Rincon Costa L., Colombo J., Rahal P., Roberto Valêncio C., Carvalho Mauad E., Maria Kerr L. and Santiago Hidalgo G.

(2008).

A MEDICAL INFORMATION SYSTEM TO MANAGE A CANCER DATABASE.

In Proceedings of the Third International Conference on Software and Data Technologies - ISDM/ABF, pages 268-271

DOI: 10.5220/0001881802680271

 SciTePress

The programming language employed is PHP

Hypertext Preprocessor (PHP) and he Database

Management System (DBMS) used was MySQL.

3 SCGBT ENGINEERING

The whole SCGBT implementation was supported

by Project Management Body of Knowledge

(PMBOK) project management models and

processes, focused on four main areas: Requirements

Management, Configurations Management, Risks

Management and Tests Management (Project

Management Institute, 2004).

4 DATABASE MANAGED BY

SCGBT

The Barretos Cancer Hospital database comprises

information provided by the system’s users, patients,

doctors, tissue samples, medical forms, freezers,

departments, among others. It is possible to use data

mining, like some techniques discussed by Han &

Kamber (2006), to obtain knowledge in order to

diagnose cancer-related diseases.

Figure 1: Part of the HCB database class diagram.

Fig. 1 shows a part of the database UML class

diagram. In this diagram, the main items of the

database are shown:

 Patient: represents the patient treated at the

Hospital;

 Sample: it is a tumour sample collected from

the patient; this may be of the following types:

normal, tumour, blood, leukocytes, DNA,

RNA and serum;

 Topography: the International Classification of

Diseases for Oncology Code (ICD-O) is used

(Pan-American Health Organization, 2005);

 Morphology: the ICD-O is used for this

attribute's values;

 Freezer: is the location where the samples are

stored;

 Researcher: a sample may be removed from the

freezer for research purposes;

 Forms: show information on the patient's

history, diagnosis, clinical state, treatment and

prognosis;

 Doctor: is the doctor in charge of the patient.

5 SCGBT FUNCTIONALITIES

SGCBT comprises a number of functionalities,

providing full handling of the data on each patient

on record, as well as the tumour samples and their

characteristics. The next sections show the main

SCGBT's functionalities.

5.1 Patients

SCGBT comprises functionalities that handle patient

data, such as inclusion, update, removal and

viewing. In order to retrieve these data, the system

offers an interactive interface for the definition of

searches by the users, known as patient filtering. By

means of this interface, the user is able to put

together his/her patient search according to certain

parameters. The user is able to add or remove search

parameters, which include sample location,

topography, morphology, patient’s age, type of

sample, name, among others.

5.2 Samples

To handle the tumour tissue samples data, add,

remove, change and view samples functionalities are

available. The samples’ morphology and topography

fields use ICD-O, which associates a code and a

description to each morphology and topography.

A MEDICAL INFORMATION SYSTEM TO MANAGE A CANCER DATABASE

269

5.3 Forms

Each sample is associated to a single patient. For

each one of these samples, it is possible to fill out,

update and view its relevant forms. Such forms hold

data on the tumour's identification and history,

diagnosis, clinical stage, treatment and prognosis.

All forms stored in the database are easily viewed

and changed as required.

5.4 Freezers, Users and Doctors

It is possible to enter new freezers on record,

specifying its physical dimensions such as number

of shelves, racks, drawers, boxes and positions. The

system also offers the possibility of handling these

data. Thus, operations such as freezer searches and

changes can be easily performed. In order to

guarantee security and access control, SCGBT

encompasses user management, allowing the control

of users entered in the system, by means of

privileges. There is also information management

with regard to the doctors in charge of the each

patient’s diagnosis, who are associated with various

departments within the Hospital.

5.5 Reports

SCGBT makes several types of reports available in

order to extract data from the cancer database.

Several types of sample and patient reports are

contemplated. Data collection and management, by

means of our computer system, began in 2006 and at

the present juncture, after about two years’ time, the

Tumour Bank has almost ten thousand samples from

almost three thousand patients, 1383 (52.55%) of

whom are male, and 1249 (47.45%) are female.

With regard to the samples, 2306 are normal tissue

samples, 3221 are tumour tissue samples, 353 are

serum-type samples, 325 are leukocyte-type samples

and 3698 are blood-type samples. Fig. 2 shows some

data collected from one of the patient sample

reports.

Figure 2: Number of samples per histological type.

The forms are yet to be filled out in their entirety

since they are in the implementation stage. At the

present juncture, there are thirteen forms filled out

on penis cancer, fifty-eight on kidney cancer and

twenty-one on bladder cancer. Forms are established

in order to provide data to publish papers on cancer,

such as the paper on penis cancer (Babeto et al.,

2007). Fig. 3 provides some data on the number of

tumour samples collected per patient’s organ.

Figure 3: Number of tumour tissue samples per

topography.

6 THE BARRETOS CANCER

HOSPITAL AND THE AC

CAMARGO HOSPITAL IN SÃO

PAULO DATABASES

INTEGRATION

An important segment of this project is the

integration of the Barretos Cancer Hospital SCGBT

with the central bio-repository kept by the A.C.

Camargo Cancer Hospital in São Paulo (AC

Camargo Cancer Hospital, 2008). This bio-

repository is meant to receive and maintain, in a

centralized manner, the data from the associated

cancer research centers. By means of a data

communication system, Barretos Cancer Hospital

will provide its relevant data to this bio-repository.

At the present juncture, the data transmission model

is being prepared. Its basis will be the YAML data

structuring language (YAML Ain’t Markup

Language), a language that is similar to the widely-

known XML, but which is easier for humans to read

and understand (YAML, 2008).

7 CONCLUSIONS

The purpose of this paper is to introduce SCGBT,

which manages a cancer database. The use of human

tissue in the study is vital, since within the last few

ICSOFT 2008 - International Conference on Software and Data Technologies

270

decades there has been a decrease in the use of

animal cellular lineage and models in the study of

cancer. This trend has taken place concurrently with

the development of molecular studies and also with

the conception of a the neoplasic phenomenon as a

heterotypical process in which both the neoplasic

cell and the issue environment in which it develops

play a key role, since, in addition to the genetic

factors associated with the tumour, the individual-

related factors interfere with the tumour and its

response to treatment (Marahatta, 2005).

8 FUTURE WORK

As future work the integration with other tumour

banks will be developed. Another task to be

performed is the inclusion of reports and charts that

may provide a view of the distribution of the various

cancer-related data by geographic region (Carr et al.,

2003).

ACKNOWLEDGEMENTS

We wish to express our appreciation to FAPESP and

PROPG (Pró-reitoria de pós-graduação) for

providing financial support for this work; to

Fundação Pio XII, to IBILCE – UNESP, to Tamara

Colaiacovo for their collaboration to this project and

Dr. Geraldo Santiago Hidalgo, pathologist

responsible for the beginning of this project.

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