Laboratories Medical Bioinformatics set up at Medical Sciences University

دست‌یابی به تکنولوژی‌های جدید در علوم زیستی و پزشکی، همچون توالی‌یابی نسل بعد، زمینه پیشرفت سریع‌تر از پیش مطالعات را فراهم نموده است. از این رو، حجم بسیار عظیمی از اطلاعات اولیه فراهم می‌گردد و همچنان نیز رو به افزایش است. طراحی سیستم‌های پیشرفت‌های که تلفیقی از محاسبات کامپیوتری، علم آمار، تکنولوژی اطلاعات وهوش مصنوعی باشند، جهت ذخیره، پردازش و تفسیر این اطلاعات روبه افزایش، الزامی است(1). علوم ذکرشده با عنوان ابزارهای بیوانفورماتیکی جهت حل مسائل پیچیده زیستی و نتیجه‌گیری منطقی به خدمت گرفته می‌شوند. ژنومیک، ترانس کریپتومیک، پروتئومیک و متابولومیک، زمینه‌های اصلی مطالعات بیوانفورماتیک تلقی می‌گردند(2). امروزه، ابزارهای بیوانفورماتیکی متعددی به صورت دسترسی آزاد وonline توسط پایگاه داده‌ها و نرم‌افزارهای تحت وب، یا به صورت قابل ذخیره و اجرا در ویندوز با عنوان نرم‌افزار دسک تاپ و یا نرم‌افزارهایی قابل خریداری در اختیار محققان قرارگرفته‌اند(3). ظهور ابزارهای بیوانفورماتیکی و محاسبات کامپیوتری انقلابی در مطالعات زیستی و پزشکی ایجادکرده است. این ابزارها برای ذخیره، مدیریت، پردازش و تجزیه تحلیل داده‌های خام به دست آمده از تکنیک‌های پیشرفته‌ای چون توالی یابی نسل بعد و نتایج مطالعات معتبرمنتشرشده توسعه یافته‌اند(4). علاقمندی محققان سراسرجهان و رشد فزاینده دانش در این حیطه‌ی علمی، دست یابی به یافته‌های جدید و ظهور تکنیک‌های پیشرفته، محققان امروز را با حجم گسترده‌ای از داده‌های اولیه روبرو ساخته است. به کارگیری این داده‌های اولیه جهت سرعت بخشیدن به روند مطالعات امری اجتناب‌ناپذیر است. برقراری ارتباط و تفسیر منطقی این حجم از داده‌ها بدون کمک ابزار‌های بیوانفورماتیکی امکان‌پذیر نیست. ابزارهای بیوانفورماتیکی با اهداف عملکردی متنوع و با قابلیت به‌روزرسانی‌های مداوم جهت تسهیل وسرعت بخشید به مطالعات و نتیجه‌گیری‌های دقیق علم فراهم گردیده‌اند. با استفاده ازاین ابزارها در کم‌ترین زمان و با صرف کم‌ترین هزینه می‌توان بر اساس نوع هدف پیشرو به نتایج معتبری دست یافت(5). پس از معرفی ابزارهای بیوانفورماتیکی به جامعه علمی، پیشرفت سریع و گسترده‌ای درمطالعات مربوط به این زمینه به وجود آمد. ظهور این ابزارها آن چنان مورد استقبال محققان واقع شد که به سرعت درصد بالایی از مقالات معتبر منتشرشده به این حوزه اختصاص یافت. معرفی ابزارهای حاضر یا جدید و به کارگیری این ابزارها در مطالعات سلولی-مولکولی و ژنتیکی اصلی ترین مباحث در مقالات مربوطه هستند(6). در حال حاضر شاهد رشد چشم‌گیر به کارگیری این ابزارها در انواع زمینه‌های مطالعاتی در سطح آزمایشگاه و بالین هستیم(7). کاربرد ابزارهای بیوانفورماتیکی مربوطه در آینده نزدیک، نتایج ارزنده‌ای در زمینه‌ی معرفی بیومارکرهای جدید تشخیص، درمان و تهیه‌ی پروفایل اختصاصی به منظور شخصی سازی پزشکی به دست خواهد آمد. بی‌شک بدون دانستن بانک‌های اطلاعاتی و پایگاه‌های داده، پیدا کردن ارتباطات و کاربردی سازی این حجم عظیم اطلاعات امکان‌پذیر نخواهد بود. باتوجه به این که لایسنس این نرم‌افزارها بعضا دارای هزینه‌های زیادی است و بستر سخت‌افزاری پرهزینه‌ای که برای اجرای این نرم‌افزارها نیاز است، وجودآزمایشگاه‌های تخصصی در این حیطه را بیش از قبل ضروری می‌نماید. ازاین رو هدف بیان تجربه طراحی و پیاده‌سازی آزمایشگاه بیوانفورماتیک در دانشگاه‌های علوم پزشکی، گام‌ها و اهداف مشخص آن است

Designing and Implementation of Retina Image Drawing System and Automatic Report Generation from Retina Examinations

Introduction: Electronic medical records as one of major parts of electronic health records is an important application of Medical Informatics. EMR includes different types of data, Graphical items being one of these data types. To this end, a standard structure for storing and recovering and finally exchanging this data type is required. In order to standardize information items in this research, UMLS standard is used. In this research, graphical information from fondues designing in retina surgery forms is used for the task of implementation. Implementation: Three-layer software architecture is used for implementation of this system, which includes user interface, data base access and business logic. XML database is used for storing and exchanging of data. User interface is designed by the means of Adobe Flash. Also in the user interface for eye examinations, appropriate icons compatible with current pathologies in retina examinations are considered and UMLS codes are used for standardizations purposes. Results: As this project is independently implemented in Adobe Flash, it can be run in most of electronic patient records software. For evaluation purposes of this research, an EMR system for eye clinics is used. Tree structure is used for data entry and finally a text report based on the entered data will be generated. By storing graphical items in this software editing and searching in medical concepts and also comparing features will be available. Conclusion: One of the data items that we encounter in various medical records is graphical data. In order to cover the patient’s complete electronic medical records, the Electronic Implementation of this information is important. For this purpose, graphical items in retina surgery forms were used and finally a software application for drawing retina picture was developed. Also, XML files were used for the purpose of storing valuable medical data from the pictures, and also UMLS were applied for the standardization purpose. The developed software is currently being used in some of eye clinics in Ira

Use association rules to study the relation between variables that affect high blood pressure

Introduction :Due to the increasing development of industrial societies, special diseases were spread in this regard, particularly in Iran, because of improper life style of eating and physical activity, the prevalence of these diseases is high. One of these diseases is high blood pressure, which is the origin of many other diseases and thus, increase costs of the health budget is allocated to it. Usually the types of jobs, lack of exercise and poor diet can have a large impact on the disease. Methods :In this study, we try to use data mining algorithms; important relation between disease and high blood pressure are effective features, data on 1000 patients who entered our survey. Results and conclusions: This review was undertaken with association rules employment physical factors and smoking in people with low blood pressure have been seen. Obesity BMI above the low green fruit consumption in people with high blood pressure has been seen together

Semantic-Web Architecture for Electronic Discharge Summary Based on OWL 2.0 Standard

ABSTRACT Introduction: Patients’ electronic medical record contains all information related to treatment processes during hospitalization. One of the most important documents in this record is the record summary. In this document, summary of the whole treatment process is presented which is used for subsequent treatments and other issues pertaining to the treatment. Using suitable architecture for this document, apart from the aforementioned points we can use it in other fields such as data mining or decision making based on the cases. Material and Methods: In this study, at first, a model for patient’s medical record summary has been suggested using semantic web-based architecture. Then, based on service-oriented architecture and using Java programming language, a software solution was designed and run in a way to generate medical record summary with this structure and at the end, new uses of this structure was explained. Results: in this study a structure for medical record summaries along with corrective points within semantic web has been offered and a software running within Java along with special ontologies are provided. Discussion and Conclusion: After discussing the project with the experts of medical/health data management and medical informatics as well as clinical experts, it became clear that suggested design for medical record summary apart from covering many issues currently faced in the medical records has also many advantages including its uses in research projects, decision making based on the cases etc

Designing and Implementation of Fuzzy Case-based Reasoning System on Android Platform Using Electronic Discharge Summary of Patients with Chronic Kidney Diseases

Introduction: Case-based reasoning (CBR) systems are one of the effective methods to find the nearest solution to the current problems. These systems are used in various spheres as well as industry, business, and economy. The medical field is not an exception in this regard, and these systems are nowadays used in the various aspects of diagnosis and treatment. Methodology: In this study, the effective parameters were first extracted from the structured discharge summary prepared for patients with chronic kidney diseases based on data mining method. Then, through holding a meeting with experts in nephrology and using data mining methods, the weights of the parameters were extracted. Finally, fuzzy system has been employed in order to compare the similarities of current case and previous cases, and the system was implemented on the Android platform. Discussion: The data on electronic discharge records of patients with chronic kidney diseases were entered into the system. The measure of similarity was assessed using the algorithm provided in the system, and then compared with other known methods in CBR systems. Conclusion: Developing Clinical fuzzy CBR system used in Knowledge management framework for registering specific therapeutic methods , Knowledge sharing environment for experts in a specific domain and Powerful tools at the point of care

The Usage of Association Rule Mining to Identify Influencing Factors on Deafness After Birth

Background: Providing complete and high quality health care services has very important role to enable people to understand the factors related to personal and social health and to make decision regarding choice of suitable healthy behaviors in order to achieve healthy life. For this reason, demographic and clinical data of person are collecting, this huge volume of data can be known as a valuable resource for analyzing, exploring and discovering valuable information and communication. This study using forum rules techniques in the data mining has tried to identify the affecting factors on hearing loss after birth in Iran. Materials and Methods: The survey is kind of data oriented study. The population of the study is contained questionnaires in several provinces of the country. First, all data of questionnaire was implemented in the form of information table in Software SQL Server and followed by Data Entry using written software of C # .Net, then algorithm Association in SQL Server Data Tools software and Clementine software was implemented to determine the rules and hidden patterns in the gathered data. Findings: Two factors of number of deaf brothers and the degree of consanguinity of the parents have a significant impact on severity of deafness of individuals. Also, when the severity of hearing loss is greater than or equal to moderately severe hearing loss, people use hearing aids and Men are also less interested in the use of hearing aids. Conclusion: In fact, it can be said that in families with consanguineous marriage of parents that are from first degree (girl/boy cousins) and 2nd degree relatives (girl/boy cousins) and especially from first degree, the number of people with severe hearing loss or deafness are more and in the use of hearing aids, gender of the patient is more important than the severity of the hearing los

Designing Decision Support System to Detect Drug Interactions Type 2 Diabetes

Background and Aim: Type II Diabetes is the most common diseases of metabolic disorders and the treatment of oral anti-diabetic drug use takes place But The problem of using multi-drug and interactions at the same time is an issue that has always been a major challenge And diagnosis of drug interactions, particularly in Diabetic patients due to the problem with the disease is very important. The purpose of this studying is, to design a clinical assistant decided to use this approach to determine the type II diabetes drug interactions this makes it easy for those who are active in the field. Materials and Methods: Study is Developmental that to determine the content of the system a self-made checklist was used. Checklist Validity and reliability has been confirmed by four professors. The Research community to determine the content of the system was country endocrine that are 124 people.  The sample size was calculated using Cochran that was 57 people. The Score of checklist was calculated in SPSS version 20 .finally, the checklist was approved by at least 70% points. The system by using Microsoft SQL server 2008 and visual Studio 2012 development environment was designed in C#.net. In the end, In order to evaluate the software to determine the level of satisfaction, usability and ease of use, designed systems sharing with all Medical Informatics students of Tehran University of Medical Sciences. For this purpose a self-made questionnaire was used. Questionnaire Validity has been confirmed by four professors and reliability was assessed by Cronbach method. Results: The results of the survey are showing that the majority of students found out and believed the software is useful and easy to use and generally expressed their satisfaction software. Conclusions: The methodology provides a suitable approach for analysis and modeling of data in the medical field and the performance is good

Applying data mining techniques to determine important parameters in chronic kidney disease and the relations of these parameters to each other.

Introduction: Chronic kidney disease (CKD) includes a wide range of pathophysiological processes which will be observed along with abnormal function of kidneys and progressive decrease in glomerular filtration rate (GFR). According to the definition decreasing GFR must have been present for at least three months. CKD will eventually result in end-stage kidney disease. In this process different factors play role and finding the relations between effective parameters in this regard can help to prevent or slow progression of this disease. There are always a lot of data being collected from the patients' medical records. This huge array of data can be considered a valuable source for analyzing, exploring and discovering information. Objectives: Using the data mining techniques, the present study tries to specify the effective parameters and also aims to determine their relations with each other in Iranian patients with CKD. Material and Methods: The study population includes 31996 patients with CKD. First, all of the data is registered in the database. Then data mining tools were used to find the hidden rules and relationships between parameters in collected data. Results: After data cleaning based on CRISP-DM (Cross Industry Standard Process for Data Mining) methodology and running mining algorithms on the data in the database the relationships between the effective parameters was specified. Conclusion: This study was done using the data mining method pertaining to the effective factors on patients with CKD