BIOMEDICAL

INFORMATICS
(R4EC4111S)
PARVATHY LAKSHMY
ASSISTANT PROFESSOR
ELECTRONICS DEPT
VJTI
MEDICINE?
BIOMEDICINE?
INFORMATICS?
BIOMEDICAL INFORMATICS?
MEDICAL INFORMATICS
=MEDICINE+INFORMATICS

• MEDICINE: Is an old discipline of science and an art of

healing comprising a variety of practices to maintain and
restore health.
• INFORMATICS: Science of information researching in
computational methods therefore in using computers.
• MEDICAL INFORMATICS: Scientific field that deals
with the storage, retrieval and optimal use of biomedical
information, data and knowledge for problem solving and
decision making.
INADEQUACY OF TRADITIONAL
PAPER RECORDS

• Difficulty in obtaining information either about a patient or

a general issue related to patient management is a
frustrating job for medical practitioners
• This attracts them to move on with automated paper less
computer-based patient information.
• The complexity associated with automating medical
records is best appreciated if we analyse the processes
involved in the creation and use of such records.
USE OF COMPUTERS IN
BIOMEDICINE
• Biomedical application of computers invokes different images
based on the nature of one’s involvement in the field.
• Medical computer science is the subdivision of computer
science that applies to deal with larger field of medical topics
• Biomedical computing is where computers are involved for
purposes relating to biology and medicine.
• Biomedical informatics is broader than biomedical computing
which focuses on the nature of fields where computations are
applied.
NATURE OF MEDICAL DATA

• Medical information different from information in physics and engineering

• Includes the essence of uncertainty
• Contains high level processes carried out on complex objects like organisms
• Person using computers to analyse descriptions of these high-level processes faces serious
difficulties.
• Medical informatics include computers to process very low level descriptions to high level
descriptions that are systematically different.
• Improvements in hardware and software makes computers more suitable for medical applications.
CLINICAL DATA STANDARDS

• A standard can be defined as a set of rules and definitions that specify how to carry out a
process or produce a product.
• Common language for different systems and organisations to understand and use data
effectively.
• Enhance data quality, reduce redundancy, streamline data analysis.
• Clinical data standards are used to store and communicate information related to
healthcare so that its meaning is unambiguous.
NEED FOR CLINICAL STANDARDS

• As we acquire more patient data from Electronic Health Record(EHR), standards help us
make a sense of it.
• Makes it easier to parse data. Thus, vulnerable patients quickly get the care they need.
• Better care means more risk gaps closed.
COMMON CLINICAL STANDARDS

• CDISC, or Clinical Data Interchange Standards Consortium, is a non-profit organization

that develops data standards for clinical data collection and analysis.
i. Study Data Tabulation Model (SDTM)-Standard for formatting and organising data
for clinical trials. It’s easier to review, interpret and share data making it efficient for
more effective reviews and faster access to data.
ii. The Analysis Dataset Model (ADaM)-Provides datasets ready for statistical analysis of
clinical data.
 OTHER EXAMPLES

• Integrating the Healthcare Enterprise

• Omaha System

• ASC X12 (EDI) – transaction protocols used for transmitting patient data. Popular in the United States for transmission of billing data.

• CEN's TC/251 provides EHR standards in Europe

I. EN 13606, communication standards for EHR information.

II. HISA (EN 12967), a services standard for inter-system communication in a clinical information environment.

• DICOM – an international communications protocol standard for representing and transmitting radiology (and other) image-based data, sponsored by
NEMA (National Electrical Manufacturers Association)

• HL7 (HL7v2, C-CDA) – a standardized messaging and text communications protocol between hospital and physician record systems,

• Fast Healthcare Interoperability Resources (FHIR) – a modernized proposal from HL7 designed to provide open, granular access to medical
information

• ISO – ISO TC 215 provides international technical specifications for EHRs. ISO 18308 describes EHR architectures
 DATA IN NARRATIVE TEXTS

• The Clinical Narrative is a tool that allows therapists to describe and demonstrate their
practice within a specific case (over several days or treatment sessions) or at a specific
point in time.
• It provides the therapist with a tool for self-reflection on their current practice
• It enables the therapist to depict his/her current clinical practice.
• It presents information in a way that promotes discussion with colleagues.
 DATA IN NARRATIVE TEXTS

• Patient narrative is a summary of AEs occurring in a clinical trial patient/subject.

• The purpose of writing patient narratives is to provide a concise summary of
identified/specific adverse events (AEs) occurring in a patient to conclude causal
relationship between the investigational drug and AE.
• It should be written in a structured way with clear, concise, and logical flow of
information.
• In addition, it should also include patient identifier, age, sex, race (height and weight, if
relevant), disease being treated (if relevant), prior medications, medical history, and
active/ongoing medical conditions.
PRESENTATION OF NARRATIVE TEXTS

• The logical flow to describe events in a patient narrative is as described below:

i. Clinical course of the events, with an indication of timing of event corresponding to study drug
administration.
ii. Nature, intensity/severity, and outcome of the event
iii. Relevant laboratory findings
iv. Treatment administered for the event
v. Action taken with respect to the study drug
vi. Postmortem findings (if applicable).
vii. Investigator's and sponsor's assessment (if required) on causality.
TYPES OF NARRATIVE TEXTS

• The type of narratives depends on whether the trial is ongoing (interim analysis) or completed.
• For completed studies, if the number of narratives is large (approximately >150–200), narrative writing
activity usually starts along with cleaning of database.
• If the number of narratives is less (<150), narrative writing activity may start along with CSR(Clinical
Study Report) preparation.
• For studies under interim analysis (ongoing studies), it is advisable to initiate narrative writing activities
well before the data cutoff date and per protocol recommendations.
• In such cases, only the events which occurred before the cutoff date will have the narratives written for.
• Narratives may be written in text or tabular format depending on the requirement.
DATA SOURCES FOR NARRATIVE TEXTS

• Primary data source which includes clinical database (patient profiles in the form of
pdf/excel) or patient listings in the form of pdf/excel/doc, or case report form)

• Supplementary data sources such as Argus/Council for International Organization of

Medical Sciences/MedWatch forms/data clarification forms that aid in providing details
about the events and its course in the narrative.
NARRATIVE
WRITING
PROCESS
Narrative writing is a complex
process that involves various
stakeholders.
PROCESS

• The process begins with template finalization which is a crucial step in the NWP as it
avoids subjectivity.
• Finalized sample narratives need to be clear, concise, and appropriate, as they form the
basis for drafting further batches.
• Thus, an agreement with all the stakeholders/reviewers on the content/template of sample
narratives is desirable.
• Finally, the compiled batch of narratives is shared with the respective stakeholders before
publishing.
CHALLENGES IN NARRATIVE WRITING PROCESS

• Large number of resources required for any given project.

• Maintaining consistency in the narratives due to multiple resources working on the same project,
• Requirement of quick turnaround time and timely delivery with high quality,
• Not having standardize data sources/patient profiles for most of the programs.
• High variability in template finalization before and after sample narratives due to differences in opinion of
the reviewers.
• Change in reviewers during the intermediate/later stages of the project,.
• Delay in review cycles.
• Not receiving timely clinical team consensus on the addressed comments and pending queries.
MITIGATION STRATEGIES

• Excellent project management skills for efficient resource utilization.

• Automation of narratives.
• Standardization of data sources/patient profiles throughout the process.
• Finalization of template before starting sample narratives, in consensus with the clinical team.
• Rigorous follow-ups and proactive communication with all the stakeholders.
• Standardization of the review process.
• Regular calls with clinical team to address review comments or pending queries.
EFFECTIVE EXECUTION OF NARRATIVE
WRITING
• Review of data sources-Every data point in the template should be mapped against the
patient profile. Missing/discrepant data, if any, should be highlighted on an immediate
basis, and its inclusion or deletion in the narrative needs to be justified.
• Data validation-Narratives that are generated with the aid of automation tool needs
validation of data against the data sources to ensure quality. Any discrepancies should be
fixed immediately, to avoid such errors in the future batches.
• Quality calibration-Helps in tracking inter- and intra-variability while performing QC of
the document.
AUTOMATION OF NARRATIVES

• Automation in narrative writing is a current trend that every pharmaceutical industry is

adopting to provide quality and consistency within the narratives batch.
• The tool which helps in creating automated narratives, extracts relevant information for
all the identified patients in desired format/template.
• This tool is very helpful for studies with large volume of narratives (usually >150).
AUTOMATION OF NARRATIVES

The tool which helps in creating automated narratives, extracts relevant information for all the identified
patients in desired format/template. This tool is very helpful for studies with large volume of narratives
(usually >150).
The key features of autogenerated narratives are:
• Consistency in narratives
• High-quality narratives with minimal/no error
• Preformatted and editable narratives generation, which gives flexibility to modify based on the need
• Decrease turnaround time for overall narratives
• Ability to generate graphs and bar diagrams
MEDICAL REVIEW-AUTOMATION

• Medical and scientific review of the narratives is a must, even if the narratives are
generated with an automation tool.
• Narratives should make sense from a scientific perspective; hence a thorough medical and
scientific review is desirable to conclude events summary.
• A medical reviewer possesses in-depth knowledge of the therapeutic area and usually
verifies medical clarity of the events, safety data reported in the narrative, and flow and
alignment of contents according to the applicable regulatory requirements.
GENOMIC DATA

• Genomic data is data related to the structure and function of an organism's genome.
• Genomic data includes information like the sequence of molecules in an organism’s genes.
• It includes the function of each gene, the elements that control gene expression, and the
interactions between different genes and proteins.
• Genomic data science combines genetics and computational biology research with
statistical data analysis and computer science.
• Genomic data science integrates multiple datatypes to models which can predict the risk of
common diseases based on an individual's genetic information.
GENOMIC DATA

• Genomic data typically includes the following information:

• RNA: Molecule that transports genetic information in a cell and creates proteins. Scientists use
RNA in genomics for applications like gene expression, RNA interference, and translation.
• DNA: Genetic material of all living organisms. The DNA sequence contains information about
the structure and function of genes. Scientists study DNA data to identify and characterize
disease-causing mutations, understand how genes interact, and discover new genes.
• Proteins: Molecules composed of amino acids, which are involved in many cellular processes.
Proteins play a role in DNA sequences, gene expression, and other cellular activities.
APPLICATIONS OF GENOMIC DATA

• Life Sciences Research: To understand and explore the evolutionary history of

organisms.
• Genetic disease diagnosis: To diagnose and monitor genetic diseases like cancer, genetic
disorders, and inherited diseases.
• Drug Development: To investigate diseases or medical conditions, identify and assess
drug targets and develop new treatments.
• Forensic Science: To identify suspects in criminal cases.
• Population Genetics: To study population genetics and evolutionary history
GENOME DATA ANALYSIS TECHNOLOGIES

Genomic data analysis involves the use of various technologies to identify patterns and trends in
genetic data. They are:
• Bioinformatic tools
• Machine learning
• Statistical software
• Sequencing technology
• Visualization tools
• Big data tools
GENE EXPRESSION AND PROTEIN DATA

• Gene expression is the process by which the information encoded in a gene is turned into
a function. This mostly occurs via the transcription of RNA molecules that code for
proteins or non-coding RNA molecules that serve other functions.
• Genes are frequently expressed in the form of the types of proteins they create.
• The sequence of any protein that is created is extracted from underlying DNA through
the process of RNA transcription.
• A technology that allows biologists and machine learning scientists to analyse gene
expression data is that of microarrays.
GENE EXPRESSION AND PROTEIN DATA

• Measuring and analysing gene expression is important, as the level of expression of a particular
gene within a cell can give large amounts of information.
• There are various gene expression analysis methods, including serial analysis of gene expression
(SAGE), microarrays, and RNA sequencing (RNA-Seq).
How it Works?
• When genes are expressed, the genetic information on the DNA is first copied to a molecule of
mRNA .
• The mRNA molecules then leave the cell nucleus and enter the cytoplasm, where they participate in
protein synthesis by specifying the amino acids that make up individual proteins (translation).
GENE EXPRESSION AND PROTEIN DATA

• Gene expression be thought of as an “on/off switch” to control when and where RNA
molecules and proteins are made and as a “volume control” to determine how much of
those products are made.
• The process of gene expression is carefully regulated, changing substantially under
different conditions and cell types. The RNA and protein products of many genes serve to
regulate the expression of other genes.
• Where, when, and how much a gene is expressed can also assessed by measuring the
functional activity of a gene product or observing a phenotype associated with a gene.
GENE EXPRESSION AND PROTEIN DATA

• With current technologies, we can measure mRNA expression of every gene in the entire genome.
• This is a powerful tool to help us measure which genes are turned on, how much and where.
• Classically, we can also measure gene expression by observing a phenotype or a trait. Examples of those would
be to measure a protein activity.
• If a protein activity can be measured, the gene that encodes for that protein is probably turned on or we can define
it as turned on.
• We can also look for patterns and traits.
• So, for example, if a beautiful butterfly wing with multiple colours is the result of different genes being turned on
in different places in the butterfly wing, then we can measure that gene expression simply by observing the wing
of the butterfly and marking the locations of the colours.
GENE EXPRESSION AND PROTEIN DATA

• Messenger RNA (abbreviated mRNA) is a type of single-stranded RNA involved in

protein synthesis.
• mRNA is made from a DNA template during the process of transcription. The role of
mRNA is to carry protein information from the DNA in a cell’s nucleus to the cell’s
cytoplasm (watery interior), where the protein-making machinery reads the mRNA
sequence and translates each of these into its corresponding amino acid in a growing
protein chain.
GENE EXPRESSION AND PROTEIN DATA

• mRNA really is a form of nucleic acid, which helps the human genome which is coded in
DNA to be read by the cellular machinery.
• Between the DNA code itself, and the machinery that uses DNA to make proteins, there
must be a translator. And mRNA is the translated form of DNA that the machinery can
recognize and use to assemble amino acids into proteins.
• It is a fundamental link between what we think of as being the code of life and the actual
cell being able to construct a living organism.
• mRNA is a crucial piece of the fundamental way in which the living organism is created.
HEALTH INFORMATION SYSTEMS

• Powerful Information and Communication Technology(ICT)-based tools able to make health care
delivery more effective and efficient.
• Comprises of different applications that support the needs of health care organizations, clinicians
and patients in collecting and managing all the data related to both clinical and administrative
processes.
• These data can be used across several systems for many different purposes.
• They must be integrated with the data from other entities to be effective-especially for patient
data.
• Must be subject to strict rules in terms of confidentiality and security safeguards.
HEALTHCARE INFORMATION SYSTEMS

• Six elements that make Healthcare information systems important:

i. The gravity associated with information mismatches

ii. The personal nature of most of the information managed by health information systems.
iii. The professional-driven and hierarchical nature of health care organizations.
iv. The multidisciplinary of the people who access HCISs.
v. The conclusions for learning and adaptation associated to the implementation of an HCIS.
HOSPITAL INFORMATION SYSTEMS

• A Hospital Information System (HIS) is a set of organizational structures, information

flows and ICT-based solutions that support core and secondary processes of a hospital.
• Responsible for supporting secondary care and are the combination of a variety of
interconnected systems that manage a huge amount of narrative, structured, coded and
multimedia data.
• The HIS not only manages complex and widespread processes but store and make
accessible all the information needed by the staffs of the hospital.
HOSPITAL INFORMATION SYSTEMS

Primary (or core) processes, related to direct patient care are:

• Admission: Disease prevention, inpatient or outpatient event booking and hospital
admission;
• Anamnesis: Definition of patient’s clinical status from a medical and nursing perspective.
• Diagnosis: Definition of patient’s therapeutic and care plan;
• Care: Therapy, treatment, rehabilitation;
• Discharge and follow-up: Patient discharge and possible transfer to outpatient or home
care for follow-up activities.
HOSPITAL INFORMATION SYSTEMS

Secondary (or support) processes are :

• Strategic services: Strategy, planning and controlling, supervision of regulations.
• Administrative services: Administration and accounting, information systems, quality
assurance, human resources.
• Technology services: Clinical machinery, biotechnologies, building automation, auxiliary
systems.
• Sourcing and logistics.
HOSPITAL INFORMATION SYSTEMS

From a functional viewpoint, the main areas of an HIS are:

• The administration and management area, which supports strategic and administrative
processes
• The front-office area, which supports the admission of inpatients, outpatients, or
emergency/first aid patients;
• The clinical area, which supports the core health care processes (the processes through
which health care organizations provide treatment to patients).
ADMINISTRATION AND MANAGEMENT AREA

• The administration and management area supports processes like general administration
and procurement, planning and management control, and resource management.
• The components related to this area have the responsibility to support the company in
managing the activities of an administrative/accounting nature.
• Two main components of administration and management area are:
i. Administration and accounting suite
ii. Management of human resources
FRONT OFFICE AREA

• The front office area deals with patient reception, and distinguishes between inpatients,
outpatients and patients in the emergency unit.
• These sub-areas manage the workflows related to the waiting lists or the appointment
management.
• Common solutions are the Centralized Outpatient Booking Centre (COBC) and the
procedures related to Acceptance-Discharge-Transfer (ADT).
• The proper functioning of the COBC system is made possible by a front- and back-office
service, responsible for programming functions and access management.
FRONT OFFICE AREA

• ADT systems manage the processes related to hospitalized inpatients.

• In accordance with the hospital’s organization, ADT systems can provide the services in (i)
centralized mode, (ii) distributed in the wards, or even (iii) in mixed mode (e.g. acceptance can
be centralized while transfers and dismissals can be handled by wards).
• Emergency and first aid systems are made for both the organizational aspects of emergency
events as well as the direct impact on citizens who request services considered essential for their
health.
• These systems must also be able to support the doctor in requesting diagnostic support as well
as in making decisions as quickly and safely as possible.
CLINICAL AREA

• Most complex and most delicate area due to its broad support to all the core processes of a hospital.
• Most challenging area in terms of management, due to the involvement of critical patient data, on one
side and on the other side, to pre-existing systems implemented independently by each department or
ward in different periods.
• Clinical systems are mainly (i) Departmental systems or (ii) Electronic Medical Records
• The former support both clinical and administrative tasks in diagnostic services and are fed by the
requests coming from wards or outpatient offices.
• The latter should be responsible for the digitally-integrated management of clinical information to
support care and acts as the unique point of reference for clinical decisions.
CLINICAL AREA

• Departmental systems receive requests from COBC or from the order management systems in the
wards, they support the execution phases of tests, notify the patients regarding the execution of the
examination, and produce reports that are stored in the clinical repository.
The most common departmental systems are:
i. The Radiology Information Systems (RIS)-Manage the acquisition of radiological images, their
analysis and reporting.
ii. The Laboratory Information Systems (LIS)-Automatically manage the exam requests from the
clinical units and supports the validation of the results.
iii. The applications for the operating room.
CLINICAL AREA

• The Electronic Medical Record (EMR) is the central element of the HIS.

• To collect information on the clinical history of patients during hospitalization to support the multidisciplinary
communication between professionals, operations management and decisions.

• Five functional areas of EMR:

i. The ADT Area-Manages patient admissions, discharges and transfers within the hospital.

ii. The Diagnostic Area.-Allow the requests of exams and the delivery of reports to/from wards.

iii. The Clinical Dossier-Management of all medical and nursing sheets, including initial assessment,
anaesthesiology documents, Surgery reports etc.

iv. Therapy management-Support to prescription and administration of drugs, transfusions, nutrition, etc

v. Out-patient management-Manages admission and medical reporting for outpatients and feeds the patient’s
EMR with information like preliminary reports or follow-up examinations.
SHARED SERVICES

• Components that complement the HIS architecture.

• The shared services are:
i. Central Patients and Encoding Database: Responsibility to centrally manage patient
identifiers to make them available to other components of the HIS.
ii. Prescriptions Generation: Allows the preparation, digital signature and issue of all
prescriptions to be used outside the hospital.
iii. Order Entry: Manages ward requests for internal exams and second opinion
consultations;
SHARED SERVICES

i. Medical Reports Generation: Supports the issue of legally compliant medical reports
for all hospital services;
ii. Clinical Repository: this is a central archive of (i) all kinds of digitally-signed medical
reports, (ii) structured data, (iii) patient events (e.g. transfusions, surgery) and
(iv)many others, from exam requests to therapy prescriptions.