1.
CLINICAL SOURCES IN HEALTH CARE
• PRIMARY SOURCE
Where the data is produced (laboratories, clinical center devices, biosensors, etc.).
• SECONDARY SOURCE
Where the data is stored (repositories, Health care record, etc.).
Health Care Record (HR) = structured and systematic documentation about one single
patient’s medical history and care across the time.
Clinical Data Repository (CDR) = real-time data base that consolidates data from a variety
of clinical sources to present a unified view of a single patient.
Clinical Data Warehouse (CDW = CDR + HR) = data base containing data from múltiple
sources.
The difference between them are that CDR updates the information of the CDW
periodically.
Big Data = data that contains greater variety in big volumes, higher veloicity and
qüestionable veracity. These are known as the 4Vs.
2. DATA USES IN HEALTH CARE
• PRIMARY USE
The main purpose is to deliver Health care to the patient. There is no need to ask
permission to the patient to access rights.
• SECONDARY USE
The data is used for other than Health care provision pusposes. In this case, you need to
ask permission to the patient to use the data.
3. TYPES OF DATA
There are 6 major types of data:
- Health care record data: is obtained at the point of care at a medical facility, hospital,
clinic or practice. The data collected includes administrative and demographic
information, diagnosis, treatment, prescription drugs, laboratory tests, physiologic
monitoring data, hospitalization, patient insurance, etc.
- Administrative data: dades d'alta hospitalària comunicades a una agència
governamental
- Claims data: fa referencia a les assegurances entre els pacients i el sistema d’assistència
sanitària.
- Patient-disesase registry data: sistemes d'informació clínica que rastregen una gamma
reduïda de dades clau per a determinades condicions cròniques com la malaltia
d'Alzheimer, càncer, diabetis, malalties del cor i asma.
- Health surveys data: in order to provide an accurate evaluation of the population health.
- Clinical trials data: data on a subset of subjects in order to test a treatment before it is
introduced in a health care system.
The data can be collected in diferent formats.
- Structured: values obtained directly from the patient, such as the temperature, and are
stored in variables.
- Unstructured: images and charts.
The clinical data sometimes contains cumulative and non-cumulative data:
- Cumulative: displays the total amount of information that’s been gathered over a period
of time.
Count = indicates a quantity.
Ratio = number divided by another number
Proportion = ratio of counts where the numerator is a subset of the denominator.
Percentage = proportion expressed as a percentage.
Risk = proportion where the numerator counts events that happen prospectively.
Rate = proportion that involves a time.
- Non-cumulative: shows the amount of information gathered only at a certain point in
time.
4. VARIABLES
CLINICAL VARIABLES
ACCORDING THEIR ACCORDING THE
RELATIONSHIP POSSIBLE VALUE
INDEPENDENT QUALITATIVE
QUANTITATIVE
We can control or Don't have numerical
Numerical interpretation
change (dosi) interpretation
DEPENDENT NOMINAL
DISCRETE
Variable that we Their values are labels
Some values are possible
measure (temperature) (male/female)
ORDINAL
CONTINUOUS´
Their values represent an
order (pain score 0-10) All values are possible
5. DATA TRANSFORMATIONS
• DISCRETIZATION: NUMERIC → CATEGORICAL
The goal of discretization is to reduce the number of values a continuous variable assumes
by grouping them into a number of n intervals or bins.
Benefits: memory save, data simplification, easier to model, application of discrete
methods, can improve the performance of patient classification.
- By value
0,0,0,1,1,1,1,1,2,2,3,4,4,5,5 (discrete) → g0, g0,g0,g1,g1,g1,g1,g1,g2,g2,g3,g4,g4,g5,g5
(nominal)
0,0,0,1,1,1,1,1,2,2,3,4,4,5,5 (discrete) → 0,0,0,1,1,1,1,1,2,2,3,4,4,5,5 (ordinal)
- By rounding
37.51,38.3,36.47,39.0,39.4,36.8,37.8 (numeric) → 38, 38, 36,39,39,37,38 (ordinal)
- By truncation
37.51,38.3,36.47,39.0,39.4,36.8,37.8 (numeric) → 37, 38, 36, 39, 39, 36, 37 (ordinal)
- By size
Input = size of the grup = n
Groups of n.
- By user specification
Input = condition = baby (<2y), infant (2-16y), young (17-22), adult (22-65y), elder (>65y)
1,2,2,5,12,13,18,18,20,30,35,35,40,70,76,76 (numeric) → B,I,I,I,I,I,Y,Y,Y,A,E,E,E
(categorical)
- By binning
Separate in n equally groups.
Input = number of bins = n
S=(Max-min)/n is the size of each bin
1,2,2,5,12,13,18,18,20,30,35,35,40,70,76,76 (numeric) → (76-1)/5=15 →
[1,16),[16,31),[31,46),[46,61),[61,76] →
g1,g1,g1,g1,g1,g1,g2,g2,g2,g2,g3,g3,g3,g5,g5,g5 (categorical)
- By frequency
Input = number of bins = n
1,2,2,5,12,13,18,18,20,30,35,35,40,70,76,76 (numeric) → 16/5 = 3 values per bin →
g1,g1,g1,g2,g2,g2,g3,g3,g3,g4,g4,g4,g5,g5, g5, g6→g5 (nominal)
• CONTINUITY: CATEGORICAL → NUMERIC
The goal of continuity is to convert a nominal variable into a numeric variable by projecting
it in a continuous space.
Benefits: application of numèric methods and can improve the performance of patient
classification.
- Binary to continuous = one of the binary values (false) is converted to 0, the other one
(true) is converted to 1.
- N-ary to numèric
o Unique integers: drugs acting on the
cardiovascular system are codified as
numbers.
o Dummy coding: the use of a drug d in a treatment is marked with 1/0 in the
corresponding new numeric column d.
d1, d2, d1, d1, d3, d4, d2, d4, d3 → 1000, 0100, 1000, 1000, 0010, 0100, 0001,
0010
o Dummy coding with comparison group: the use of a drug d≠g in a treatment is
marked with 1/0 in the corresponding new numeric column d. Drug g does not
have a column.
d1, d2, d1, d1, d3, d4, d2, d4, d3 (comparison group d2) → 100, 000, 100, 100,
010, 001, 000, 001, 010
o Effect coding with comparison group: the use of a drug d≠g in a treatment is
marked with 1/0 in the corresponding new numeric column d. Drug g does not
have a column. Drug g has all d≠g columns to -1.
d1, d2, d1, d1, d3, d4, d2, d4, d3 (comparison group d2) → 100, -1-1-1, 100, 100,
010, 001, -1-1-1, 001, 010
6. WRONG, MISSING, AND CENSORING DATA
Wrong data = the values of the data is incorrect because:
- The person introducing it made a mistake
- Wrong default values
- Values out of range
Missing data = the value of the data is unknown because:
- A clinical Device is disconnected
- The data was not taken
- The data is protected/private/unavailable
Censoring data = the value of the data is partially unknown because…
- The data was approximated during introduction
- Device does not reach the values measured (e.g., scale registering weights until 150kg,
and patient is over weighted).
Dealing with types of data:
1. Detect: not always possible
2. Correct: several alternatives such as remove instances, remove feature, encoding,
imputation (replace or predict) or leave as NA and use algorithms capable to manage
them.
7. BIG DATA IN HEALTH CARE
Data can have different sizes:
- Bit = 1/8 byte
- Nibble = ½ byte
- Byte = 8 bits
- Megabyte = 1024 kilobytes
- Gigabyte = 1024 megabytes
- Terabyte = 1024 gigabytes
- Petabyte = 1024 terabytes
- Exabyte = 1024 petabytes
Big Data is known for have 4Vs = volume, velocity, variety and veracity
8. STANDARDS OF BIOMEDICAL DATA
Clinical Data Standards are used to codify clinical information, diagnoses, procedures, and
laboratory tests, ensuring consistent terminology across healthcare systems.
• INTERNATIONAL CLASSIFICATION OF DISEASES (ICD)
ICD provides alpha numeric codes to classify diseases and a wide variety of signs, symptoms,
abnormal findings, complaints, social circumstances and external causes of injury or disease.
There are different versions of ICD:
- ICD-9-CM
It consists of 3 volumes: V1-V2 for diagnosis codes, V3 for codes about surgical,
diagnostic, and therapeutic procedures.
Is coded by numbers.
Volumes 1-2 – Diseases:
Format = NNN.N[N]
Example = 540.9 -Acute appendicitis without mention of peritonitis
Volumes 3 – Procedures:
Format = NN.N[N]
Example = 38.34 -Resection of vessel with anastomosis, aorta
- ICD – 10 – CM & ICD – 10 – PCS
ICD-10-CM for diagnosis codes, replacing volumes 1 and 2. ICD-10-PCS(PCS stands for
Procedure Coding System) for procedure codes, replacing volume 3.
Is coded by a character and two numbers.
ICD-10-CM -Diseases:
Format = ANN.N[NNNA]
Example = M24.542 - Contracture, left hand
ICD-10-PCS - Procedures:
Format = XXXXXXX (alphabetic or numeric)
Example = 30243G0 -Transfusion of Autologous Bone Marrow into Central Vein,
Percutaneous Approach
- ICD – 11 – CM
Is for diagnosis codes.
Format = XXXX.X[X]
Example = 1C12.0 Whooping cough due to Bordetella pertussis
Comparision beetween ICD – 9 AND ICD - 10:
Comparision beetween ICD10 and ICD11
ICD has been reviewed to accommodate for the needs of multiple use cases and users in
recording, reporting, and analysis of health information. ICD-11 comes with:
- Improved usability: more clinical detail with less training time (you can reach a disease
more faster)
- Updated scientific content
- Clinical detail: enables coding of all clinical detail (more details of a disease)
- Computerization: made eHealth ready for use in electronic environaments
- Interoperability: linked to relevant other classifications and terminologies
- Multilingual: full multilingual support (translations and outputs)
• DIAGNOSIS – RELATED GROUPS (DRG)
DRG = is a classification of the services that acute health care centers can provide. DRGs were
intended to describe all types of patients in an acute hospital setting. It has been used in the US
to determine how much medicare pays the hospital for each service, since patients within each
category are clinically similar and are expected to use the same level of hospital resources. DRGs
are assigned to patients by a grouper program based on ICD diagnoses, procedures, age, sex, etc.
• INTERNATIONAL CLASSIFICATION OF PRIMARY CARE
It classifies patient data and clinical activity in the domains of general/family practice and
primary care, taking into account the frequency Distribution of problems seen in theses domains.
Comparision beetween ICPC and ICD
ICD ICPC
It is oriented to primary care.
Covers the need of hospital
It covers multiple episodes of
care where patients normally
INTENTION care over time and feal with
present for a single episode
many and undifferentiated
of care.
problems simultaneously.
Reflect the content of
CONTENT
primary care
14000-140000 codes with a
SIZE 1300 codes
complex coding System
More specicificity for all three
STRUCTURE Less specificity
elements of the encounter
MULTILINGUAL Not all types Yes
Episode of care (RFE + diagnosis + procedure) = healthcare management and billing concept
that refers to a specific period during which a patient receives a sequence of healthcare services
related to a particular health issue, condition, or treatment.
RFE (symptoms) = Patient’s Reason for Encounter (e.g., headache)
Diagnosis = differential knowledge acquired about the patient’s physical or psychical state.
Procedure = treatment action(s) or test(s) started on the patient.
• CLASSIFICATION OF FUNCTIONING, DISABILITY AND HEALTH (ICF)
ICF = it is the WHO framework for measuring health and disability at both individual and
population levels.
ICF has 4 chapters: b, d, e, s
Format = A-N-NN-N
Example = d4100 – Lying down
• CURRENT PROCEDURAL TERMINOLOGY (CPT)
Current Procedural Terminology = it is a medical code system describing clinical procedures and
services (either medical, surgical, and diagnostic) addressed to physicians, health insurance
companies and accreditation organizations.
CPT coding is similar to ICD-9 and ICD-10 coding, except that it identifies the services rendered,
rather than the diagnoses.
Three categories of CPT codes:
- Category I: coding procedures and contemporary medical practices. It is organized in 6
groups (NNNNN)
- Category II: Clinical laboratory services (NNNNA). Complementary to category I, but have
not attached costs.
- Category III: Emerging technologies, services, and procedures (NNNNA). New things that
are expecting to be incorporated in category I.
• ANATOMICAL THERAPEUTIC CHEMICAL CLASSIFICATION SYSTEM (ATC)
ATC = codification system in which drugs are classified at five levels.
Format = A-NN-A-A-NN
Levels:
- Level 1: Anatomical main Group (A): 14 groups
- Level 2: Therapeutic Subgroup (NN)
- Level 3: Therapeutic/Pharmacological Subgroup (A)
- Level 4: Chemical/therapeutic/pharmacological Subgroup (A)
- Level 5: Chemical Substance (NN)
• LOGICAL OBSERVATION IDENTIFIERS NAMES AND CODES (LOINC)
Logical Observation Identifiers Names and Codes (LOINC) = an international standard to assist
in the electronic exchange and gathering of clinical results (such as laboratory tests, clinical
observations, outcomes management and research).
LOINC has two parts:
- Laboratory: to describe results of laboratory and microbiology tests
- Clinical: to refer to a variety of non-lab concepts (e.g., ECG, cardio echo, ultrasound).
Each code has six dimensions or parts:
- Component (Analyte): the substance or entity being measured or observed.
- Property: the characteristic or attribute of the analyte.
- Time: the interval of time which an observation was made.
- System (Specimen): The specimen or thing upon which the observation was made.
- Scale: how the observation value is qualified or expressed: quantitative, ordinal,
nominal.
- Method (optional): how the observation was made.
Example = code 806-0 (parts Leukocytes: NCnc: Pt: CSF: Qn: Manual count) stands for “manual
count of white blood cells in cerebral spinal fluid specimen”.
- NCns = number concentration
- Pt = Point in time
- CSF = cerebral spinal fluid
- Qn = quantitative.
• SYSTEMATIZED NOMENCLATURE OF MEDICINE (SNOMED CT)
Systematized Nomenclature of Medicine - Clinical Terms = it is the most comprehensive,
multilingual and codified clinical terminology developed in the world. SNOMED CT is also a
terminology product that can be used to encode, retrieve, communicate, and analyze clinical
data, enabling healthcare professionals to represent information in an appropriate, accurate, and
unambiguous way. Terminology is constituted, in a basic way, by concepts, descriptions and
relationships. These items are intended to accurately represent clinical knowledge and
information in the healthcare setting.
Diagrams:
• UNIFIED MEDICAL LANGUAGE SYSTEM (UMLS)
UMLS = set of files and software that brings together many health and biomedical vocabularies
and standards to enable interoperability between computer systems.
The UMLS integrates and distributes key terminology, classification and coding standards, and
associated resources to promote creation of more effective and interoperable biomedical
information systems and services, including electronic health records.
9. INTEROPERABILITY
Interoperability is the ability of diverse systems and organizations to work together seamlessly.
That means exchanging information and using the information that has been exchanged.
- Syntactic Interoperability: when two or more systems are capable of communicating and
exchanging data by using the same data formats or communication protocols XML and
JSON are examples of data exchange formats
- Semantic Interoperability: ability to automatically interpret the information exchanged
meaningfully and accurately in order to produce useful results for end users. To achieve
semantic interoperability, both sides must obey a common information exchange
reference model The content of the information exchange requests are unambiguously
defined what is sent is the same as what is understood.
10. EHR SYSTEMS
Electronic Health Record (EHR) = it is an electronic platform that collects medical information
about a person and it is stored on a computer. It includes information about a patient’s Health
history such as diagnosis, medicines, tests, etc. This information can be shared between any type
of health care professional and all of them can access to this data. Can be shared between Health
care centers.
Personal Health records = it contains the same information as EHRs but in this case, it is designed
to be set up, accessed and managed by patients. Example = aplicació la meva salut.
Electronic medical records = is a digitalized form of a paper chart that is consistently updated
and contains comprehensive medical and clinical information from 'one' healthcare provider's
practice, including demographics, medical conditions, medications, vital signs, immunizations,
etc. It can’t be shared between clinical centers; each hospital has the own medical record of each
patient.
10.1. PARTS OF AN HER
The parts of an EHR are:
• Health Data and Information: contain certain data about patients.
The difference between data and information is that data are symbols representing
numbers, letters, words, whereas information is an assignment of a meaning to data that
allows decision making and knowledge generation. In other words, data are values or
variables, and information is the explication and the meaning of the data. For example,
the data is 37º and the information is that patient has fever. The data can be introduced
in EHRs in either a structured and unstructured format.
There are different categories of EHR data and information:
- Patient demographics
- Patient list of problems and diagnosis
- List of medications
- List of allergies
- Clinical documentation
- Patient orders
- Medication and administration record (MAR)
• Results management: contain the results of the clinical tests, diagnostics tests and
consultive exams (ECG, MRI, CT, potassium level, complete blood count, etc.).
• Order entry and management: contain the treatment orders asked by the Health Care
professionals.
Computerized provider order entry (CPOE) is an application that allows health care
providers to use a computer to directly enter medical orders electronically in inpatient
and ambulatory settings, replacing the more traditional order methods of paper, verbal,
telephone, and fax.
Benefits:
- Reduction of errors because hand-writing
- Automatic filling of fields in the order
- Automatic incorporation of orders in the EHR of the patient
- Electronic prescription
- Time reduction
- Automatic detection of medication errors and interactions
- Paper elimination and cost reduction
• Clinical decision support: contain some tools for decision support.
Clinical decision support (CDS) is a component in EHR that uses patient’s data and
information to assist the provider, nurse, and other professionals to make optimal
decisions about a patient’s treatment plan. CDS and CPOE proved a beneficial symbiosis
working together.
This component was not possible in paper-based health records.
• Electronic communication and connectivity: facilitate secure data communication
between different units in the same health care center or among centers.
It allows data communication:
- Data sources: where HER data is produced
- Data storages: where HER data is stored
- Data uses: where HER data is consumed / required.
It also allows EHR access to Internet.
It is related to IT security.
• Patient support: this component provide support to the patients.
These modules can be accessed by patients providing patient-oriented support and
educative information.
An example would be that if you enter in the app “la meva salut” you can found some
tips to avoid covid.
• Administrative processes: this component allows health care organization around the
patient.
It is normally used during admission, discharge (alta) or visit.
It uses to be centered on demographic information, the patient receives a medical record
identifier, patient’s insurance or payer information and patient locations (rooms, ICU
rooms, etc.).
• Reporting and Population Health Management: this module extract summary
information required by National Health Care systems.
This component in an EHR is used by health care centers to report their activities and
information to federal, state and local governmental institution and to report to the
hospital.
Automating EHR data extraction should be achieved with HER modules implementing
theses extractions and processing algorithms. There components reduce time, costs and
accuracy during reporting.
10.2. EHR SOFTWARE STRATEGIES
Ad hoc strategy = the hospital IT staff develops their own system.
Off-the-shelf strategy = the hospital purchases a software and customizes it.
- Single EHR: a single software is available with modules for financial, billing, human resources,
material management, etc. It’s a neat compact solution.
- Best-of-breed strategy: many vendors solutions are analyzed and the best components of
each are purchased and integrated. It involves intensive interface development between
components.
- Best-of-suite strategy: there is a core EHR to which other software systems are integrated.
10.3. HEALTH INFORMATION SYSTEMS (PAST, PRESENT AND FUTURE
CHALLENGES)
I. Shift from paper-based to computer-based processing and storage, as well as the
increase of data in health care settings
II. Shift from institution-centered departmental and, later, hospital information systems
towards regional and global HIS
III. Inclusion of patients and health consumers as HIS users, besides health care
professionals and administrators
IV. Use of HIS data not only for patient care and administrative purposes, but also for health
care planning as well as clinical and epidemiological research
V. Shift from focusing mainly on technical HIS problems to those of change management
as well as of strategic information management
VI. Shift from mainly alpha-numeric data in HIS to images and now also to data on the
molecular level
VII. Steady increase of new technologies to be included, now starting to include ubiquitous
computing environments and sensor-based technologies for health monitoring
10.4. EHR STANDARDS
The most important standards are:
• HL7
It is a set of international standards for transfer of clinical and administrative data
between software applications that are used by various healthcare providers.
They ate produced and maintained by Health Level Seven International.
HL7 version 3 offers a Reference Information Model to standardize the fromat of HL7
messages and documents
- HL7 messages in v3 are not as much used as HL7 v2 messages
- HL7 v3 documents are based on the Clinical Document Architecture, which
specifies document types for sharing, exchange, and reuse. It uses XML notation
- Unlike messages, documents do not contain rules for transmission
- Documents can be combined with other standards
HL7 CDA provides a standard for the representation, persistence and communication of
clinical documents for exchange between systems. A CDA document is a tree structure
in which higher levels can contain lower level CDA structures.
A CDA document is an XML file composed of:
- Header: identifies the patient, provider, document type, etc.
- Body: contain the complete content and an optional encoded part that can be
safely ignored by recipients which are unable to process it.
Classes (levels) of CDA documents:
- Level 1 (Body): with a NonXMLBody. It is composed ot two parts (human
readable representation of the document and machine processable part)
- Level 2 (Section): with a StructuredBody containing textual sections. Each one of
the body components.
- Level 3 (Entry): with a StructuredBody containing textual sections with codified
entries for machine processing. It allows semantic interoperability.
• OpenEHR
OpenEHR is an open standard that specifies all the architectural components needed to
create health information systems that are interoperable, highly maintainable and very
flexible. It describes the management and storage, retrieval, and exchange of health
data in EHRs. It has three basic components:
o Reference Model (RM) = is a hierarchy of data structures and ins NON-
MODIFICABLE. It describes all the basic classes in openEHR. The classes are
organized in packages:
- Package EHR_extract - Package EHR
- Package demographic - Package integration
- Package composition - Package common
- Package data_structures - Package data_types
- Package support
o Knowledge or Archetype Model (AM) = composed of models to describe
templates or archetypes (prototips). Each archetype defines a topic-related set
of data groups and elements and each one has a concept name, description,
purpose, use and possible misuses.
There are 4 basic classes to describe archetypes:
- Composition
- Section
- Entity: can be an observation (information on what data components
represent blood pressure), evaluation (data units to the evaluation of
gender), action (what are the features of a procedure), instruction
(elements describing the activity) or admin (relevant components to get
captured at admission time such as room, bed, point of care, etc.).
- Cluster
OpenEHR templates are combinations and constraints on archetypes to create
context-specific clinical data sets and documents such as clinical notes, discharge
summary documents, or messages that will be used in EHR systems.
To make a template, is important to follow the steps:
1. Determine how many organizational models are used (how many
sections)
2. Select the archetypes that will have each section
3. Set default values in the primary archetypes
4. Specialize some archetypes
The openEHR Clinical Knowledge Manager (CKM) is an international, online
clinical knowledge resource to manage openEHR archetypes and templates that
has gathered an active community of interested and motivated individuals from
around the world focused on furthering an open and international approach to
clinical informatics for sharing health information between individuals, clinicians
and organizations; between applications, and across regional and national
borders.
The new archetypes can be generated by different ways:
- From scratch: we can generate an archetype for a new concept.
- By specialitzation: we can take an existing archetype and refine it to
represent a more specific archetyp.
- By composition: we can take several existing archetypes and combine
them to form a new more complex archetype.
o Service Model (SM) = includes definitions of basic services in the health
information environment.
• EHRcom
EHRcom was the European Standard for an information architecture to communicate
Electronic Health Records (EHR) of a patient.
This standard was intended to support the interoperability of systems and components
that need to communicate (access, transfer, add or modify) EHR data via electronic
messages or as distributed objects:
- preserving the original clinical meaning intended by the author
- reflecting the confidentiality of that data as intended by the author and patient.
It is the ISO 13606 standard, which defines a architecture for communicationg part or all
of the electronic Health record of a single subject of care (patient) between EHR systems,
or between EHR systems and a centralized EHR data repository.
