What is Biomedical Informatics ?

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What is Biomedical Informatics ?
James J. Cimino, M.D. National Library of
Medicine Woods Hole BioMedical Informatics
Course June 2, 2008
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Biomedical Informatics is...
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Biomedical Informatics is...
The field that concerns itself with the
cognitive, information processing and
communication tasks of medical practice,
education and research, including the information
science and the technology to support these
tasks. Greenes RA. Shortliffe EH. JAMA 1990
Feb 23 263(8)1114-20.
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Biomedical Informatics is...

• The art and science of organizing knowledge of
  human health and disease, and making it useful
  for problem solving

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• The art is getting longer and longer, the brain
  of the learner has its limitsthe time is too
  short for a man already burdened to the breaking
  point.
• - William Osler

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The Spectrum of Problem Solving

• Science base of biology and medicine
• Collection and interpretation of signals
• Application of science and data in clinical care
• Extension of clinical care to populations

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Whats in a Name?

• Bioinformatics
• Really biomolecular informatics
• Medical informatics
• Really clinical informatics
• Biomedical informatics
• Covers both and more

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Building Blocks

• Representation of data and knowledge
• Storage and retrieval of information (structured
  and unstructure)
• Signal processing
• Natural language processing
• Decision analysis
• Expert systems
• User interface design
• Standards

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Application Areas

• Biomolecular modeling
• Digital imaging systems (PACS)
• Cardiology systems
• Electronic health records
• Telemedicine
• Public health information systems
• Educational tools

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Biomedical Informatics is...

• Concepts
• Technologies
• Skills

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Forces Propelling Informatics Toward Increasing
Importance

• Health care costs
• Medical errors and decision support
• Functional genomics
• Explosive growth of the literature
• Personal health records
• Privacy
• Translational research
• Public health disasters

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Case Presentation

• The patient is a 50 year old, Native American
  female who present to the emergency room (ER)
  with the chief complaint of lip numbness, nausea
  and chest pain.
• The patient was generally well until about one
  half hour prior to arrival in the ER, while
  eating dinner at as seafood restaurant in Rock
  Harbor, MA. She was finishing a dinner of New
  England clam chowder, lobster, steamed clams, and
  corn on the cob when she noted onset of symptoms.
  Others in her party ate fish and chips, although
  two other people ate the clam chowder none at
  the steamers.
• She gives a history of hypertension and states
  that she was getting a "capsule, half green, half
  blue-green" from her private doctor. She also
  reports that she was treated in the past for
  tuberculosis while she was pregnant, but doesn't
  remember what she was treated with or for how
  long. She reports that she was at another
  hospital on the other side of town, where she had
  a liver biopsy. She reports that he thinks the
  diagnosis was "hemachromatosis". The patient
  reports an allergy to Bufferin.
• Physical examination revealed a well-developed,
  well-nourished diaphoretic female in moderate
  respiratory distress. Vital signs showed a pulse
  of 110, a respiratory rate of 8, an oral
  temperature of 100.3, and a blood pressure of
  150/100. Examination revealed rales over both
  lower lung fields. Abdominal exam revealed a
  tender, palpable liver edge. Neurologic exam
  reveals dysarthria, diffuse muscle weakness, and
  hyperreflexia.
• Chem7 (serum) Glucose 100 (70-105) Chem7
  (plasma) Glucose 150 (75-110)
• CBC Hgb 15 (12.0-15.8), Hct 45 (42.4-48.0), WBC
  11,000 (3,540-9,060), Platelets 145K (165-415K)
• A fingerstick blood sugar was 80
• Urinalysis showed protein of 1 and glucose of 0
• A blood culture was positive for
  methicillin-resistant Staphylococcus aureus
  (MRSA)
• ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST
  segment 2mm elevated and
• T-waves down in leads I, L, V5 and V6
• Chest X-ray Left upper lobe infiltrate, left
  ventricular hypertrophy
• The patient's nurse reported that the patient
  seemed more worried about who would care for her
  elderly father if anything happened to her.
• A medical student reviewing the case wonders
  whether paralytic shellfish poisoning could cause
  a myocardial infarction she decides to do a
  literature search.
• The patient was treated with activated charcoal
  and stomach lavage, followed by enteric-coated
  aspirin. Due to worsening respiratory
  insufficiency, she was intubated and placed on
  mechanical ventilation.

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Health Information in the Case
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Issues in Cognitive, Information Processing,
Communication, Practice, Education and Research

• How do we find out what medication the patient is
  on?
• How do we get her records from another
  institution?
• How do we get the right records?
• How do we keep the clinicians from getting
  overwhelmed?
• How do we recognize her potential allergy?
• How do we facilitate retrieval of relevant
  evidence?
• How do facilitate application of expert systems?
• How do we assess the patients genetic
  predispositions?
• What do we have to report for public health, and
  how?
• How do we exploit the information to gain new
  knowledge?
• Why is this all hard to do?

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Biomedical Informatics is...
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Biomedical Informatics Course

• Application areas
• Bioinformatics
• Clinical systems
• Order entry
• Telemedicine
• Consumer systems
• Personal records
• Public health
• Disaster informatics
• Education
• Issues
• Privacy
• Evaluation
• Managing teams

• Building blocks
• Databases
• Controlled terminology
• Decision analysis
• Evidence-based practice
• Image informatics
• Internet
• Information resources
• Bibliographic resources
• Expert systems
• Personal skills
• Web pages
• Databases

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American Medical Informatics Association
www.amia.org
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American Medical Informatics Association
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National Library of Medicine Training Programs
http//www.nlm.nih.gov/ep/GrantTrainInstitute.html
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Final Project

• This year's project will focus on a Harmful Algal
  Bloom (HAB), commonly referred to as Red Tide, in
  the Northeast. Most species of algae and
  phytoplankton are not harmful, including most Red
  pigmented algae. However a small number of
  species, Alexandrium spp., Gymnodinium catenatum,
  Pyrodinium bahamense produce potent neurotoxins
  that affect higher forms of life in the food web.
  Humans can be affected when they eat shellfish or
  fish that feed upon the harmful algae. The effect
  in humans, Paralytic Shellfish Poisoning (PSP),
  is caused by Saxitoxins.  Symptoms are purely
  neurological and their onset is rapid. Duration
  of effects is a few days in non-lethal cases.
  Symptoms include tingling, numbness, and burning
  of the perioral region, ataxia, giddiness,
  drowsiness, fever, rash, and staggering. The most
  severe cases result in respiratory arrest within
  24 hours of consumption of the toxic shellfish.
  If the patient is not breathing or if a pulse is
  not detected, artificial respiration and CPR may
  be needed as first aid. There is no antidote,
  supportive therapy is the rule and survivors
  recover fully.   The project will focus upon a
  fictional HAB of Alexandrium spp. effecting Cape
  Cod during tourist season. The MBL staff will set
  up skeleton site using Drupal. The students will
  create a portal for the public and health
  professionals to monitor the event and its
  effects. They will learn the basics of Drupal,
  creating an RSS feed, using Twitter and Google
  Earth. The students will be in charge of
  populating the website however MBL staff will be
  available to help them as needed.

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Work Times and Location

• Breaks
• Meals
• Wednesday afternoon
• After evening workshops
• Wireless Internet

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Biology Homework
1. Understanding basic physical concepts Place
the following in a logical order Chromosome
Codon Gene Gene Pool Genome
Nitrogen Atom Nucleotide Proton
Gene Pool Genome Chromosome Gene Codon Nucleotide
Nitrogen Atom Proton
Proton Nitrogen Atom Nucleotide Codon Gene Chromos
ome Genome Gene Pool
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Biology Homework
2. Understanding how concepts relate to each
other Place the following in a logical order
Amino acid sequence Biologic pathway
Cellular function Disease DNA sequence
Epidemic Organism function Protein
function Protein structure RNA sequence
DNA sequence RNA sequence Amino acid
sequence Protein structure Protein function
Biologic pathway Cellular function Organism
function Disease Epidemic
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Biology Homework
3. Relating chemicals and processes Match the
processes on the left with all the related
chemicals on the right (each may be used once,
more than once, or not at all) Replication
DNA
Transcription
RNA Translation
Protein Products Post-Translation
Modification
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Biology Homework
4. Understanding jargon Which of these does not
belong Genome Proteome
Phenome Metronome
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Biology Homework
5. Relating science and popular culture The
movie Gattaca depicts a world where genetic
testing is used for everything from job
placement, to identity verification, to mate
selection. What is the signiciance of the name
of the company, Gattaca Corporation, that is
referenced in the film's title? (IMDB will be
not help here negative points if you dont know
what IMDB is)
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Biology Homework
6. Understanding Mendalian inheritance When a
single location in a genetic sequence varies
among members of a species, it is referred to as
a single nucleotide polymorphism, or SNP.
Image that there is a particular SNP in the human
genome that can be any of the four nucleotides
(A, T, C or G). If your mother, father, brother
and you are all tested for this SNP and the
following Mother A Father T
You AT Your Brother AC a) What is the
likely explanation for you having AT? b) What is
the likely explanation for your brother having AC?
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Biology Homework
7. Understanding the nuances of RNA-protein
translation When the SNP in Question 6, above,
was tested in a large group of people that ate
shellfish contaminated with toxic algae, all of
those with any combination of A, T and C
developed paralytic shellfish poisoning.
However, those people with the rarest SNP, G, did
not develop the disease. As it happens, this SNP
is actually the third nucleotide in a codon in a
gene. The first two nucleotides are CC. What is
the likely explanation for the obsersvation that
people with the G variety of the SNP seem to be
protected? (Hint you may find the table at
http//learn.genetics.utah.edu/content/begin/dna/t
ranscribe/ to be helpful)
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Biology Homework
7. Understanding the nuances of RNA-protein
translation DNA RNA Amino Acid Protein
Function CCA GGT
CCT GGA CCC GGG CCG GGU
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Biology Homework
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Biology Homework
7. Understanding the nuances of RNA-protein
translation DNA RNA Amino Acid Protein
Function CCA GGT
CCT GGA CCC GGG CCG GGU
CCA GGT Glycine .GLY
Susceptible CCT GGA Glycine
.GLY Susceptible CCC GGG Glycine
.GLY Susceptible CCG GGU
Glycine .GLY Protected?