Disease Informatics: Terms and Jargon to begin with

1
Disease Informatics Terms and Jargon to begin
with

• R. P. Deolankar

2
General Terms
3
Data and Information

• Data
• Numbers
• Words
• Images
• Information is derived from the data
• Information
• It is the knowledge derived from analysis of the
  data
• Inferences can be drawn from information
• The inferences drawn from earlier work provides
  the basis for projected work

4
Target information and Information gap

• Target information
• Information which is required but not available
• The information goal intended to be attained
• Information gap
• Total information required to hit the information
  target minus available information

5
Research question and Hypothesis

• Research question
• This is the question, if answered, could
  eliminate the information gap
• The cycle of setting the information target,
  locating the information gap and raising new
  research questions is the part of process of
  research
• Hypothesis
• This is a tentative answer to the research
  question
• The hypothesis is tested by performing the
  experiment
• After testing, hypothesis is either accepted or
  rejected
• Postulation
• Hypothesis that cannot be tested and hence taken
  for granted
• A statement as the basis of a theory

6
(Disease phenomenon is the result of several
causes, not just one)Multiple hypotheses

• More effective way of organizing research
• Provides stimulus for study and fact-finding
• See the interaction of the several causes
• Promotes much greater thoroughness
• Leads to lines of inquiry that we might otherwise
  overlook
• Avoids the pitfall of accepting weak or flawed
  evidence for one hypothesis when another provides
  a more elegant solution
• Precautions
• Keeping a written list of multiple hypotheses is
  necessary
• Difficult to test
• Vacillation is preferable to the premature rush
  to a false conclusion

7
Thomas Chrowder ChamberlinAuthor of Method of
Multiple Working Hypotheses
8
What is ontology?

• Incomplete information gives rise to speculation
• Hierarchical structuring of speculations about
  things within a particular domain is ontology
• Ontology is the statement of a logical theory

9
Disease Ontology

• Controlled Medical Vocabulary
• Facilitate mapping of diseases and associated
  conditions to codes such as ICD, SNOMED and
  others
• Disease Ontology (DO) is developed at the
  Bioinformatics Core Facility in collaboration
  with the NuGene Project at the Center for Genetic
  Medicine, USA

10
Clinical event

• Clinical related to the health or disease
• Event something that happens at a given place
  and time
• Depicted at both the ends of cause and effect
  diagram
• Link of a Disease Causal Chain
• Backend event Event occurring earlier to the
  focused event
• Frontend event Event occurring next to the
  focused event

11
Biomarker

• Indicator of event of health / disease / clinical
  history
• Usually biochemical metabolite
• Indicator of normal biologic processes,
  pathogenic processes, or pharmacologic responses
  to a therapeutic intervention.

12
Disease Causal Chain

• Diagram depicting chain or net
• Links of chain are events
• Progress from one event to other is shown by
  Cause and effect diagram
• Journey from one event to the other is driven by
  factors

13
Model organism

• Animal model in study of diseases
• Discoveries made in the animal model provides
  insight into the human disease study
• Studies include pathogenesis, potential causes
  and treatments of diseases
• Basis common descent of all living organisms,
  and the conservation of metabolic and
  developmental pathways and genetic material over
  the course of evolution
• Research performed using poor quality animals
  could be misguiding

14
Component cause

• Belief in one cause one effect is a major error
  in disease investigation
• Single component cause does not result in disease
• Virus is a component cause in a viral disease
• Subset of sufficient causes does not result in a
  disease but could predispose
• Most causes of interest to the epidemiologist are
  actually components of a sufficient cause

15
Sufficient cause

• Sufficient causes are constellation of component
  causes that could result in a disease
• Factors contributing susceptibility to virus are
  also component causes of viral disease
• Disease can originate from either of several
  different sufficient causes

16
Book by Rothman and Greenland
17
NCL-60 lines

• Cell lines for anticancer drug screening
• Developed by the National Cancer Institute,
  Maryland, USA
• Reflect diverse cell lineages lung, renal,
  colorectal, ovarian, breast, prostate, central
  nervous system, melanoma, and hematological
  malignancies
• Such panels could be prepared for other diseases
  also

18
Algorithm

• A precise rule or set of rules
• A sequence of instructions
• Specify how to solve some problem

19
Metathesaurus

• Vocabulary for information retrival
• Integrated from synonyms and antonyms for common
  words and phrases (thesauri)
• e.g. Unified Medical Language System to integrate
  into a single system the terminology of the
  biomedical sciences

20
SNOMED CT and SNOMED RT

• SNOMED Sytematized NOMencalture of MEDicine
• CT for Clinical Terms
• RT for reference terminology

21
UMLS Unified Medical Language System

• UMLS is a metathesaurus
• Developed by the National Library of Medicine
  (NLM)
• Contains Knowledge Sources (databases) and
  associated software tools (programs)
• Useful for developers of computer system

22
UML Unified Modeling Language Not to be
confused with UMLS

• A standardized general-purpose modeling language
  in the field of software engineering
• UML includes a set of graphical notation
  techniques
• Creates abstract models of specific systems
• Diagrams structure (Class, Component, Composite
  structure, Deployment, Object and Package
  diagrams), behavior (Activity, State and Use
  case) and interaction (Communication, Interaction
  overview, Sequence and Timing)

23
Semantic Network

• Knowledge diagram with graphic notation
• Looks like flow chart
• Contains patterns of interconnected nodes and
  arcs

24
SPECIALIST Lexicon

• SPECIALIST is the name of Natural Language
  Processing (NLP) System
• Lexicon (dictionary like document) developed
  using SPECIALIST is SPECIALIST lexicon
• Vocabulary encompassing English and biomedical
  terminology
• The lexicon entry for each word or term records
  the syntactic, morphological, and orthographic
  information needed by the SPECIALIST NLP System

25
Genetic terminology
26
Essential genes

• Genes required for growth to a fertile adult
• Essential for viability

27
Housekeeping genes

• Involved in basic functions needed for the
  sustenance of the cell
• Constitutively expressed
• They are always turned ON e.g. actin

28
Disease-associated genes

• Alleles carrying particular DNA sequences
  associated with the presence of disease
• e.g. Gene UNC-93B deficiency as a genetic
  etiology of Herpes Simplex Encephalitis
• Lack of Stat1 interferon signaling gene enhances
  pathogenesis of a viral disease

29
Gene Ontology (GO)

• The Gene Ontology (GO) is a project
• Provides a controlled vocabulary to describe gene
  and gene product attributes in any organism
• (the molecular function of gene products their
  role in multi-step biological processes and
  their localization to cellular components)

30
Epigenetic

• Relating to, being, or involving a modification
  in gene expression
• It is independent of the DNA sequence of a gene
• DNA methylation, chromatin remodeling,
  transcription factors etc

31
Paralogs Paralogous genes

• Two genes or clusters of genes at different
  chromosomal locations in the same organism
• Have structural similarities indicating that they
  derived from a common ancestral gene
• Have diverged from the parent copy by mutation
  and selection or drift.

32
Homologs Homologous genes

• Homologs Having the same relative position,
  value, or structure, something (as a chemical
  compound or a chromosome) that is homologous
• Homologous sequences are of two types
  orthologous and paralogous

33
Orthologs orthologous genes

• Orthologous genes genes that have evolved
  directly from an ancestral gene
• This is in contrast to paralogous genes

34
Interlogs

• Suppose protein molecules (from one species of
  animal say human) A and B interact homologous
  protein molecules (from another species of animal
  say dog) A and B also interact, then interlogs
  are
• Resembling pair of protein-protein interactions
  (e.g. A-B and A'-B')
• Can be observed parallelly in two different
  organisms

35
Interologous Interaction Database

• Web-accessible database to facilitate
  experimentation and integrated computational
  analysis with model organism Protein-Protein-Inter
  action networks

36
Regulogs

• Sets of co-regulated genes for which the
  regulatory sequence has been conserved across
  multiple organisms
• The quantitative method assigns a confidence
  score to each predicted regulog member on the
  basis of the degree of conservation of protein
  sequence and regulatory mechanisms

37
Translational medicine ("Bench to bedside"
research)

• Clinical Research orienting interaction between
  basic research and clinical medicine,
  particularly in clinical trials

38
Systems biology

• Relatively new biological study field
• Focuses on the systematic study of complex
  interactions in biological systems
• Uses a new perspective (integration instead of
  reduction) to study complex interactions

39
Predictive medicine

• Identifying biological markers in order to enroll
  individuals at high risk for developing a disease
  in special early detection trials

40
Meta-analysis

• In statistics, a meta-analysis combines the
  results of several studies that address a set of
  related research hypotheses

41
Bayesian approach

• Statistical approach based on Bayes' theorem
• Application of Bayes theorem Bayes' theorem can
  be applied to calculate the probability that a
  positive medical test result of a disease is a
  false positive hence retesting is planned
• Bayes' theorem can be also be applied to
  calculate the probability of a false negative

42

• Omics terms

43
Genomics

• The branch of genetics that studies organisms in
  terms of their genomes (their full DNA sequences)

44
Pharmacogenomics

• Study of how an individual's genetic inheritance
  affects the body's response to drugs
• Tailor-made for individuals and adapted to each
  person's own genetic makeup
• Greater efficacy and safety
• Environment, diet, age, lifestyle, and state of
  health all can influence a person's response to
  medicines

45
Nutrigenomics

• Study of molecular relationships between
  nutrition and the response of genes
• Personalized nutrition based on genotype

46
Phenomics

• Field of study concerned with the
  characterization of phenotypes
• Phenotypes arise via the interaction of the
  genome with the environment

47
Transcriptome and transcriptomics

• Transcriptome
• The complete set of RNA products (mRNAs, or
  transcripts in a particular tissue at a
  particular time) that can be produced from the
  genome
• Transcriptomics
• The study of the transcriptome

48
Proteome and proteomics

• Proteome
• PROTEin complement to a genOME
• Proteomics
• The qualitative and quantitative comparison of
  proteomes
• The comparison under different conditions to
  further unravel biological processes

49
Metabolome and Metabolomics

• Metabolome
• It represents the collection of all metabolites
  in a biological organism, which are the end
  products of its gene expression
• Metabolomics
• Study of metabolome under different conditions