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Overview of Health Informatics
ITI
BMI-Dept
Overview of Health Informatics
Fellowship
Week5
Day 10ITI, BMI-Dept
7/5/2010 2
1-Bioinformatics Definitions2-System Biology3-Bioinformatics vs Computational biology4-Bioinformatics vs Clinical informatics5-Bioinformatics Elements6-For whom is Bioinformatics7-Bioinformatics challenges8-Bioinformatics today and future9-Genomics, Proteomics and Pharmacogenomics10-Gene Databases11-Human Genome Project12-Private sectors corporation
Agenda
Bioinformatics Definitions
• “…the computational branch of molecular biology.”1
• “the study of how information is represented and analyzed in biological systems, starting at the molecular level”2
• “field of science in which biology, computer science and information technology merge to form a single discipline”3
Bioinformatics Definitions Cont.
“The systematic development and application of computing systems and computational solution techniques to the analysis of biological data obtained by experiments, modeling, database search, and instrumentation.” 4
In Vivo è In Vitro è In Silico
System Biology11
• “the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life.”
• “tries to understand how proteins and genes interact at a cellular level”2
• Build upon results of HGP
• Moving from understanding single component è understanding All components and interactions among them, as a System, which is true!!
• Please visit: http://www.systemsbiology.org/
Source: http://sysbio.ist.uni-stuttgart.de/
Bioinformatics vs Computational biology
• Computational biology focuses on applying the Computer science techniques to develop models and simulations of biological systems.
• Bioinformatics focuses of analysis and generation of new knowledge from available data using the information and communication technologies.
Biology
Computer Science
Information Technology
Bioinformatics
Bioinformatics Vs Clinical informatics2
“Whereas clinical informatics deals with the management of information related to the delivery of health care, bioinformatics focuses on the management of information related to the underlying basic biological sciences”
• Both are complex and related to living systems.• Clinical Informatics deals with:
– Social systems of medicine– Cognitive processes of medicine– Technologies required to understand human
physiology
Bioinformatics Elements
I. Biological data
II. Algorithm
III. Software
IV. Hardware
V. Bioinformatician
Bioinformatics Elements cont.
I. Biological data:
• DNA è Genome
• RNA è Transcriptome
• Protein è Proteome
• Biological Pathways
• Mutations
• …..etc.
Bioinformatics Elements cont.
II. Algorithm:“An algorithm is an effective
method for solving a problem using a finite sequence of instructions. Algorithms are used for calculation, data processing, and many other fields.” 5
E.g. Gotoh's algorithm and Myers-Miller's algorithm, for Glopal Alignment, based on Dynamic Programming
Bioinformatics Elements cont.
III. Software:A program or
computational tool used to solve a problem depending on a specific Algorithm.
E.g. Binding Affinity Prediction of Protein-Ligand (BAPPL).
Please visit: http://www.scfbio-iitd.res.in/software/drugdesign/bappl.jsp
Bioinformatics Elements cont.
IV. Hardware:
PCs, Servers, Super computers, Networks,…etc.
E.g. NCBI and EBI Networks
Bioinformatics Elements cont.
V. Bioinformatician:Skills Required:§A basic knowledge of molecular biology§ Experience with one or more of Molecular Biology software packages § Operating system's§ Computer Programming Language§ Database Management Systems
For whom is Bioinformatics
People from1:
• Biology
• Medical field
• Computer science
• Pharmaceutical fields
• Legalization authorities
• Investing companies
• …etc.
Bioinformatics challenges6
• Lots of data à what does it mean?• Collecting data à using data à predicting data
• Genome annotation (functional genomics)– What does this piece of DNA do?
• Protein structure is related to function (protein folding)– Can we predict structure from sequence and basic physics?
[Source: www.shis.uth.tmc.edu/about-us/Informatics-Bernstam%20presentation.ppt]
Bioinformatics today and future cont.
1. Molecular medicine – More drug targets– Personalised medicine– Preventative medicine– Gene therapy
2. Microbial genome applications – Waste cleanup– Climate change– Alternative energy sources– Biotechnology– Antibiotic resistance– Forensic analysis of microbes– The reality of bio-weapon creation– Evolutionary studies
3. Agriculture CropsInsect resistanceImprove nutritional qualityGrow crops in poorer soils and that are drought resistant
4. Animals5. Comparative studies
Please visit: http://www.ebi.ac.uk/2can/bioinformatics/bioinf_realworld_1.html
Source: http://www.ebi.ac.uk/
-“At this point Bioinformatics seems
practice of medicine.”
-“At this point Bioinformatics seems like a field remote from medicine, but that will change with pharmacogenomics and personal genetic profiles ”7
- “...bioinformatics to align with the practice of medicine.”7
- Proteomics èmore receptor and more specific drug
targeting.
PharmacogenomicsèPersonalized Medicine
- New Diagnostic and Prognostic techniques2
- Diagnosing about 3000 hereditary diseases
Mutual benefits between bio and clinical informatics.6
Build models of: Molecules, Cells, Tissues, Organisms, Systems. For
application in simulation s of drug interactions.6
Important Opservations6
• Different people respond to drugs differently– Many drugs– Many genetic differences between people
• In addition, genetics influence– Risk factors à are you going to get the disease? (e.g.
smoking à emphysema, heart disease)– Operative risk
• How to collect and use these data?• Memory is not enough, need some tools
[Source: www.shis.uth.tmc.edu/about-us/Informatics-Bernstam%20presentation.ppt]
Genomics, Proteomics and Pharmacogenomics7
• Genomics: the field that analyzes genetic material from a species
• Proteomics: the study of gene expression at the level of proteins
• Pharmacogenomics: the study of genetic material to look for drug targets
Patient genetic Profile
Patient genetic Profile
EHR
Pharmacogenomics Knowledge base
• Mission: collect, encode, and disseminate knowledge about the impact of human genetic variations on drug response
• Process: – Curate primary genotype and phenotype data– Annotate gene variants and gene-drug-disease
relationships via literature review– Summarize important PGx genes and drug
pathways• Provide Tutorials, for searching and using
PharmGKB• Please visit: http://www.pharmgkb.org/
Gene Databases8
Sequence DatabasesThere are three major co-operating DBs (EMBL-EU, GenBank-USA, DNA Data Bank-Japan) containing millions of sequences with billions of nucleotides from several organisms with exponential growth.
Secondary Sequence DatabasesSuitable for Microarray experiments. Contain better annotation and meta-information. Example: UniGene, TIGR, RefSeq
Genomic DatabasesExamine sequences for microarrays from a genomic perspective Contain gene names and annotations (rather than gene sequences) organized per organism. Example: Ensembl, CMR (Microbial Genomes).
Gene Expression Databasesèè
For more databases that are related to Bioinformatics, please visit: – http://www.biw.kuleuven.be/vakken/i287/bioinformatica.htm– http://en.wikipedia.org/wiki/Category:Bioinformatics_databases– http://www.uni-konstanz.de/FuF/Bio/Bioinformatik/bivli_db.htm– http://www.techcuriosity.com/resources/bioinformatics/bioinformatics_databases.php
[Source: http://www.imbb.forth.gr/people/poirazi/journal-club/2005-06/Simeonides20-12-05.ppt]
Data Growth
Source: http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html
Year Base Pairs Sequences
1982 680,338 606
2008 99,116,431,942 98,868,465
Year Yearly Totally
1982 28 99
2009 6435 57177
http://www.pdb.org/pdb/statistics/contentGrowthChart.do?content=molType-protein&seqid=100
Growth of Protein Structures in Protein Data Bank
(1982 - 2009)
0
10000
20000
30000
40000
50000
60000
1982
1984
1986
1988
1990
1992
1994
1996
1998
2000
2002
2004
2006
2008
Yearly
Total
Source: http://www.biw.kuleuven.be/vakken/i287/bioinformatica.htm
EMBL, GenBank, DDBJ
SWISS-PROT, TrEMBL, PIR-PSD
dbEST, TGI, Mendel ESTs, Bodymap
3DInSightMolMovDB
PDB, EBI-MSD, NDB
National center for Biotechnology Information (NCBI)7
• Created 1988
• Part of NIH NLM
• Host 10 different genetic databases
• The Largest “Biomedical Research Center”
• Provide access to about 1, 000 organisms genome
• Please visit:
http://www.ncbi.nlm.nih.gov/sites/gquery
Human Genome Project (HGP)
• 1990-2003• International Collaborative
research Project.• “…Goal was the complete
mapping and understanding of all the genes of human beings”9
• Sequencing, Identifying location and Mapping of about 25, 000 genes.
• 3 000, 000 SNPs have been identified by mid-2007.7
• Please check: http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606
(courtesy National Library of Medicine)
What is after HGP?!!10
• National Institute of Health initiated the Human Microbiome Project (HMP).
• Sequencing 600 Health related microbes.• 5 year project.• Aims to: • Developing a reference set of microbial genome sequences and
preliminary characterization of the human microbiome• Relationship between disease and changes in the human
microbiome• Development of new technologies• Development of new tools for computational analysis• Establishing a Data Analysis and Coordinating Center (DACC)• Establishing a resource repository• Ethical, legal and social implications (ELSI) of HMP research• Please visit : http://nihroadmap.nih.gov/hmp/
Private sectors corporation10
• Celera Genomics è Genetic Mapping and Pharmacogenomics.
• DNA Direct è Genetic Testing and Counseling
• Decode Genetics Corporation, Iceland initiative, deCodeMeè Genome Analysis for diagnosing about 29 common diseases.
• Oracle Corporation and Thailand Initiative.
• Others…!!!
References1. Jean-Michel Claverie. Cedric Notredame. Bioinformatics for Dummies 2nd Edition. Wiley 2007.
2. Edward H. Shortliffe. James J. Cimino. Biomedical Informatics: Computer Applications in Health Care and Biomedicine 3rd
Edition. Springer. 2006.
3. NCBI. A Science Primer. www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html (Accessed December 6 2009).
4. Helge Weissig. Introduction to Bioinformatics. http://www.bioinformaticscourses.com/bioinform/ . 2003.
5. Wikipedia. Algorithm. http://en.wikipedia.org/wiki/Algorithm. (Accessed December 6 2009).
6. Elmer V. Bernstam, School of Health Information Sciences and Internal Medicine, UT – Houston. Health Informatics Presentation: www.shis.uth.tmc.edu/about-us/Informatics-Bernstam%20presentation.ppt (Accessed December 6 2009).
7. Robert E. Hoyt. Melanie Sutton. Ann Yoshihashi. Medical Informatics: Practical Guide for the Healthcare Professional 2nd
Edition. Lulu.com. 2008.
8. Alexandros Kanterakis. Heraklion, Crete. MineGene Presentation: http://www.imbb.forth.gr/people/poirazi/journal-club/2005-06/Simeonides20-12-05.ppt.17-5-2005. (Accessed December 6 2009)
9. National Human Genome Research institute , National Institute of Health. Human Genome Project: http://www.genome.gov/(Accessed December 6 2009)
10. National Institute of Health. Human Microbiome Project: http://nihroadmap.nih.gov/hmp/ (Accessed December 7 2009).
11. Institute for System Biology. http://www.systemsbiology.org/Intro_to_ISB_and_Systems_Biology/Systems_Biology_--_the_21st_Century_Science (Accessed Decemeber 07 2009)