Biology and Biomedical Informatics Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org - PowerPoint PPT Presentation

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Biology and Biomedical Informatics Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org

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Title: Biology and Biomedical Informatics Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org


1
Biology andBiomedical InformaticsRobert Arp,
Ph.D.Ontology Research Group (ORG)www.org.buffa
lo.eduNational Center for Biomedical Ontology
(NCBO)www.bioontology.org
2
BIOLOGY Bios Greek forlife Logos
Greek forwordrational accountstudy
ofscience of
3
BIOLOGY So, biology is ascience, the
sciencethat studies life andliving things.
What is science?
4
Some Important Scientific Literature
  • Journals
  • Scientific American (all lay persons should
    subscribe to this)
  • Skeptic (ditto for this)
  • Nature (technical)
  • Science (technical)
  • Books
  • What is This Thing Called Science, by Chalmers
    (McGraw-Hill)
  • Scientific Method in Practice, by Gauch
    (Cambridge)
  • Science A History, by Gribbin (Penguin)
  • Evolution What the Fossils Say, by Prothero
    (Columbia)

5
Sciencethe systematic attempt on the part of
researchers to develop theories to explain the
phenomena of our experience so as to classify,
describe, organize, explain, explore, predict
and, ultimately, control the phenomena.
6
Sciencethe systematic attempt on the part of
researchers to develop theories to explain the
phenomena of our experience so as to classify,
describe, organize, explain, explore, predict
and, ultimately, control the phenomena.
7
phenomena of our experience Things that are
publicly observable, 5 senses-able, testable,
repeatedly, directlyThings that are publicly
observable, 5 senses-able, testable, repeatedly,
indirectly
molecules, cells, crystals, cats, dogs,
ecosystem, solar system, Milky Way
gravity, electromagnetism, strong force, weak
force, subatomic particles
8
Can you, I, anyone, and everyone experience it or
sense it with one of the 5 senses directly or
indirectly, repeatedly, by testing it in a
controlled environment? Yes scientificNo
non-scientific
5
9
NOT the 4 Ms M indin terms of soulM
oralityright and wrongM eaningpurpose in
lifeM agnificent Beingsgod or godsthese are
outside the realm of the phenomena of our
experience (OK to study and believe in, but not
in science proper)
10
NOT these other Mseither M iraclesM
artians or other aliensM ind-control like
ESPM agic these are outside the realm of the
phenomena of our experience (OK to de-bunk, but
not in science proper)
11
Intelligent Design- The universe was createdby
some superior intelligentmind (SSIM)- Life
itself was created by SSIM- The highly complex
things in the universe (e.g., eyes, flagellums,
blood clotting) could not have evolved and had to
be created by SSIM
12
Intelligent Design- The universe was created by
somesuperior intelligent mind (SSIM)- Life
itself was created by SSIM- The highly complex
things in the universe (e.g., eyes, flagellums,
blood clotting) could not have evolved and had to
be created by SSIM
  • Unfortunately for Intelligent Design
  • Not part of the phenomena of our experience
  • Cant be publicly observed, repeated, tested
    either directly or indirectly
  • There just is no science of Intelligent Design

False, too
13
Some Literature on Intelligent Design
  • Science, Evolution, and Creationism, by the
    National Academy of Sciences
  • Evolution vs. Creationism, by Scott (University
    of California)
  • The Edge of Evolution The Search for the Limits
    of Darwinism, by Behe (InterVarsity)
  • Debating Design From Darwin to DNA, edited by
    Dembski Ruse (Cambridge)

14
Intelligent DesignDoes it belong in ascience
classroom?Or, is it more appropriate for a
religion or history class?How about the study
of souls? whats right and wrong?the meaning
of life?
15
Sciencethe systematic attempt on the part of
researchers to develop theories to explain the
phenomena of our experience so as to classify,
describe, organize, explain, explore, predict
and, ultimately, control the phenomena.
16
THESCIENTIFIC METHOD
17
systematic attempt on the part of
researchersScientific Method1 ask relevant
question2 do background search3 construct
hypothesis4 test hypothesis with experiment5
analyze results of experiment6a if
hypothesis is confirmed (true) go to 76b if
hypothesis is not confirmed (false) or partially
true7 report results8 use results to
construct more hypotheses
18
Car wont start
19
Car wont start
Hypotheses?
20
Car wont start
Hypotheses?
Battery?
21
Car wont start
Hypotheses?
Battery?
How do you test this Hypothesis?
22
Sciencethe systematic attempt on the part of
researchers to develop theories to explain the
phenomena of our experience so as to classify,
describe, organize, explain, explore, predict
and, ultimately, control the phenomena.
23
to develop theories to explain Theory-
essentially a truth, body of facts- coherent
system- confirmed hypotheses- laws (WHAT GOES
UP DOPPLER EFFECT)- deductions from these
laws- overall reliable predictions
24
to develop theories to explain Theory-
essentially a truth, body of facts- coherent
system- confirmed hypotheses- laws (WHAT GOES
UP DOPPLER EFFECT)- deductions from these
laws- overall reliable predictions
E.g., Atomic, Big Bang, Evolution
25
And reliable predictions lead to - Developing
better drugs to fight disease- Developing early
warning systems for tornadoes, floods,
earthquakes- Safer highways- Spaceships and
exploration and the list goes on and on
26
So much for ScienceWhat is Biology?
27
Biologythe systematic attempt on the part of
researchers to develop theories to explain the
organic (living) phenomena of our experience so
as to classify, describe, organize, explain,
explore, predict and, ultimately, control the
phenomena.
28
Some Biology Literature
  • Journals
  • Journal of Biology (technical)
  • PLoS Biology (http//biology.plosjournals.org/)
  • Science Magazine (all science, too)
  • Books
  • Biology, by Raven et al. (McGraw-Hill)
  • Biology Life on Earth, by Audesirk et al.
    (Prentice-Hall)
  • The Epic History of Biology, by Serafini (Basic)

29
biochemistrymolecular biologymicrobiologycellul
ar biologyphysiologybotanyzoologyecologyevolu
tionary biology
30
and many more branchesand sub-branches
31
to explain theorganic (living) phenomena of our
experience
One Goal of Biology
32
So what is Life?- ReplicationDNA, RNA-
Encapsulationcell wall, barrier-
Self-Movementgrowth, repair- Adaptationhomeosta
sis- Use of Energy in Multiple Ways-
Hierarchically-Organized System
?
33
So what is Life?- ReplicationDNA, RNA-
Encapsulationcell wall, barrier-
Self-Movementgrowth, repair- Adaptationhomeosta
sis, fitness- Use of Energy in Multiple Ways-
Hierarchically-Organized System
D. Koshland, The Seven Pillars of Life In
Science (2002) 295 2215-2216
34
- is a single cell alive? - the organelles that
make up a cell? (Mitochondrion, Golgi Apparatus)
- a virus? - a prion? (abnormal protein) -
the ecosystem itself?
35
Biologythe systematic attempt on the part of
researchers to develop theories to explain the
organic (living) phenomena of our experience so
as to classify, describe, organize, explain,
explore, predict and, ultimately, control the
phenomena.
36
classify, describe, organizeHomo sapiens
(species)is_a Homo (genus)is_a hominid
(family)is_a primate (order)is_a placental
(subclass)is_a mammal (class)is_a vertebrate
(subphylum)is_a chordate (phylum)is_a animal
(kingdom)is_a eukaryote (domain)
37
What I DoBIOMEDICAL INFORMATICSThe science
associated with the collection, categorization,
management, storage, processing, retrieval, and
dissemination of biomedical knowledge and
information using computational tools with the
overall goal to improve patient care, medical
education, and health science research
classify, describe, organize
38
What I DoBIOMEDICAL INFORMATICS Combination
of BiologyMedicineHealth CareComputer
ScienceInformation Science
classify, describe, organize
39
Some Biomedical Informatics Literature
  • Chen, H., Fuller, S., Friedman, C., Hersh, W.
    (2005). Medical informatics Knowledge management
    and data mining in biomedicine. The Netherlands
    Springer.
  • Goldstein, D., Groen, P., Ponkshe, S., Wine, M.
    (2007). Medical informatics 20/20 Quality and
    electronic health records through collaboration,
    open solutions, and innovation. New York Jones
    Bartlett.
  • Polanski, A., Kimmel, M. (2007).
    Bioinformatics. London Springer.
  • van Bemmel, J., Musen, M. (Eds.). (1997).
    Handbook of medical informatics. The Netherlands
    Springer.
  • Xiong, J. (2006). Essential bioinformatics.
    Cambridge Cambridge University Press.

40
New York State Center of Excellence in
Bioinformatics Life SciencesUniversity at
Buffalo
41
Information Science
  • science associated with the collection,
  • categorization, management, storage,
  • processing, retrieval, and dissemination of
  • knowledge and information, often times
  • using computational tools think librarian,
  • but a librarian with computational skills
  • OVERALL GOAL
  • KNOWLEDGE SHARING

42
What I DoBIOMEDICAL INFORMATICS More
specifically, I help biomedical researchers(A)
classify their data and information in their
labs(B) build links between and among all of
their labs so that they can share the data and
information with each other
classify, describe, organize
43
What I DoBIOMEDICAL INFORMATICS More
specifically, I help biomedical researchers(A)
classify their data and information in their
labs(B) build links between and among all of
their labs so that they can share the data and
information with each other
classify, describe, organize
with domain ontologies
with formal ontologies
44
Domain Area of study like biology, law,
psychology, or any other science or discipline
you would find at a university
45
Domain Ontology A classification kind of
like Periodic Table of the ElementsKingdoms
of Biology in some domain (like biology, law,
psychology, or any other science or discipline
you would find at a university)
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Only more complex in terms of the objects and
their relationships to one another
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Crazy and overwhelming, isnt it?
55
So, instead of using a STANDARD like the Periodic
Table of Elements, people start classifying
things their own different waysthis results in
56
SILO EFFECT
57
SILO EFFECT
58
PROBLEMDE-SILOING all of this domain data and
information so that it may be queried
effectively, shared, andre-used(like
Google-izing it)
59
SOLUTION
60
FORMAL ONTOLOGY- Upper-level- Applicable to
any domain
61
Assists in making communication between and among
domain ontologies possible by providing -
Common language- Common formal framework for
reasoning
62
So, just as ENGLISH is a common world language
enabling different people to communicate in
common So too, FORMAL ONTOLOGY is a common
language enabling different domain ontologies
to communicate in common
63
Formal Ontology is like a backbone or spine
making communication, interoperability, and
optimal dissemination of information possible
between and among domain ontologies.
64
From this To this
65
Some Domain and Formal Ontology Literature
  • Arp, R. (2007). Philosophical ontology, domain
    ontology, formal ontology. The Reasoner, 1,
    12-13.
  • Bittner, T., Donnelly, M., Winter, S. (2006).
    Ontology and semantic operability. In S.
    Zlatanova D. Prosperi (Eds.), Large-scale 3D
    data integration Challenges and opportunities
    (pp. 139-160). Boca Raton, FL CRC Press.
  • Ceusters, W., Smith, B., van Mol, M. (2003).
    Using ontology in query answering systems
    Scenarios, requirements and challenges.
    Proceedings of the 2nd CoLogNET-ElsNET Symposium,
    Amsterdam, 2, 5-15.
  • Grenon, P., Smith, B. (2004). SNAP and SPAN
    Towards dynamic spatial ontology. Spatial
    Cognition and Computation, 1, 1-10.
  • Grenon, P., Smith, B. (2004a). A formal theory
    of substances, qualities and universals. In A.
    Varzi and L. Vieu (Eds.), Proceedings of FOIS
    2004. International Conference on Formal
    Ontology and Information Systems (pp. 49-59).
    Amsterdam IOS Press.
  • Mars, N. (Ed.). (1995). Towards very large
    knowledge bases Knowledge building and knowledge
    sharing. Amsterdam IOS Press.
  • Menzel, C. (2003). Ontology theory. In J.
    Euzenat, A. Gomez-Perez, N. Guarino, H.
    Stuckenschmidt (Eds.), Ontologies and semantic
    interoperability (pp. 13-30). Hamburg IOS Press.
  • Smith, B. (2003). Ontology. In L. Floridi (Ed.),
    Blackwell guide to the philosophy of computing
    and information (pp. 155-166). Malden, MA
    Blackwell.
  • Smith, B., Ceusters, W. (2007). Ontology as the
    core discipline of biomedical informatics
    Legacies of the past and recommendations for the
    future direction of research. In G. Crnkovic S.
    Stuart (Eds.), Computing, philosophy, and
    cognitive science (pp. 121-145). Cambridge
    Cambridge Scholars Press.
  • Smith, B., Kumar, A., Bittner, T. (2004). Basic
    Formal Ontology for bioinformatics. Available at
    http//www.uni-leipzig.de/akumar/JAIS.pdf.

66
Thank YouRobert Arp, Ph.D.Ontology Research
Group (ORG)www.org.buffalo.eduNational Center
for Biomedical Ontology (NCBO)www.bioontology.org
New York State Center of Excellence in
Bioinformatics Life SciencesThe University at
Buffalo(716) 881-7905 Office(850) 509-4503
Cellrarp_at_buffalo.eduhttp//www.org.buffalo.edu/r
arp/
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