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

Bios = Greek for:
“life”
Logos = Greek for:
“word”
“rational account”
“study of”
“ science of ”

So, biology is a science, the science that studies life and living things.

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)

Science: the 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.

Science: the 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.

phenomena of our experience…
Things that are publicly observable, 5 senses-able, testable, repeatedly, directly: molecules, cells, crystals, cats, dogs, ecosystem, solar system, Milky Way
Things that are publicly observable, 5 senses-able, testable, repeatedly, indirectly: gravity, electromagnetism, strong force, weak force, subatomic particles

M ind…in terms of “soul”
M orality…right and wrong
M eaning…purpose in life
M agnificent Beings…god or gods
…these are outside the realm of the phenomena of our experience (OK to study and believe in, but not in science proper)

M iracles…
M artians… or other aliens
M ind-control… like ESP
M agic…
…these are outside the realm of the phenomena of our experience (OK to de-
bunk, but not in science proper)

- The universe was created by some superior 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

Intelligent Design:
- The universe was created by some superior 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
- Can’t be publicly observed, repeated, tested either directly or indirectly
False, too…
- There just is no science of Intelligent Design

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)

Intelligent Design:
Does it belong in a science classroom?
Or, is it more appropriate for a religion or history class?
How about… the study of souls?
…what’s right and wrong?
…the meaning of life?

Science: the 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.

systematic attempt on the part of researchers…
Scientific Method
1 = ask relevant question
2 = do background search
3 = construct hypothesis
4 = test hypothesis with experiment
5 = analyze results of experiment
6a = if hypothesis is confirmed (true) = go to 7
6b = if hypothesis is not confirmed (false) or partially true
7 = report results
8 = use results to construct more hypotheses

How do you test this Hypothesis?

Science: the 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.

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

to develop theories to explain…
Theory: E.g., Atomic, Big Bang, Evolution
- essentially a truth, body of facts
- coherent system
- confirmed hypotheses
- laws
(WHAT GOES UP… DOPPLER EFFECT…)
- deductions from these laws
- overall… reliable predictions

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…

Biology: the 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.

• 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)

biochemistry molecular biology microbiology cellular biology physiology botany zoology ecology evolutionary biology…

…and many more branches and sub-branches
…
Biological Science
… …
…
…
…
…
…

- Replication…DNA, RNA
- Encapsulation…cell wall, barrier
- Self-Movement…growth, repair
?
- Use of Energy in Multiple Ways
- Hierarchically-Organized System

- Replication…DNA, RNA
- Encapsulation…cell wall, barrier
- Self-Movement…growth, repair
- Adaptation…homeostasis, fitness
- Use of Energy in Multiple Ways
- Hierarchically-Organized System
D. Koshland, “The Seven Pillars of Life”
In Science (2002) 295: 2215-2216

(Mitochondrion, Golgi Apparatus)

Biology: the 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.

classify, describe, organize…
Homo 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)

What I Do: classify, describe, organize…
BIOMEDICAL INFORMATICS
The 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…

What I Do: classify, describe, organize…
BIOMEDICAL INFORMATICS
Combination of:

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.

New York State Center of
Excellence in Bioinformatics
& Life Sciences
University at Buffalo

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

What I Do: classify, describe, organize…
BIOMEDICAL 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

What I Do: classify, describe, organize…
BIOMEDICAL INFORMATICS
More specifically, I help biomedical researchers:
(A) classify their data and information in their labs with domain ontologies
(B) build links between and among all of their labs so that they can share the data and information with each other with formal ontologies

A classification kind of like:
Periodic Table of the Elements
Kingdoms of Biology in some domain (like biology, law, psychology, or any other science or discipline you would find at a university)

…Only more complex in terms of the objects and their relationships to one another

Crazy and overwhelming, isn’t it?

So, instead of using a STANDARD like the Periodic Table of Elements, people start classifying things their own different ways… this results in…

Data
SILO EFFECT
Data
Data
Data
Data
Data Data

Data
SILO EFFECT
Data
Data
Data
Data
Data Data

DE-SILOING all of this domain data and information so that it may be queried effectively, shared, and re-used
(like Google-izing it)

- Upper-level
- Applicable to any domain

Assists in making communication between and among domain ontologies possible by providing:
- Common language
- Common formal framework for reasoning

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…

Formal Ontology is like a “backbone” or “spine” making communication, interoperability, and optimal dissemination of information possible between and among domain ontologies.
Formal Ontology
E.G., Basic Formal Ontology
Data Data Data Data Data Data Data

From this…
To this…
Data
Data
Data
Data
Data
Data
Formal Ontology
E.G., Basic Formal Ontology
Data
Data Data Data Data Data Data Data

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.

Robert Arp, Ph.D.
Ontology Research Group (ORG) www.org.buffalo.edu
National Center for Biomedical Ontology (NCBO) www.bioontology.org
New York State Center of Excellence in Bioinformatics & Life Sciences
The University at Buffalo
(716) 881-7905 = Office
(850) 509-4503 = Cell rarp@buffalo.edu
http://www.org.buffalo.edu/rarp/