Biology and Biomedical Informatics Biology and Biomedical Informatics Robert Arp, Ph.D. Ontology Research Group (ORG) National Center.

Biology andBiology andBiomedical Biomedical InformaticsInformatics

Robert Arp, Ph.D.Ontology Research Group (ORG)

www.org.buffalo.eduNational Center for Biomedical Ontology (NCBO)

www.bioontology.org

BIOLOGY

Bios = Greek for:“life”

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

BIOLOGY

So, biology is ascience, the sciencethat studies life andliving things.

What is science?

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:

Things 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

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

NOT the 4 Ms:

M ind…in terms of “soul”M orality…right and wrongM eaning…purpose in lifeM 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)

NOT these other Mseither:

M iracles…M 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)

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

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- Can’t be publicly observed, repeated, tested either directly or indirectly- There just is no science of Intelligent Design

False, too…

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 ascience 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.

THESCIENTIFIC METHOD

systematic attempt on the part of researchers…Scientific Method1 = ask relevant question2 = do background search3 = construct hypothesis4 = test hypothesis with experiment5 = analyze results of experiment

6a = if hypothesis is confirmed (true) = go to 76b = if hypothesis is not confirmed (false) or partially true

7 = report results8 = use results to construct more hypotheses

Car won’t start

Car won’t start

Hypotheses?

Car won’t start

Hypotheses?

Battery?

Car won’t start

Hypotheses?

Battery?

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:- 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

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…

So much for Science…

What is Biology?

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.

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)

biochemistrymolecular biologymicrobiologycellular biologyphysiologybotanyzoologyecologyevolutionary biology…

…and many more branchesand sub-branches

…to explain theorganic (living)

phenomena of our experience

One Goal

of Biology

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

?

So… what is Life?- 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

- is a single cell alive?

- the organelles that make up a cell? (Mitochondrion, Golgi Apparatus)

- a virus?

- a prion? (abnormal protein)

- the ecosystem itself?

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:

BIOMEDICAL 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…

What I Do:

BIOMEDICAL INFORMATICS Combination of:

BiologyMedicineHealth CareComputer ScienceInformation Science

classify, describe, organize…

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

Information Sciencescience associated with the collection,categorization, management, storage,processing, retrieval, and dissemination ofknowledge and information, often timesusing computational tools… think librarian,but a librarian with computational skills…

OVERALL GOAL:

KNOWLEDGE SHARING

What I Do:

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

classify, describe, organize…

What I Do:

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

classify, describe, organize…

with domain ontologies

with formal ontologies

Domain:

Area of study like biology, law, psychology, or any other science or discipline you would find at a university

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)

…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

Data

Data

Data

Data Data

Data

SILO EFFECT

Data

Data

Data

Data

Data Data

Data

SILO EFFECT

PROBLEM:DE-SILOING all of this

domain data and information so that it may

be queried effectively, shared, and

re-used(like Google-izing it)

SOLUTION:

FORMAL ONTOLOGY:

- 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.

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

From this…

To this…

Data

Data

Data

Data

Data Data

Data

Data

Data

Data

Data

Data

Data

Data

Formal Ontology E.G., Basic Formal Ontology

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.

Thank YouThank YouRobert 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

[email protected]://www.org.buffalo.edu/rarp/