ontology - and reloaded and revolutions
DESCRIPTION
TRANSCRIPT
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontology- and Reloaded and Revolutions
in Life Science
Jie Bao
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontology
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Once upon a time there is a Graduate called Neo
who like thinking
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
And ask his advisor silly questions Architect: Hello Neo. Neo: Who are you? Architect: I am the Architect. I created the Matrix. I
have been waiting for you. You have many questions and although the process has altered your consciousness you remain irrevocably human, ergo some of my answers you will understand and some of them you will not. Concordantly, while your first question maybe the most pertinent you may or may not realize it is also the most irrelevant. Ultimately, you are just one Cell.
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Meaning of the World
A Cell?
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Cell?
From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Cell?
From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Cell?
From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Cell?
From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Cell?
From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Cell?
From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Names and Meaning
You do need to learn more about names and their meanings to be the One. In another word, you have to learn ontology.
Ontology? It is another unknown word….
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
What is Ontology
• the American Heritage® Dictionary: The branch of metaphysics that deals with the nature of being.
• Merriam-Webster : 1: a branch of metaphysics concerned with the nature and relations of being. 2 : a particular theory about the nature of being or the kinds of existents
Then use dictionary!
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
What is Ontology(2)
• 1. <philosophy> A systematic account of Existence.• 2. <artificial intelligence> (From philosophy) An explicitformal
specification of how to represent the objects, concepts and other entities that are assumed to exist in some area ofinterest and the relationships that hold among them. For AI systems, what "exists" is that which can be represented. ..... Formally, an ontology is the statement of a logicaltheory.
• 3. <information science> The hierarchical structuring of knowledge about things by subcategorising them according to their essential (or at least relevant and/or cognitive) qualities.
Source: The Free On-line Dictionary of Computing, © 1993-2005 Denis Howe
And google!
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
What is Ontology(3)
• Aristotle: Science of Being (Metaphysics, IV, 1)
• Tom Gruber: An ontology is a specification of a conceptualization. (T. R. Gruber. A translation approach to portable ontologies. Knowledge Acquisition, 5(2):199-220, 1993 )
And learn from those people
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
This is an ontology
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Another Ontology
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Yet Another Ontology
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Keys of Ontologies
A set of controlled vocabulary that classify concepts and define the relationship between them
• Terms: Neo, Cell, Smith, Agent,Program, fights• Relations
– Neo is a Cell– Smith is an Agent– An Agent is a Program– Neo fights Smith
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
What is Not an Ontology
• Controlled vocabulary, with no relations. – Like PDB ID
• Dictionaries – they are not formal specification
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Why Ontology
What I can do once I have an ontology?
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Annotation
In this study, we report the isolation and molecular characterization of the B. napus PERK1 cDNA, that is predicted to encode a novel receptor-like kinase. We have shown that like other plant RLKs, the kinase domain of PERK1 has serine/threonine kinase activity. In addition, the location of a PERK1-GTP fusion protein to the plasma membrane supports the prediction that PERK1 is an integral membrane protein…these kinases have been implicated in early stages of wound response…
Function: protein serine/threonine kinase activity ; GO:0004674 (IDA)
Component:integral to plasma membrane ; GO:0005887 (IDA)
Process: response to wounding ; GO:0009611 (NAS)
You may annotate data precisely with ontology terms
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Reasoning
– Recognising semantic similarity in spite of syntactic
differences (Neo is the One)
– Recognising implicit consequences given explicitly
stated facts ( (given ontology)-> Smith is a Program)
This is what we called “machine understandability”, Neo
You may infer implicit facts from known facts
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontology
Reloaded
Ontologies in life science
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
More Gradute-advisor conversion• Neo: Why am I here?
• Architect: Your life is the sum of a remainder of an unbalanced equation inherent in the programming of the matrix. You are the eventuality of an anomaly which despite my sincerest efforts I have been unable to eliminate from what is otherwise a harmony of mathematical precision. While it remains a burden deciduously avoided it is not unexpected and thus not beyond a measure of control, since we have known the control of you cells with knowledge about your biological existence. Which has led you inexcerably here?
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
More Gradute-advisor conversion
Can you give me an example of your knowledge about biological existences ?I assume it is a ontology – the study of existence
Let’s Start with GO
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
GO?
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
GO - Gene Ontology
Cellular Component
Molecular Function Biological Process
is NOT an ontology only about Gene
This is a typical ontological misunderstanding
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Cellular Component
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Molecular Function
insulin binding. insulin receptor activity
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Molecular Function
drug transporter activity
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Biological Process
cell division
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Biological Process
Courtship behavior of Homo Sapiens
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Anatomy of a GO term
id: GO:0006094name: gluconeogenesisnamespace: processdef: The formation of glucose fromnoncarbohydrate precursors, such aspyruvate, amino acids and glycerol.[http://cancerweb.ncl.ac.uk/omd/index.html]exact_synonym: glucose biosynthesisxref_analog: MetaCyc:GLUCONEO-PWYis_a: GO:0006006is_a: GO:0006092
unique GO IDterm name
definition
synonymdatabase ref
parentage
ontology
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontology Structure
cell
membrane chloroplast
mitochondrial chloroplastmembrane membrane
is-apart-of
DAG(directed acyclic graph)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
What other ontologies in life science
There are many! EC, SCOP, CATH, MIPS. MGED… Let’s see some trait ontologies.
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Phenotype (Trait) OntologiesExample: Plant Ontology (http://www.plantontology.org)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Animal Trait Ontology
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research LaboratoryATO Editor
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
ATO Editor Features
• Collaborative Ontology Building– Concurrent editing– Hierarchical management– Partial Locking
• Scalable Database storage
• Modular ontology representation
• Partially reusable ontology
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
OBO• Open Biomedical Ontologies - http://obo.sourceforge.net/
And more…
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
OBO Format• format-version: GO_1.0
!any comment here typeref: relationship.types subsetdef: goslim "Generic GO Slim" version: $Revision: 1.11 $ date: April 18th, 2003 saved-by: jrichter remark: Example file
[Term] id: GO:0003674 name: molecular_function def: "The action characteristic of a gene product." [GO:curators] subset: goslim
[Term] id: GO:0016209 name: antioxidant activity is_a: GO:0003674 def: "Inhibition of the reactions brought about by dioxygen or peroxides. \ Usually the antioxidant is effective because it can itself be more easily \ oxidized than the substance protected. The term is often applied to \ components that can trap free radicals, thereby breaking the chain \ reaction that normally leads to extensive biological damage." \ [ISBN:0198506732]
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontology
- Revolutions
Ontology for Matrix
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
More Gradute-advisor conversion
Ontologies are really funny. Could you tell me how useful they are other than helping you to design efficient biological cells?
Basically, ontologies help us a lot in design the Matrix. To represent the real world, we need a formalism to do Knowledge Representation.
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Semantic WebThe first prototype of Matrix is based on so called “Semantic Web”
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Semantic Web
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Ontologies based on Logics
• Matrix, or semantic web, are designed based on the formal presentation of concepts and their relations. The underlying magic is logics, especially the Description Logics, which is much complex than the OBO ontologies e.g. GO.
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Web Ontology Language• OWL is a syntax of descrption logics
and first generation Matrix language.
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
DL and OWL
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
DL and OWL(2)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Evolution of Web Ontology Languages
XMLXML
HTMLHTML
RDFSRDFS
SHOESHOE
OILOIL
DAML-ONTDAML-ONT
OWLOWLRDFRDF
Revision
Extendvocabularies
Combinevocabularies
Extend HTML tagsfor semantic description
Define vocabularies
OWL-SOWL-S
SGMLSGML
DAML-SDAML-S
For Webservices
1992 1998 1999 2000 2001 2002 2003
DAML(DAML+OIL)
DAML(DAML+OIL)
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Protégé – Ontology Editor
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Architect: Ontologies do open the road to the series of revolutions leading to the final Matrix
Neo: That’s an interesting talk. If I were you, I would hope that we will meet again, Dr. Arch.
Architect: We will.
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
References• Amelia Ireland. GO : the Gene Ontology (talk)• Tom Shi: Introduction to GO (talk)• Chintan O. Patel and Yves A. Lussier Rerepresenting Biomedical
Ontologies using the Web Ontology Language -A Checklist . SOFG 2004
• Zhi-liang Hu, Jie Bao, Max F. Rothschild, Vasant Honavar, and James M. Reecy. (2006) Developing Frameworks and Tools for Animal Trait Ontology (ATO) . Plant and Animal Genome XIV Conference. Poster Track. January 14-18, 2006,San Diego, California.
• Ian Horrocks, Peter F. Patel-Schneider, and Frank van Harmelen. From SHIQ and RDF to OWL: The making of a web ontology language. Journal of Web Semantics, 2003.
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
Questions
Computer Science 672, Spring 2006, Iowa State University. Feb 27. 2006
Iowa State University Department of Computer ScienceArtificial Intelligence Research Laboratory
A dictionary of Matrix• First Matrix: a complete but inconsistent system• Later Matrices: incomplete but consistent Systems• Zion: formulae not decidable in Matrix (due to
Gödel incompleteness)• Matrix Reload: incorporate new facts from the One• Neo – a learning program to collect new facts, from
non-logic worlds• Oracle – heuristic program• Architect – A distributed reasoner which can
integrate knowledge in matrix and Neo.