Biological Ontologies

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Biological Ontologies

• Neocles Leontis
• April 20, 2005

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What Is An Ontology?

• An ontology is an explicit description of a
  domain of knowledge
• Concepts -- Entities and Relations
• Properties and attributes of Entities and
  Relations
• Constraints on properties and attributes
• Individuals (Instances)
• An ontology defines
• a common vocabulary
• a shared understanding of the domain of knowledge
• Commitments on how to use the vocabulary

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What Is Ontology Engineering?

• Ontology Engineering Defining terms in the
  domain and relations among them
• Defining concepts in the domain (Classes)
• Arranging the concepts in a hierarchy
  (Subclass-Superclass hierarchy)
• Defining which attributes and Properties classes
  can have (slots) and constraints on their values
  (facets)
• Defining individuals and filling in slot values
  (instantiation)

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Why Develop an Ontology?

• To share common understanding of the structure of
  information
• among people
• among software agents
• To enable reuse of domain knowledge
• to avoid re-inventing the wheel
• to introduce standards to allow interoperability
  between ontologies

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More Reasons

• To make domain assumptions explicit
• easier to change domain assumptions
• easier to understand and update legacy data
• To separate domain knowledge from the operational
  knowledge
• re-use domain and operational knowledge separately

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An Ontology Is Often Just the Beginning
Databases
Declare structure
Ontologies
Knowledge bases
Provide domain description
Problem-solving methods
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Ontology-Development Process

• In Logical order

In reality - an iterative process
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Protégé

• Graphical ontology-development tool
• Supports a rich knowledge mode
• Open-source and freely available
  (http//protege.stanford.edu)

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Authoring Program (Protégé 2000)

• Enforces the implementation of foundational
  principles and definitional desiderata
• Frame-based architecture compatible with OKBC
  protocol Open Knowledge Base Connectivity
• Frames are used to represent anatomical concepts
• Frames allow for distinguishing between class and
  instance
• Protégé allows for selective inheritance of
  attributes
• Protégé enhances specificity and expressivity of
  attributes by assigning them their own attributes.

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Determine Domain and Scope
determinescope
considerreuse
enumerate terms
defineclasses
defineproperties
defineconstraints
createinstances

• What is the domain that the ontology will cover?
• Who is going to use the ontology?
• For what are they (we) going to use the ontology?
• For what types of questions should the
  information in the ontology provide answers
  (competency questions)?
• Answers to these questions may change during the
  lifecycle

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RNA Ontology Scope DOMAIN

• RNA Sequences (1D) -- Coding and Non-Coding
• RNA 2D structures
• RNA 3D structures
• Alignments of homologous RNA sequences
• Relationships between alignments and 3D
  structures

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RNA Ontology ScopeWHO?

• Molecular biologists biochemists
• Structural biologists
• Evolutionary biologists
• Nanotechnologists

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RNA Ontology Scope WHAT?

• How to improve prediction of RNA 3D structure
• How to improve sequence alignments of homologous
  RNAs
• To identify and annotate RNA genes in genomes
• How are RNA 3D structure and evolution coupled?
• How is RNA evolution coupled to biological
  evolution

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Consider Reuse
considerreuse
determinescope
enumerate terms
defineclasses
defineproperties
defineconstraints
createinstances

• Why reuse other ontologies?
• to save the effort
• to interact with the tools that use other
  ontologies
• to use ontologies that have been validated
  through use in applications

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Enumerate Important Terms
enumerate terms
considerreuse
determinescope
defineclasses
defineproperties
defineconstraints
createinstances

• What are the terms (entities) we need to talk
  about?
• What are the properties and attributes of these
  entities?
• What are the relationships between entities?

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Define Classes and the Class Hierarchy
defineclasses
considerreuse
enumerate terms
determinescope
defineproperties
defineconstraints
createinstances

• A class is a concept in the domain
• a class of wines
• a class of wineries
• a class of red wines
• A class is a collection of elements with similar
  properties
• Instances of classes
• a glass of California wine youll have for lunch

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Class Hierarchy
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Class Inheritance

• Classes usually constitute a taxonomic hierarchy
  (a subclass-superclass hierarchy)
• A class hierarchy is usually an IS-A hierarchy
• an instance of a subclass is an instance of a
  superclass
• If you think of a class as a set of elements, a
  subclass is a subset

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FMA -- High Level Scheme

• FMA (AT, ASA, ATA, Mk)
• AT Anatomy taxonomy (assigns anatomical
  entities as class concepts
• ASA Anatomy Structural Abstraction -- includes
  structural relationships among entities of the AT
• ATA Anatomical Transformation Abstraction --
  relationships that describe morphological
  physical transformations of anatomical entities
• MK Metaknowledge -- principles and sets of rules

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ASA -- High Level Scheme

• ASA (Dt, PPt, Bn, Pn, SAn)
• Dt Dimensional taxonomy
• PPt Physical Properties taxonomy
• Bn Boundary network
• Pn Partonomy network
• SAn Spatial Association network

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Boundary Network (Bn)

• Specification of boundaries is critical for
  segmentation of images and volumetric datasets
• Definition Boundary Non-material physical
  anatomical entity of two or fewer dimensions that
  delimits anatomical entities that are of one
  higher dimension than the bounding entity

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Boundary Network (Bn)

• Inverse Relationships
• -bounded by-
• -bounds-
• Real vs. Virtual BoundariesRea boundaries
  correspond to its surface and designate
  discontinuities between constitutional parts of
  anatomical entities

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Partonomy Network (Pn)

• Inverse Relationships
• -has part-

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Rule of Dimensional Consistency

• Distinguishes between boundary and partonomy
  relationships.
• Parthood relations -- only allowed for entities
  of the same dimension
• Ex Cavity of stomach (3D) -has part- Cavity of
  pyloric antrum (3D)
• Ex Internal surface of stomach (2D) -has part-
  Internal surface of pyloric antrum (2D)

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What to Reuse?

• Ontology libraries
• DAML ontology library (www.daml.org/ontologies)
• Ontolingua ontology library (www.ksl.stanford.edu/
  software/ontolingua/)
• Protégé ontology library (protege.stanford.edu/plu
  gins.html)
• Upper ontologies
• IEEE Standard Upper Ontology (suo.ieee.org)
• Cyc (www.cyc.com)

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RNA Ontology Consortium

• To share common understanding of the structure of
  information
• among people
• among software agents
• To enable reuse of domain knowledge
• to avoid re-inventing the wheel
• to introduce standards to allow interoperability

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What to Reuse? (II)

• General ontologies
• DMOZ (www.dmoz.org)
• WordNet (www.cogsci.princeton.edu/wn/)
• Domain-specific ontologies
• UMLS Semantic Net
• GO (Gene Ontology) (www.geneontology.org)
• FMA (Foundational Model of Anatomy)

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Foundational Model of Anatomy
http//sig.biostr.washington.edu/projects/fm/index
.html

• Reference ontology for biomedical informatics
• Representation of Anatomical Entities and
  Relationships
• Symbolic modeling of the structure of the human
  body at the highest level of granularity
• Evolving Resource for knowledge-based
  applications requiring anatomical information

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FMA Modeling Challenges

• Representing complex structural relations
• Representing different levels of granularity
• Developing a model that is scalable to a very
  large number of concepts
• Using consistent organizational principles