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Principles and Practice of Ontology Development: Making Definitions Computable. Chris Mungall LBL. Why make definitions computable?. Doing the work all by yourself is hard, boring and error prone Automate using reasoning Bonus: Makes the definitions easier for humans

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principles and practice of ontology development making definitions computable

Principles and Practice of Ontology Development: Making Definitions Computable

Chris Mungall

LBL

why make definitions computable
Why make definitions computable?
  • Doing the work all by yourself is hard, boring and error prone
  • Automate using reasoning
  • Bonus:
    • Makes the definitions easier for humans
    • Enables better visualization
biology is modular most ontology classes are compositional
Biology is modular, most ontology classes are compositional

phalanx

p

pf

ph

distal

phalanx

proximal

phalanx

pp

dp

autopod

hand

foot

ppf

dpf

dph

pph

(adapted from diagram by

David Hill and Joel Richardson)

history
History
  • “Cross-products”
    • Hill, D. P. and Blake, J. A. and Richardson, J. E. and Ringwald M: Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res 2002
  • Formal Concept Analysis
  • Description Logics 1980s-present
    • Galen – Rector et al
    • GONG – Wroe, Stevens et al
logical definitions
Logical definitions
  • Genus-differentia form
    • Text definition is genus-differentia form
      • Distal phalanx of hand:
        • “A distal phalanx that is part of a hand.”
        • or “A distal phalanx[ID:2]that is part of a hand[ID:3].”
    • OWL:
      • ‘distal phalanx of hand’ EquivalentTo ‘distal phalanx’and part_ofsome hand
    • OBO-Format
      • [Term]
      • id: ID:1 ! distal phalanx of hand
      • intersection_of: ID:2 ! distal phalanx
      • intersection_of: part_of ID:3 ! hand
editing logical definitions
Editing logical definitions
  • OBO-Edit
    • Cross-product tab
      • Genus
      • Differentia
    • Parent Editor
      • select links to make them ‘intersections’
  • Protégé 4
    • Equivalent Classes
      • Enter expression
using a reasoner
Using a reasoner
  • Given:
    • ‘distal phalanx of hand’ EquivalentTo ‘distal phalanx’ and part_ofsome hand
    • ‘phalanx of hand’ EquivalentTo phalanxand part_ofsome hand
    • ‘distal phalanx’ is_a phalanx
  • A reasoner can infer that:
    • ‘distal phalanx of hand’ is_a ‘phalanx of hand’

dp

ph

dph

uses of a reasoner
Uses of a reasoner
  • Ontology authoring
    • Time saving
      • Automatically inferring is_a polyhierarchy
    • Quality Control
      • detecting inconsistencies
  • Data integration and discovery
    • Less applications… so far
reasoners
Reasoners
  • OBO-Edit
    • Rule Based Reasoner
  • OWL Reasoners (Protégé 4)
    • Pellet
    • FaCT++
    • HermiT
difference between obo and owl reasoning
Difference between OBO and OWL reasoning
  • OBO format expresses a subset of OWL
    • We thought this would be enough for most users
    • But this turned out not to be true
    • E.g. Lacks part
    • See talk later today
  • Sufficient for basic anatomical classification
modularity and external ontologies
Modularity and external ontologies
  • Modularity principle:
    • Multiple orthogonal ontologies
    • Use classes from O1 as building blocks in O2
    • E.g.
      • astrocyte differentiation
      • anucleate cell
  • BUT: Can pose problems for large external ontologies
    • CHEBI
    • PRO
import
Import
  • application can choose to follow import chain
    • if it doesn’t, then there are dangling references
  • the full import closure can be large!

CL

GO-BP

imports

ontology based

application

large import closure
Large Import Closure

CL

GO-BP

AO

GO-CC

PRO

CHEBI

ontology based

application

bridge files
Bridge files
  • current solution used by NIF, GO

CL

BP

BP-xp-CL

more

advanced application

basic application

mireot minimal information for retrieval of external ontology terms
MIREOT - Minimal Information for Retrieval of External Ontology Terms
  • current solution used by OBI, PRO, hemo-CL

BP

CL (full)

CL subset

copy

  • ontology author “MIREOT”s in subset of external ontology
deploying cell obo
Deploying cell.obo
  • Typical User
    • inferred links materialized
    • external ontology links removed
  • Advanced User
    • asserted links only
    • external links present
    • minimal external classes included
ontology publishing pipeline
Ontology publishing pipeline

cell_edit.obo

cell_public.obo

cell_basic.obo

reasoner

filter

GO/PRO/etc subset

GO/PRO/etc subset

obo2owl

obo2owl

obo2owl

cell_edit.owl

cell_public.owl

cell_basic.owl

reasoner

filter

GO/PRO/etc subset

GO/PRO/etc subset

summary
Summary
  • Many ontologies are seeing the benefits of using computable definitions
    • e.g. fly anatomy
    • GO slow to adopt, lots of legacy issues to work out
  • Better to employ them from the outset
    • DC_CL
    • Hemo_CL