Lexical Issues in Anatomical Ontologies

1
Lexical Issues in Anatomical Ontologies

• Sarah Luger
• www.xspan.org
• based on work with
• Stuart Aitken and Bonnie Webber

2
XSPAN Objectives

• To support access to tissue-based genetic
  information that is indexed by anatomy across
  species, via anatomy ontology integration.
• homology relationships
• function similarities
• lineage relationships
• cell types

3
A Mapping Problem

• Mouse Tail

4
A Mapping Problem

• C. Elegans Tail

• Mouse tail to C. elegans tail
• Same name, different function

5
A Mapping Problem

• In mouse
• embryo/ organ system/ sensory organ/ eye/ optic
  stalk/ optic nerve
• In drosophila
• larva/ larval organ system/ larval nervous
  system/ larval central nervous system/ larval
  brain/ medulla anlage/ optic nerve
• Mouse optic nerve to drosophila optic nerve
• Same name, same function
• The ontologies show different paths.

6
A Mapping Problem

• Identify and exploit relationships between
  tissues across the key model organisms given
• Mouse 3559 anatomical parts
• Drosophila 506 anatomical parts
• C. Elegans 242 anatomical parts
• Zebrafish 1200 anatomical parts
• Human 2328 anatomical parts
• Can their terminologies and anatomical ontogolies
  suggest what parts may be similar (homologous)?

7
Lexical Analysis

• Language processing
• normalize, remove stop words, stemmed and
  lemmatized and then treated as unordered set
• Use more than the leaf label
• Context, terms are not unique
• Important terms spread across path
• The last term is weighted more than all prior
  terms combined. This filters out some garbage
  when comparing similar root-to-leaf paths with
  vastly different levels of specificity.

8
Weighting Example

• EMAPA.18237Mouse/ embryo/ organ system/ sensory
  organ/ eye/ lens/ capsule
• 0 1 2 4 8
  16 32
• EHDAA.9045 100 match
• Human/ embryo/ organ system/ sensory organ/ eye/
  lens/ capsule
• 0 1 2 4
  8 16 32
• EHDAA.4727 87 similar or 55/63
• Human/ embryo/ organ system/ sensory organ/ eye/
  lens vesicle/capsule
• 0 1 2 4 8
  8 32

9
Weighting Example

• EHDAA.9045
  Human/ embryo/
  organ system/ sensory organ/ eye/ lens/ capsule
• EMAPA.18979
  Mouse/ embryo/
  organ system/ visceral organ/ reproductive
  system/ female/ ovary/ capsule
• EMAPA.18679
• Mouse/ embryo/ organ system/ visceral organ/
  renal urinary system/ metanepheros/ excretory
  component/ cortex/ capsule

10
Methodology

• Use a similarity threshold to limit the number of
  results.
• Resultant pairs have one to many mappings
• EMAPA 18237 EHDAA.9045
• EMAPA 18237 EHDAA.4727
• Tissue pairs then structurally assessed by taking
  the ontologies as graphs with directed but
  unlabeled edges.
• Examine intra-species relationships
• Check relative positions of the terms between
  species
• Judge comparisons as contradictory, supported, or
  no evidence.

11
Mouse-Human Results

• Threshold Matched Pairs Support
• 100 1223 90.4
• 96 1763 84.7
• 94 3037
  92.8
• This improvement follows from the larger set of
  lexical matches having more common terms near the
  top of the ontology, which permits paths that
  were previously being rejected.

12
Mouse-Human Results

• Mappings between human and mouse terms, where the
  x-axis represents thresholds of lexical
  similarity.

13
Human-Drosophila Results

• Fewer matches so we chose lexical similarity
  levels of 75, 66 and 50.
• Some contradictory mappings appear at 50.
• The proportion of compatible mappings drops as
  the comparison threshold is reduced.
• An increase in mapping score is again observed.

14
Future Work

• Different name, same function
• Introduces the need for synonym tables.
• Working with an anatomist to include synonyms in
  the mouse anatomy.
• Zebrafish is also working on this.
• Discover more differences in ontology terms and
  free-text terms.

15
Ontologies, Mapping and Synonyms
gonad

• drosophila
• isa
• whole organism
• part of
• organ system
• isa
• reproductive system
• isa
• male reproductive system
• part of
• testis

C. elegans part of organ system isa
sex-associated system isa
male-associated system isa male
reproductive system isa male
gonad
testis
16
COBrA Ontology Mapping
17
COBrA A GO editor
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COBrA A GO editor
19
Structural Analysis