www.xspan.orgbio-ontologies workshop 20041 cross-species mapping between anatomical ontologies:...
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www.xspan.org Bio-ontologies Workshop 2004 1
Cross-species Mapping between Anatomical Ontologies:
Terminological and Structural Support
bySarah Luger, Stuart Aitken & Bonnie Webber
[email protected], [email protected],[email protected]
XSPAN/University of Edinburgh
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A Mapping Problem
• Mouse Tail
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A Mapping Problem
• C. Elegans Tail
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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
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A Mapping Problem
• Given– Mouse: 3559 anatomical parts– Drosophila: 506 anatomical parts– C. Elegans: 242 anatomical parts
• Can their terminologies and anatomical ontogolies suggest what parts may be similar (homologous)?
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A Mapping Problem
• Mouse tail to C. elegans tail– Same name, different function
• Mouse optic nerve to drosophila optic nerve– Same name, same function– The ontologies show different paths.
• The goal is to suggest the anatomical parts that maybe similar. Does language suggest similarity? What clues can we use?
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A Related Problem• In two different models of human anatomy, do parts with
similar names always denote similar tissues?
• In GALEN:Lobe of left lung
Maps in FMA to:
Upper Lobe of left lung Lower lobe of left lung
• Extrapolate from intra-human to inter-species comparisons.
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XSPAN Project
University of EdinburghSchool of Biomedical SciencesSchool of Informatics
Heriot-Watt UniversitySchool of Mathematical and Computer Sciences
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XSPAN• A framework for recording
expert knowledge about anatomy.
• A Web server with information about evolutionary, functional, developmental and cellular anatomy:
– Homology relationships– Functional similarities– Lineage relationships– Cell types
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XSPAN: Background
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Current Species Comparisons
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Example Ontologies: COBrA
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Comparison ExamplesEarlier I gave the impression that comparison between
terms was based on a “short form.” That is not exactly true. The short form needs to be understood in context.
mouse . embryo . organ system . sensory organ . ear . external ear . pinna . mesenchyme
mouse . embryo . organ system . visceral organs . alimentary system . gut . foregut . pharynx . associated mesenchyme
mouse . embryo . organ system . nervous system . central nervous system . brain . forebrain . telencephalon . corpus striatum . caudate nucleus . head
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Comparison Motivation
• Two motivations for using more than the leaf label:– Context is important as terms are not uniquely
denotated across the ontologies.– The important terms are spread across the
labels of the path, they are not restricted to the leaf terms.
• This reflects the choices biologists made in grouping and structure.
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Lexical Analysis
• Normalize terms to limit the effect of different descriptive styles including dealing with American and English variants.
• Compare content words by removing stop words.
• Ensure comparable forms of words by stemming and lemmatizing.
• Results are then treated as an unordered set.
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Lexical Analysis Examples
• Use example pairing for comparison:
1) arch of aorta2) aortic sinus3) visceral muscle of larval heart
1’) arch aort
2’) aort sinu3’) viscer muscl larval heart
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Lexical Analysis Examples mouse . embryo . organ system . cardiovascular system .
heart . aortic sinus
drosophila . embryo . embryonic organ system . embryonic circulatory system . embryonic . larval dorsal vessel . embryonic . larval heart . visceral muscle of larval heart
1. Node comparison or leaf node in a tree. aortic sinus to visceral muscle of larval heart
2. Path-based comparison or sequence of node labels from root to leaf.
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Methodology• Tissue pairs assessed structurally.• Use a similarity threshold to limit the
number of results.• Resultant pairs have one to many
mappings:EMAPA: 16039 FBbt: 00000052EMAPA: 16039 FBbt: 0000111EMAPA: 16039 FBbt: 00006005EMAPA: 16069 FBbt: 00001056EMAPA: 16103 FBbt: 0000125
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Structural Analysis
• Evaluate structural similarity by taking the ontologies as graphs with directed but unlabeled edges.– First examine the intra-species relationships– Check to see if the relative positions are
consistent between species.– There may not be evidence.
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Structural Analysis
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Results
• Node-based comparisons– Approximately 80% of lexical mappings have
support from the ontology.– Less than 16% of proposed mappings have
either no evidence for or against, or are contradictory across the three comparisons.
• Path-based comparisons– With lexical mappings at 75% similarity, the
number of contradictory matches was reduced to zero.
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Results
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Pairwise Results
C. elegans 2732
Mouse 79% positive 2121
15% no evidence 358
6% contradictory 254
C. elegans 1625
Drosophia 82% positive 1337
2% no evidence 32
16% contradictory 256
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Pairwise ResultsDrosophila 2732
Mouse 78% positive 2121
13% no evidence 358
9% contradictory 254
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Future Work Average path length in nodes
Mouse 7.9
Drosophila 6.4
C. elegans 6.0
Weighting paths helps normalize specificity.
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Future Work
mouse . organ systems . circulatory system . heart . valve muscle1 2 4 8 16
The last term is weighted more than all prior terms combined. This filters out the “garbage” when comparing similar root-to-leaf paths with vastly different levels of specificity.
drosophila . organ system . upper torso . circulatory system . 1 2 4 8
valve network . heart . valves . valve muscles 16 32 64 128
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Future Work
• Augment the three m.o. datasets with synonyms and abbreviations.– Some are provided in the anatomies, but not
systematically or consistently– Introduce synonyms from an anatomical
reference.
• Establish the effect of additional information on previous results.
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References• Aitken, J.S., B.L. Webber and J.B.L. Bard. Part-
of Relations in Anatomical Ontologies: A Proposal for RDFS and OWL Formalisations. Proc PSB 04, 9:166-177(2004)
• Zhang, S., and O. Bodenreider. Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain. Proc PSB 04, 9:250-261(2004)
• Zhang, S., P. Mork and O. Bodenreider. Lessons Learned from Aligning Two Representations of Anatomy. To be published in KR-MED 2004.