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Lexical Issues in Anatomical Ontologies

Lexical Issues in Anatomical Ontologies. Sarah Luger www.xspan.org based on work with Stuart Aitken and Bonnie Webber. To support access to tissue-based genetic information that is indexed by anatomy across species, via anatomy ontology integration. homology relationships

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Lexical Issues in Anatomical Ontologies

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  1. Lexical Issues in Anatomical Ontologies Sarah Luger www.xspan.org based on work with Stuart Aitken and Bonnie Webber BIONLP

  2. 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 XSPAN Objectives BIONLP

  3. A Mapping Problem • Mouse Tail BIONLP

  4. A Mapping Problem • C. Elegans Tail • Mouse tail to C. elegans tail • Same name, different function BIONLP

  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. BIONLP

  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)? BIONLP

  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. BIONLP

  8. Weighting Example • EMAPA.18237:Mouse/ embryo/ organ system/ sensory organ/ eye/ lens/ capsule 0 1 24816 32 • EHDAA.9045: 100% match Human/ embryo/ organ system/ sensory organ/ eye/ lens/ capsule 0 1 24816 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 BIONLP

  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 BIONLP

  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. BIONLP

  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. BIONLP

  12. Mouse-Human Results Mappings between human and mouse terms, where the x-axis represents thresholds of lexical similarity. BIONLP

  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. BIONLP

  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. BIONLP

  15. drosophila isa whole organism part of organ system isa reproductive system isa male reproductive system part of testis Ontologies, Mapping and Synonyms gonad C. elegans part of organ system isa sex-associated system isa male-associated system isa male reproductive system isa male gonad testis BIONLP

  16. COBrA: Ontology Mapping BIONLP

  17. GO term data search hyperlink COBrA: A GO editor BIONLP

  18. COBrA: A GO editor BIONLP

  19. Structural Analysis BIONLP

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