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ANATOMY AND TIME Barry Smith

ANATOMY AND TIME Barry Smith. SNAP AND SPAN. To understand relations between universals. Reference to times and instances are important A derives from B concept A derives from concept B. Official OBO definition. term: derived_from definition: Any kind of temporal relationship,

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ANATOMY AND TIME Barry Smith

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  1. ANATOMY AND TIMEBarry Smith

  2. SNAP AND SPAN

  3. To understand relations between universals • Reference to times and instances are important • A derives from B • concept A derives from concept B

  4. Official OBO definition • term: derived_from • definition: Any kind of temporal relationship, • such as derived_from, translated_from

  5. Better Definition • A derives from B • for any instance x of A there is some instance y of B such that x exists earlier than y and

  6. What is an anatomy standardization for? • Anatomy: • across species (human, mouse) (SAEL) • across time (development, growth, aging) • from generic (normal + abnormal) • to instance-based) • Tied to: genomic • clinical (disease pathways)

  7. FMA = (AT, ASA, ATA, Mk) • AT = Anatomy Taxonomy • ASA = Anatomical Structural Abstraction • Mk = Metaknowledge

  8. FMA = (AT, ASA, ATA, Mk) • ATA, or Anatomical Transformation Abstraction describes the time-dependent morphological transformations of the concepts represented in the taxonomy during the human life cycle, which includes prenatal development, postnatal growth and aging;

  9. FMA = (AT, ASA, ATA, Mk) • ATA, or Anatomical Transformation Abstraction describes the time-dependent morphological transformations of the concepts represented in the taxonomy during the human life cycle, which includes prenatal development, postnatal growth and aging;

  10. single-cell zygote • multi-cell zygote • morula • early blastocyst • gastrula • new born • infant • adolescent • young adult

  11. A sequence of SNAP ontologies

  12. development processes aging processes growth processes physiological processes together with SPAN ontologies for processes/transformations SNAP

  13. each of these at a plurality of levels of granularity cellular subcellular molecular physiological processes SNAP

  14. time SNAP

  15. canonical vs. instantiated time

  16. undeformed  deformed time

  17. these are not instances undeformed  deformed time

  18. WINDOWS ON REALITY undeformed  deformed time

  19. SYMBIOSIS OF KNOWLEDGE ABOUT UNIVERSALS AND INSTANCES undeformed  deformed time

  20. undeformed  deformed time

  21. undeformed  deformed human chimpanzee mouse fly yeast bacteria time

  22. undeformed  deformed human chimpanzee mouse fly yeast bacteria time

  23. A Proposed Standardization • relations

  24. A Proposed Standardization • OBO Relations Ontology

  25. A Proposed Standardization • OBO Relations Ontology • is part of • is member of (a collection) • is location of -- is contained in … • is connected to • is later than – is simultaneous with … • is bearer of • is function of • causes • is functioning of

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