1 ANATOMY AND TIME Barry Smith. 2 SNAP AND SPAN 3 To understand relations between universals Reference to times and instances are important A derives.

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Presentation transcript:

1 ANATOMY AND TIME Barry 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 together with SPAN ontologies for processes/transformations physiological processes development processes aging processes growth processes SNAP

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

14 SNAP time

15 time canonical vs. instantiated

16 time undeformed  deformed

17 time undeformed  deformed these are not instances

18 time undeformed  deformed WINDOWS ON REALITY

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

20 time undeformed  deformed

21 time undeformed  deformed human chimpanzee mouse fly yeast bacteria

22 time undeformed  deformed human chimpanzee mouse fly yeast bacteria

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