anatomy and time barry smith

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ANATOMY AND TIME

Barry Smith

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SNAP AND SPAN

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To understand relations between universals

Reference to times and instances are important

A derives from B

concept A derives from concept B

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Official OBO definition

term: derived_from

definition: Any kind of temporal relationship,

such as derived_from, translated_from

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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

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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: genomicclinical (disease pathways)

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FMA = (AT, ASA, ATA, Mk)

AT = Anatomy Taxonomy

ASA = Anatomical Structural Abstraction

Mk = Metaknowledge

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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;

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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;

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single-cell zygote

multi-cell zygote

morula

early blastocyst

gastrula

new born

infant

adolescent

young adult

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A sequence of SNAP ontologies

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together with SPAN ontologies for processes/transformations

t i m et i m ephysiological processes

t i m

e

t i m

e

development processest i m

e

t i m

e

aging processest i m et i m egrowth processes

SNAP

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each of these at a plurality of levels of granularity

t i m et i m e

physiological processes

SNAP

t i m et i m e

t i m et i m e

t i m et i m e

t i m et i m e

t i m et i m e

molecular

subcellular

cellular

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SNAP

time

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time

canonical vs. instantiated

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timeunde

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timeunde

form

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these are not instances

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timeunde

form

ed

d

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WINDOWS ON REALITY

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timeunde

form

ed

d

efor

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SYMBIOSIS OF KNOWLEDGE ABOUT UNIVERSALS AND INSTANCES

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timeunde

form

ed

d

efor

med

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timeunde

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d

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hum

an c

him

panz

ee m

ouse

fly

ye

ast

bact

eria

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timeunde

form

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d

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hum

an c

him

panz

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ouse

fly

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A Proposed Standardization

relations

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A Proposed Standardization

OBO Relations Ontology

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A Proposed Standardization

OBO Relations Ontologyis part ofis member of (a collection)is location of -- is contained in …is connected to

is later than – is simultaneous with …is bearer ofis function ofcausesis functioning of