1 ANATOMY AND TIME Barry Smith
Dec 30, 2015
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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
form
ed
d
efor
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timeunde
form
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efor
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these are not instances
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timeunde
form
ed
d
efor
med
WINDOWS ON REALITY
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timeunde
form
ed
d
efor
med
SYMBIOSIS OF KNOWLEDGE ABOUT UNIVERSALS AND INSTANCES
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timeunde
form
ed
d
efor
med
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timeunde
form
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d
efor
med
hum
an c
him
panz
ee m
ouse
fly
ye
ast
bact
eria
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timeunde
form
ed
d
efor
med
hum
an c
him
panz
ee m
ouse
fly
ye
ast
bact
eria
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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