The idea underlying biomedical ontology is that, if common terms are used to annotate or tag heterogeneous data collected by scientists working in different disciplines, then these data will be more easily reused for integration and
analysis. To this end, the terms in ontologies need to be carefully defined. Smith examines definitions
of terms central to ageing research in this light, focusing on the Gene Ontology (GO), the Foundational Model of Anatomy Ontology (FMA) and the Plant Ontology (PO).
20. • How to distinguish age-related causes (aging
processes) from other causes of death?
• Roughly: age-related causes = processes
normally part of the normal aging process
• What does ‘normally’ mean?
20
21. 21
has 83281 types and 3 million relations
representing canonical adult human anatomy
= the Bauplan generated by the coordinated
expression of the organism’s own structural
genes.
Canonical anatomy contrasted with variant anatomy
and with instantiated anatomy
Canonical ≠ statistically normal
Foundational Model of Anatomy Ontology
22. Foundational Model of Anatomy (FMA)
Pleural
Cavity
Interlobar
recess
Mesothelium
of Pleura
Pleura(Wall
of Sac)
Visceral
Pleura
Pleural Sac
Parietal
Pleura
Anatomical Space
Organ
Cavity
Serous Sac
Cavity
Anatomical
Structure
Organ
Serous Sac
Mediastinal
Pleura
Tissue
Organ Part
Organ
Subdivision
Organ
Component
Organ Cavity
Subdivision
Serous Sac
Cavity
Subdivision
22
39. In the life cycle of plants we have alternating generations:
gametophyte = whole plant in haploid stage; male and
female gametes fuse to produce the zygote from which the
sporophyte arises
sporophyte = whole plant in diploid stage (the dominant form
in vascular plants such as ferns); produces spores from
which the gametophyte arises.
whole plant
development stage
PO:0007033
gametophyte
development stage
PO:0028003
sporophyte
development stage
PO:0028002
life of whole plant
PO:0025337
PP
39
47. GO:0010259: multicellular
organismal aging
Definition: An aging process
that has as participant a whole
multicellular organism.
Multicellular organism aging
includes loss of functions such
as resistance to disease,
homeostasis, and fertility, as well
as wear and tear. Multicellular
organisms aging includes
processes like cellular
senescence and organ
senescence, but is more
inclusive.
47
48. GO:0007568: aging
Definition: A developmental process that is a deterioration
and loss of function over time. Aging includes loss of
functions such as resistance to disease, homeostasis, and
fertility, as well as wear and tear. Aging includes cellular
senescence, but is more inclusive. May precede death
(GO:0016265) and may succeed developmental maturation
(GO:0021700).
48
GO requires a term for
developmental aging
53. 53
honour of Dr. Leonard Hayflick, co-author
with Paul Moorhead, of the first paper
describing it in 1961. Cells can also be
induced to senesce by certain toxins,
irradiation, or the activation of certain
oncogenes. In response to DNA damage
(including shortened telomeres), cells
either age or self-destruct (apoptosis,
programmed cell death) if the damage
cannot be easily repaired. In this 'cellular
suicide', the death of one cell, or more,
may benefit the organism as a whole. For
example, in plants the death of the water-
conducting xylem cells (tracheids and
vessel elements) allows the cells to
function more efficiently and so deliver
water to the upper parts of a plant. The
ones that do not self-destruct remain until
destroyed by outside forces. Though they
no longer replicate, senescent cells remain
metabolically active and generally adopt
phenotypes including flattened cell
morphology, altered gene expression and
secretion profiles (known as the
senescence-associated secretory
phenotype) and positive senescence
54. 54
The End: Senescence and Cell
Death (With Yuan Zhong and Jared
Taylor) - Plants, like animals, employ cell
death as a normal and necessary part of
life. Cell death occurs during
developmental processes, including
embryo and leaf development, vascular
tissue development, and various
reproductive processes. Pathogen
infection can initiate the hypersensitive
response which can include a rapid cell
58. 58
age-dependent behavioral decline
GO:0035982
synonym (exact): behavioral aging
Definition:
A developmental process that arises as an
organism progresses toward the end of its
lifespan that results in a decline in behavioral
activities such as locomotory behavior, and
learning or memory.
61. Acknowledgements
61
Gene Ontology (GO)
Jane Lomax (EBI)
Chris Mungall (Berkeley)
iPlant
Ramona Walls (University of Arizona)
Plant Ontology (PO)
Pankaj Jaswal, Laurel Cooper, Justin Elser
(Oregon State University)
Dennis W. Stevenson, Ciaran Maloney
(New York Botanical Gardens)
Ontology for General Medical Sciences (OGMS)
Werner Ceusters (Buffalo)
Lindsay Cowell (Texas)
Albert Goldfain (Syracuse)
Alan Ruttenberg (Buffalo)
Richard Scheuermann (J. Craig Venter Institute)