Ontology of aging and death
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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).
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Ontology of aging and death
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- 16. death boundary_of life of organism every instance of death boundary_of life of some organism ? every life of an organism has_boundary some death 16 Metabolism Death Life and afterlife of organism Regions of Time Abiotic chemistry
- 17. aging part_of life of organism every instance of aging part_of life of some organism NOT: every instance of life of organism has_part aging 17 because a life may be cut short by early death Thus also NOT: death boundary_of process of aging death may not follow any process of aging NOT: aging has_boundary death premature aging may be followed by a period of rejuvenation
- 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
- 23. canonically (normally) human beings have 32 teeth • This is part of the Bauplan of human beings canonically (normally) death is the terminal boundary of a process of aging • This is part of the life plan of human beings 23
- 25. 25 The Gene Ontology represents what is normal in the realms of • cellular components • molecular functions • biological processes = roughly, what pertains to ‘wild type’, as opposed to experimentally modified, organisms = what happens when genes, proteins function normally in the development of an organism
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- 34. GO:0043473 pigmentation Definition: The deposition or aggregation of coloring matter in an organism, tissue or cell. 34
- 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
- 40. whole plant development stage PO:0007033 gametophyte development stage PO:0028003 sporophyte development stage PO:0028002 life of whole plant PO:0025337 plant spore stage PO:0025375 gametophyte vegetative stage PO:0025340 gametophyte dormant stage PO:0025342 gametophyte reproductive stage PO:0025341 gametophyte senescent stage PO:0025343 sporophyte senescent stage PO:0007017 sporophyte dormant stage PO:0007132 sporophyte reproductive stage PO:0007130 sporophyte vegetative stage PO:0007134 plant zygote stage PO:0028002 PP is_a part_ of 40 Plant Stage Ontology (principal whole plant development stages)
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- 42. Life cycle of Selaginella apoda (Felsen Moosfarn) 42 http://www.youtube.com/watch?v=BTXkh34BmZs
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- 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
- 49. Vascular plant life cycle 49
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- 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
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- 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)