6/15/20151 relational taxonomy tree and biodatabase by huhn-kie lee
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04/18/23 1
Relational Taxonomy Treeand
BioDataBase
by Huhn-Kie Lee
04/18/23 2
Part I.
Relational Taxonomy Tree
04/18/23 3
Relational Taxonomy Tree (RTT)
• Taxonomic hierachy– Kingdom, phylum, class, order, family, genus,
species
• Lower level inherits higher level’s property:– Properties may be stored “redundantly”
• Siblings differ by some properties:– Properties are “disparate,” so we need different
relation schemes
04/18/23 4
Relational Taxonomy Tree (RTT)
•
Carnivore herbivore
animal
Dalmatian
catsdogs
Chihuahua Russian cat Italian cat
04/18/23 5
Relational Taxonomy Tree (RTT)
•
Carnivore (prey, hunting method) Herbivore (feeding plant, chewing method)
animal
Dalmatian
catsdogs
Chihuahua Russian cat Italian cat
04/18/23 6
Relational Taxonomy Tree (RTT)
•
Carnivore Herbivore
animal
Dalmatian
Cats (meowing sound, whiskers size)Dogs (barking sound, snout size)
Chihuahua Russian cat Italian cat
04/18/23 7
Relational Taxonomy Tree (RTT)
•
Carnivore Herbivore
animal
Cats (meowing sound, whiskers size)Dogs (barking sound, snout size)
speciesID bark snout
Dalmatian Bow-bow 3 cm
Chihuahua Wow-wow 1 cm
speciesID meow whisker
Russian cat yao 2 cm
Italian cat mao 1 cm
04/18/23 8
Relational Taxonomy Tree (RTT)
•
Carnivore (prey, preying method) Herbivore
animal
speciesID prey hunting method
Dalmatian Ground hog Dig out its hole
Chihuahua rats Bark-and-chase
Russian cat rats Hide-and-attack
Italian cat squrrels Jump-and-chase
04/18/23 9
Relational Taxonomy Tree (RTT)
• Vertical query:– join a relation with its ancestor relation – “Find hunting method of a dog which barks
“bow-bow” “ (See relations in slide 6, 5)• SELECT Carn.hunting_method
FROM Dogs D, Carnivore Carn
WHERE D.speciesID = Carn.speciesID AND
D.barking_sound = “bow-bow”
04/18/23 10
Relational Taxonomy Tree (RTT)
• Horizontal query:– join any two relations (may not in same level) – “Find (barking sound, meowing sound) pair of
dogs and cats which prey on the same animal (See relations in slide 6, 5)• SELECT D.barking_sound, C.meowing_sound
FROM Dogs D, Carnivore Carn1,Carn2, Cats C
WHERE D.speciesID = Carn1.speciesID AND
C.speciesID = Carn2.speciesID AND
Carn1.prey = Carn2.prey
04/18/23 11
Multiple Inheritance from same-level parents
Carnivore (prey, hunting method) Herbivore (feeding plant, chewing method)
animal
bear
Black bear Grizzly bear
Omnivore(prey, hunt, plant, chew)
04/18/23 12
Multiple Inheritance from diff-level parents
Carnivore (prey, hunting method) Herbivore (feeding plant, chewing method)
animal
Cats(meowing sound, whiskers size)dogs
Pseudo-cat(meow,whisker,plant,chew)
04/18/23 13
Multi-Inherit Rules
AB CD
MNAdd a taxon whose attribute set is MNABCD
AB CD
MN
ABCD
04/18/23 14
Multi-Inherit Rules
AB CD
MNAdd a taxon whose attribute set is MNCDEF
AB CD
MN
EF
EF
EF
04/18/23 15
Multi-Inherit Rules
AB CD
MNAdd a taxon whose attribute set is MNBC
AB CD
MN
BC
04/18/23 16
Multi-Inherit Rules
AB CD
MNAdd a taxon whose attribute set is KL
AB CD
MN KL
04/18/23 17
Multi-Inherit Rules
AB CD
MNAdd a taxon whose attribute set is MK
AB CD
N K
M
04/18/23 18
RTT is skewed
karyote virus
Genorg
Multi-cellular
prokaryoteeukaryote
Gram+bact1,2…
bacteria archaea
Virus1, virus2….
Gram+ bact gram - bact
Archaea1,archaea2…
Gram-bact1,2…
mono-cellular
04/18/23 19
Terminal Relation
karyote
virus
Genorg
Multi-cellular
eukaryote
mono-cellular
speciesID size
AIDS virus 10 nm
human 1.7 m
… …
04/18/23 20
Non-terminal Relation
karyote
virus
Genorg
Multi-cellular
eukaryote
mono-cellular
Sub-taxon Ave. size
virus 10 nm
Karyote 1 m
-Save general trend in
each subtaxon.
04/18/23 21
Non-terminal Relation
animal plant
Sexual eukaryoteSub-taxon How to mate
animal Search-for
plant Via carrier
-Save common values of each subtaxon.
-Terminal relation would be redundant.
Asexual eukaryote
eukaryote
04/18/23 22
Part II.
BioDataBase
04/18/23 23
BioDataBase (BDB)• Want to store all the information about all
the living organisms on the planet– Too many data!– Solution: partition database into “Domains”– Each domain has its own database that stores
relevant biological infomation
• Want to find correlation between different domains’ information
04/18/23 24
BioDataBase (BDB)• Consider 3 domains and their relevant info:
– Genomics: genes of each species
– Ecology: population distribution of species
– Environment: a location’s humidity, temperature
04/18/23 25
BioDataBase (BDB)• Genomics:
– Species/gene is
many-to-many relation– Hence,
(species, gene) relation
lion
zebra geneB
geneA
geneC
speciesID geneID
lion geneA
lion geneB
zebra geneA
04/18/23 26
BioDataBase (BDB)• Ecology:
– Want to store species_A lives in location_B and the number of them is population_C
– PRIMARY KEY: (speciesID, locationID)
speciesID locationID population
lion Israel 3000
zebra Jordan 20000
tiger China 900
04/18/23 27
BioDataBase (BDB)• Environment:
– Want to store environmental factors that affect living organisms
locationID humidity temperature
Israel low 85
Jordan low 80
China high 35
04/18/23 28
BioDataBase (BDB)• Want to answer a query that spans all 3
domains: – simply join relations from 3 domains!– “Find genes that are common to (genomics)
all species that live in the area (ecology)
where humidity is low (environment)”
04/18/23 29
BioDataBase (BDB)• “Find genes that are common to all species that live in the
area where the humidity is low“ (see relations in 14,15,16)
(SELECT G.geneID, G.speciesID
FROM Genomic G, Ecology Eco, Environment Env
WHERE G.speciesID = Eco.speciesID AND
Eco.location = Env.location AND
Env.humidity = low )
DIVIDE
(SELECT Eco.speciesID
FROM Ecology Eco, Environment Env
WHERE Eco.location = Env.location AND
Env.humidity = low )
04/18/23 30
Part III.
Conclusion & cs632 Project
04/18/23 31
Conclusion• Relational Taxonomy Tree solves
– Redundancy problem: • diff. species have common attributes.
– Disparity problem: • diff. species have diff. attributes
• RTT and BDB can serve as the prototype for the infrastructure of the Library of Life Project.
04/18/23 32
Tentative Project Suggestion• There are four of us:
– Helgi, Yoni, Shobhi, mi.
• Two of us work on implementation of
mini-Relational Taxonomy Tree
• The other two of us work implement
mini-BioDataBase
• All of us implement a program that can process SQL queries on RTT & BDB
04/18/23 33
So what do you say?