6/15/20151 Relational Taxonomy Tree and BioDataBase by Huhn-Kie Lee.

04/18/23 1

Relational Taxonomy Treeand

BioDataBase

by Huhn-Kie Lee

04/18/23 2

Part I.

Relational Taxonomy Tree

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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

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•

Carnivore herbivore

animal

Dalmatian

catsdogs

Chihuahua Russian cat Italian cat

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•

Carnivore (prey, hunting method) Herbivore (feeding plant, chewing method)

animal

Dalmatian

catsdogs


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•

Carnivore Herbivore

animal

Dalmatian

Cats (meowing sound, whiskers size)Dogs (barking sound, snout size)


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•

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

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•

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

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• 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”

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• 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

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Multiple Inheritance from same-level parents


animal

bear

Black bear Grizzly bear

Omnivore(prey, hunt, plant, chew)

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Multiple Inheritance from diff-level parents


animal

Cats(meowing sound, whiskers size)dogs

Pseudo-cat(meow,whisker,plant,chew)

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Multi-Inherit Rules

AB CD

MNAdd a taxon whose attribute set is MNABCD

AB CD

MN

ABCD

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Multi-Inherit Rules

AB CD

MNAdd a taxon whose attribute set is MNCDEF

AB CD

MN

EF

EF

EF

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Multi-Inherit Rules

AB CD

MNAdd a taxon whose attribute set is MNBC

AB CD

MN

BC

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Multi-Inherit Rules

AB CD

MNAdd a taxon whose attribute set is KL

AB CD

MN KL

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Multi-Inherit Rules

AB CD

MNAdd a taxon whose attribute set is MK

AB CD

N K

M

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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

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Terminal Relation

karyote

virus

Genorg

Multi-cellular

eukaryote

mono-cellular

speciesID size

AIDS virus 10 nm

human 1.7 m

… …

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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.

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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

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Part II.

BioDataBase

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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

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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

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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

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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

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BioDataBase (BDB)• Environment:

– Want to store environmental factors that affect living organisms

locationID humidity temperature

Israel low 85

Jordan low 80

China high 35

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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)”

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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 )

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Part III.

Conclusion & cs632 Project

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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.

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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

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So what do you say?

6/15/20151 Relational Taxonomy Tree and BioDataBase by Huhn-Kie Lee.

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