shahriyar hossain , munirul islam , jesmin , hasan m jamil integration informatics laboratory,...

Shahriyar Hossain, Munirul Islam, Jesmin, Hasan M JamilIntegration Informatics Laboratory, Computer Science, Wayne State University

Department of Genetic Engineering and Biotechnology, University of Dhaka, Bangladesh

BIBM 200804/21/231

PhyQL: A Phylogenetic Visual Query Engine

Integration Informatics Research Group

04/21/23Integration Informatics Research Group2

What is a Phylogenetic Tree?

Queries:Least Common

Ancestor

Thurs 03/20/20084

<root> <node>rayfinned fish</node> <inode> <node>lungfish</node> <inode> <inode> <node>salamanders</node> <node>frogs</node> </inode> . . . </inode> </inode></root>

for $root in doc(“tree.xml")//root return <span> <h1> { $root/node/text() } </h1> </span>Integration Informatics Research Group

Phylogenetic Query Language:

Select: select a subset of trees that match a given criteria

Join: Join two trees based on a pair of nodesSubset: Subset queries retrieve part of a given tree

11/5/20085 Integration Informatics Research Group

04/21/236

Using Path Operators

SubTree Projection

Tree Join


PhyQL:

04/21/237

XSB

DB

Visual Query Interface

User

SELECT

JOIN

SUBTREE

Translator

XML /NEXUSFrom User /

Interoperable

Databases

Wrappers


Why XSB?eliminates left recursion problem

Path(X,Z) :- Path(X,Y), Edge(Y,Z)Stores intermediate results (by tabling method)Model-based (order of writing rules doesn’t matter)

Path(X,Y) :- edge(X,Y)Path(X,Y) :- Path(X,Y), edge(Y,Z)

its in-memory database queries are an order of magnitude faster than methods such as tuProlog.


:- odbc_import(conn, 'tbl_treeinfo'(‘rootId', ‘author'), tree).:- odbc_import(conn, 'tbl_nodeinfo'('nodeId', 'nodename'), node).:- odbc_import(conn, 'tbl_edge'('parentId', 'childId'), edge).

04/21/239

<tree author="stern"> <node type=“*"> <node type=“?"> <node> Stanhopea_gibbosa </node> <node> Stanhopea_vasquezii </node> </node> <node> Stanhopea_shuttleworthii </node> </node></tree>

node(Y1, ‘Stanhopea_shuttleworthii’),node(Y2, ‘Stanhopea_gibbosa’),node(Y3, ‘Stanhopea_vasquezii),edge(Y4,Y2),edge(Y4,Y3),lca(Y0,Y4,Y1),edge(Y0,Y1)


04/21/23Integration Informatics Research Group12Integration Informatics Research Group

SummaryPhyQL offers a simple web-based visual query

interfaceLogic based tree query operationsModifications to query tools only requires change in

logic rulesProposed architecture can also applied to protein-

protein interaction networks, metabolic pathways etc.

Future Work:Database Interoperability – allow retrieving integrate

phylogenetic data during query submission ReQuery – query on the result setTree Similarity Estimation

04/21/2314

Thank You!


me: http://homopan.wayne.edu/PhD Students/Munirul Islam/index.htm

Uses of Phylogenetic Trees:1. date events of

divergence of species2. what is the most

common ancestor of all living species?

3. identify geographic origins of new disease outbreaks


CrimsonUses nested subtrees to avoid long stringsZheng, Y. S. Fisher, S. Cohen, S. Guo, J. Kim, and

S. B. Davidson. 2006. Crimson: A Data Management System to Support Evaluating Phylogenetic Tree Reconstruction Algorithms. 32nd International Conference on Very Large Data Bases, ACM, pp. 1231-1234.

A B C D E

0.1

0.1.1 0.1.2

0.2

0.2.1

0.2.1.1 0.2.1.2 0.2.2

0

Dewey system:

Integration Informatics Research Group18 11/5/2008

Label Path

Root 0

NULL 0.1

A 0.1.1

B 0.1.2

NULL 0.2

NULL 0.2.1

C 0.2.1.1

D 0.2.1.2

E 0.2.2

A B C D E

Find clade for: Z = (<CS+Ds)

Find common pattern starting from left

SELECT * FROM nodesWHERE (path LIKE “0.2.1%”);


A B C D E

2

3 5

8

9

10 12 15

1

4 6

7

17

11 13 16

18

14

Depth-first traversal scoring each node with a left and right ID


Label Left Right

1 18

2 7

A 3 4

B 5 6

8 17

9 14

C 10 11

D 12 13

E 15 16

A B C D E

2

3 5

8

9

10 12 15

1

4 6

7

17

11 13 16

18

14

SELECT * FROM nodesINNER JOIN nodes AS includeON (nodes.left_id BETWEEN include.left_id AND include.right_id)WHERE include.node_id = 5 ;

Minimum Spanning Clade of Node 5


shahriyar hossain , munirul islam , jesmin , hasan m jamil integration informatics laboratory,...

Documents

query submission requery

query tools

vasquezii stanhopea

gibbosa stanhopea

visual query interfacelogic

phylogenetic data

subset of trees

subset queries