Shahriyar Hossain, Munirul Islam, Jesmin, Hasan M Jamil

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PhyQL A Phylogenetic Visual Query Engine

• Shahriyar Hossain?, Munirul Islam?, Jesmin?,
  Hasan M Jamil?
• Integration Informatics Laboratory, Computer
  Science, Wayne State University?
• Department of Genetic Engineering and
  Biotechnology, University of Dhaka, Bangladesh?
• BIBM 2008

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What is a Phylogenetic Tree?
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Queries

• Least Common Ancestor

ltrootgt ltnodegtrayfinned fishlt/nodegt
ltinodegt ltnodegtlungfishlt/nodegt
ltinodegt ltinodegt
ltnodegtsalamanderslt/nodegt
ltnodegtfrogslt/nodegt lt/inodegt
. .
. lt/inodegt lt/inodegt lt/rootgt
for root in doc(tree.xml")//root return
ltspangt lth1gt root/node/text()
lt/h1gt lt/spangt
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Phylogenetic Query Language

• Select select a subset of trees that match a
  given criteria
• Join Join two trees based on a pair of nodes
• Subset Subset queries retrieve part of a given
  tree

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Tree Join
Using Path Operators
SubTree Projection
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PhyQL
Visual Query Interface
SELECT
JOIN
User
SUBTREE
Translator
DB
XML /NEXUS From User / Interoperable Databases
Wrappers
XSB
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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 doesnt
  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).

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lttree author"stern"gt ltnode type"gt
ltnode type?"gt ltnodegt
Stanhopea_gibbosa lt/nodegt ltnodegt
Stanhopea_vasquezii lt/nodegt lt/nodegt
ltnodegt Stanhopea_shuttleworthii lt/nodegt
lt/nodegt lt/treegt
node(Y1, Stanhopea_shuttleworthii), node(Y2,
Stanhopea_gibbosa), node(Y3, Stanhopea_vasquezi
i), edge(Y4,Y2), edge(Y4,Y3), lca(Y0,Y4,Y1), edge(
Y0,Y1)
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Integration Informatics Research Group
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Summary

• PhyQL offers a simple web-based visual query
  interface
• Logic based tree query operations
• Modifications to query tools only requires change
  in logic rules
• Proposed 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 set
• Tree Similarity Estimation

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Thank You!
me http//homopan.wayne.edu/PhD Students/Munirul
Islam/index.htm
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Uses of Phylogenetic Trees

• date events of divergence of species
• what is the most common ancestor of all living
  species?
• identify geographic origins of new disease
  outbreaks

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• Crimson
• Uses nested subtrees to avoid long strings
• Zheng, 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.

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Dewey system
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Find clade for Z (ltCSDs)
Find common pattern starting from left
SELECT FROM nodes WHERE (path LIKE 0.2.1)
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Depth-first traversal scoring each node with a
left and right ID
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Minimum Spanning Clade of Node 5
SELECT FROM nodes INNER JOIN nodes AS
include ON (nodes.left_id BETWEEN include.left_id
AND include.right_id) WHERE include.node_id 5