1. 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 11/24/2015 1 PhyQL: A Phylogenetic Visual Query Engine Integration Informatics Research Group

2. 11/24/2015 Integration Informatics Research Group 2 What is a Phylogenetic Tree?

3. 11/24/2015 Integration Informatics Research Group 3

4. Queries: Least Common Ancestor Thurs 03/20/2008 4 rayfinned fish lungfish salamanders frogs. for $root in doc(“tree.xml")//root return { $root/node/text() } Integration Informatics Research Group

5. 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 11/5/2008 5 Integration Informatics Research Group

6. 11/24/2015 6 Using Path Operators SubTree Projection Tree Join Integration Informatics Research Group

7. PhyQL: 11/24/2015 7 XSB DB Visual Query Interface User SELECT JOIN SUBTREE Translator XML /NEXUS From User / Interoperable Databases Wrappers Integration Informatics Research Group

8. 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. 11/5/2008 Integration Informatics Research Group 8 :- odbc_import(conn, 'tbl_treeinfo'(‘rootId', ‘author'), tree). :- odbc_import(conn, 'tbl_nodeinfo'('nodeId', 'nodename'), node). :- odbc_import(conn, 'tbl_edge'('parentId', 'childId'), edge).

9. 11/24/2015 9 Stanhopea_gibbosa Stanhopea_vasquezii Stanhopea_shuttleworthii 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) Integration Informatics Research Group

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11. 11/24/2015 11 Integration Informatics Research Group

12. 11/24/2015 Integration Informatics Research Group 12 Integration Informatics Research Group

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14. 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 11/24/2015 14

15. Thank You! 11/24/2015 15 Integration Informatics Research Group me: http://homopan.wayne.edu/PhD Students/Munirul Islam/index.htm http://homopan.wayne.edu/PhD Students/Munirul Islam/index.htm

16. Uses of Phylogenetic Trees: 1. date events of divergence of species 2. what is the most common ancestor of all living species? 3. identify geographic origins of new disease outbreaks 11/5/2008 Integration Informatics Research Group 16

17. 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.

18. ABCDE 0.1 0.1.10.1.2 0.2 0.2.1 0.2.1.10.2.1.20.2.2 0 Dewey system: Integration Informatics Research Group 18 11/5/2008

19. LabelPath Root0 NULL0.1 A0.1.1 B0.1.2 NULL0.2 NULL0.2.1 C0.2.1.1 D0.2.1.2 E0.2.2 ABCDE Find clade for: Z = (<C S +D s ) Find common pattern starting from left SELECT * FROM nodes WHERE (path LIKE “0.2.1%”); Integration Informatics Research Group 19 11/5/2008

20. ABCDE 2 35 8 9 10 1215 1 46 7 17 111316 18 14 Depth-first traversal scoring each node with a left and right ID Integration Informatics Research Group 20 11/5/2008

21. LabelLeftRight 118 27 A34 B56 817 914 C1011 D1213 E1516 ABCDE 2 35 8 9 101215 1 46 7 17 111316 18 14 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 ; Minimum Spanning Clade of Node 5 Integration Informatics Research Group 21 11/5/2008