Exploitation of Structural Similarity in Semi-Structured Bioinformatics Data for Efficient Storage Construction Dongkyoo Shin Sejong University, InCob2007

Multimedia & Internet Laboratory, Sejong University2/20 Table of contents Abstract Background Methods Results Conclusions

Multimedia & Internet Laboratory, Sejong University3/20 Abstract (1) Background –Many researches related to storing XML data Reduce the number of joins between tables Not proper to microarray data with distinctive hierarchy –Hierarchical feature of microarray data model a few core values occurs iteratively –New approach for capturing the feature Class elements with similar structure into a group Design common database table for the group

Multimedia & Internet Laboratory, Sejong University4/20 Abstract (2) Results –Database schema created by our approach Reduce the number of table joins remarkably Improve performance of storing and loading XML-based microarray data Conclusions –Efficient way to improve performance of microarray data is mining structural similarity of elements

Multimedia & Internet Laboratory, Sejong University5/20 Background (1) DTD (Data Type Definition)-dependent base –Map one element into one table For each e  E, #(S) ≥1 OR #(A) ≥1 -> define_Class(e) For each Se  S -> Add_attributes_of_Class(e) Se  SequenceType -> Define_multivalued_att(Se, e)

Multimedia & Internet Laboratory, Sejong University6/20 Background (2) Inline technique base –Reduce the complexity of DTD (Data Type Definition) For each e, #(S) == 1 AND Se  SequenceType -> Add_Multi-valued_attribute_of_Paren-tClass(e)

Multimedia & Internet Laboratory, Sejong University7/20 Background (3) Drawback of previous approaches –DTD-dependent Database schema has the same complexity with DTD –Inline technique Strongly depend on the number of omissible elements New design approach for microarray database –Capture similar structural features of microarray data –Need fast and simple way to mine the structural features

Multimedia & Internet Laboratory, Sejong University8/20 Background (5) Microarray data and MAGE (Microarray Gene Expression) standards –Research groups share microarray data with others, and use it to solve their biological questions –MGED society’s standard definitions MIAME (Minimum Information for the Annotation of a Microarray Experiment) MAGE-OM and MAGE-ML –Exchange object model and format for MIAME –Structural feature of MAGE-OM a variety set of objects defining the same data types including complex types.

Multimedia & Internet Laboratory, Sejong University9/20 Background (6) Decision Tree –a simple model for easy understanding classification rules correlations, and effects between variables –Proper for mining structural features of MAGE-ML DTD itself (Not MAGE-ML instances !!!) Possible to classify all elements three levels: –A root, mediators group, and bottoms group

Multimedia & Internet Laboratory, Sejong University10/20 Methods (1) Classification of core features using decision tree –Terminologies for expression of a complexType e: an element defined in XML schema E: an elements set of e SE: a sub-elements set of e a: an attribute of e A: an attributes set of e SA: an attributes set for all sub-elements of e complexType: Structural information that consists of SE and (or) A of e. Lowest child: an element without a sub-element Lowest parent: an element with a sub-element that is one of the lowest child elements PG (Parent Group): a set of candidate elements to be parents of a Lowest Child LPCG (The Lowest Parent Candidate Group): a set of candidates to be Lowest Parent LCG (The Lowest Child Group): a set of Lowest child elements LPG (The Lowest Parent Group): a set of Lowest Parent elements ULPG (Upper Level Parent Group): a set of upper level parents, including elements that are neither Lowest Child nor Lowest Parent

Multimedia & Internet Laboratory, Sejong University11/20 Methods (2) Expression of a complexType –A complexType defines structural information of elements A set of arrays including data type Definition of structural similarity SEelex = {e1, e2, …, en}, SAelex = {Ae1, Ae2, …, Aen} complexType(elex) = {SEelex, SAelex} complexType(elex) == complexType(eley)

Multimedia & Internet Laboratory, Sejong University12/20 Methods (3) Decision Tree for recognizing the core features –Condition 1: If rule 1 is satisfied, then e arrives at LCG. Otherwise, it arrives at PG. –Condition 2: If rule 2 is satisfied, then e and its similar element e arrive at a new LCG. –Condition 3: If rule 3 is satisfied, then e arrives at LPG. Otherwise, it arrives at ULPG. –Condition 4: If rule 4 is satisfied, then e and elements similar to e arrive at a new LPG.

Multimedia & Internet Laboratory, Sejong University13/20 Methods (4) Classification rules –Rule 1 Decide that an element should belong to group LCG or PG For each ei  E { if(number of elements in SEei == 0){ ei is classified into LCG; }else{ ei is classified into PG; }

Multimedia & Internet Laboratory, Sejong University14/20 Methods (5) Classification rules –Rule 2 Classify multiple sets of LCG p = 0; For each ei  LCG 0 { Flag=0; If (p>0) { For q=1 to p If (complexType(ei) = complexType(element in LCGq) { ei is classified into LCGq; Flag=1; } If (Flag==0) { For each ej  LCG 0 if(complexType(ei) = complexType(ej) { p=p+1; ei and ej are classified into a new group of LCGp; }

Multimedia & Internet Laboratory, Sejong University15/20 Methods (6) Classification rules –Rule 3 Separate elements in PG into two groups: LPG and ULPG For each ei  PG { if(SEei  LCG) { ei is classified into LPG; }else{ ei is classified into ULPG; }

Multimedia & Internet Laboratory, Sejong University16/20 Methods Classification rules –Rule 4 Classify multiple sets of LPG p = 0; For each ei  LPG 0 { Flag=0; If (p>0) { For q=1 to p If (complexType(ei) = complexType(element in LPGq) { ei is classified into LPGq; Flag=1; } If (Flag==0) { For each ej  LPG 0 if(complexType(ei) = complexType(ej) { p=p+1; ei and ej are classified into a new group of LPGp; }

Multimedia & Internet Laboratory, Sejong University17/20 Result (1) Database design by the proposed decision tree

Multimedia & Internet Laboratory, Sejong University18/20 Result (2) Database space complexity Time complexity Raw schemaClassified schema Total classes Total tables Total records Total DB size710 (Kb)27 (Kb)

Multimedia & Internet Laboratory, Sejong University19/20 Result (3) Reconstructing the XML Document

Multimedia & Internet Laboratory, Sejong University20/20 Conclusions Proposed approach –Mine elements with structural similarity from XML Schema for biological information –Experimental result Mining structural similarity of object model is proper to microarray data and more efficient than previous approaches Future work –Plan to extend current classification rules to root, LCG, LPG, ULPG respectively