1. INDUS: A System for Information Integration and Knowledge Acquisition from Autonomous, Distributed and Semantically Heterogeneous Data Sources Jie Bao, Doina Caragea, Jyotishman Pathak, Adrian Silvescu, Carson Andorf, Changhui Yan, Drena Dobbs and Vasant Honavar June 28, 2005

4. Ontology-based information integration in INDUS

5. Semantically Heterogeneous Data Sources D 1 D 2 Aspartyl/asparaginyl beta-hydroxylase Beta-adrenergic receptor kinase 2 Protein Name 1.14.11.16 Peptide-aspartate beta-dioxygenase TPR TPR_REGION TPR MAQRKNAKSS GNSSSSGSGS … Q12797 2.7.1.126 Beta-adrenergic receptor kinase RGS PROT_KIN_DOM PH_DOMAIN MADLEAVLAD VSYLMAMEKS … P35626 EC Number Prosite Motifs Protein Sequence Protein ID RIIa HSP70 Pfam Domains 415 692 Length BCY1 SSE1 Gene 16.19.01 cyclic nucleotide binding (cAMP, cGMP, etc.) VSSLPKESQA ELQLFQNEIN … P07278 16.01 protein binding STPFGLDLGN NNSVLAVARN … P32589 MIPS Funcat AA Sequence Accession Number AN

13. Semantically Heterogeneous Data Data sources need to be made self-describing by specifying the relevant meta data D 1 D 2 Aspartyl/asparaginyl beta-hydroxylase Beta-adrenergic receptor kinase 2 Protein Name 1.14.11.16 Peptide-aspartate beta-dioxygenase TPR TPR_REGION TPR MAQRKNAKSS GNSSSSGSGS … Q12797 2.7.1.126 Beta-adrenergic receptor kinase RGS PROT_KIN_DOM PH_DOMAIN MADLEAVLAD VSYLMAMEKS … P35626 EC Number Prosite Motifs Protein Sequence Protein ID RIIa HSP70 Pfam Domains 415 692 Length BCY1 SSE1 Gene 16.19.01 cyclic nucleotide binding (cAMP, cGMP, etc.) VSSLPKESQA ELQLFQNEIN … P07278 16.01 protein binding STPFGLDLGN NNSVLAVARN … P32589 MIPS Funcat AA Sequence Accession Number AN

15. Attribute value hierarchy An attribute value hierarchy (AVH) is a partial order ontology over the values of attributes of data Example: MIPS Funcat Hierarchy

16. Making data sources self-describing - Ontology-extended data source Data Schema Ontology + + MIPS Funcat: MIPS Hierarchy Prosite Motifs: Motifs Length: Positive Integer Gene: Gene ID Accession Number: MIPS ID RIIa HSP70 415 692 BCY1 SSE1 16.19.01 cyclic nucleotide binding (cAMP, cGMP.) VSSLPKESQA ELQLFQNEIN P07278 16.01 protein binding STPFGLDLGN NNSVLAVARN P32589

17. INDUS: Ontology Editor

18. INDUS: Schema Editor

19. INDUS: Data Editor

22. Mappings at schema level Protein ID: Swissprot ID Protein Name: String Protein Sequence: AA String Prosite Motifs: AA String EC Number: EC Hierarchy Accession No AN: MIPS ID Gene: Gene ID AA Sequence: AA String Length: Pos Integer MIPS Funcat: MIPS Hierarchy Pfam Motifs: Motifs D 1 D 2 PID: Swissprot ID Protein: AA String GO Function: GO Hierarchy D U Source: Species String

23. Mappings at schema level Protein ID : D 1 ≡ PID : D U Accession Number AN : D 2 ≡ PID : D U Protein ID: Swissprot ID Protein Name: String Protein Sequence: AA String Prosite Motifs: AA String EC Number: EC Hierarchy Accession No AN: MIPS ID Gene: Gene Set AA Sequence: AA String Length: Pos Integer MIPS Funcat: MIPS Hierarchy Pfam Motifs: Motifs D 1 D 2 PID: Swissprot ID Protein: AA String GO Function: GO Hierarchy D U Source: Species String

24. Mappings at schema level Protein ID : D 1 ≡ PID : D U Accession Number AN : D 2 ≡ PID : D U Protein Sequence : D 1 ≡ AA Composition : D U AA Sequence : D 2 ≡ AA Composition : D U Protein ID: Swissprot ID Protein Name: String Protein Sequence: AA String Prosite Motifs: AA String EC Number: EC Hierarchy Accession No AN: MIPS ID Gene: Gene ID AA Sequence: AA String Length: Pos Integer MIPS Funcat: MIPS Hierarchy Pfam Motifs: Motifs D 1 D 2 PID: Swissprot ID Protein: AA String GO Function: GO Hierarchy D U Source: Species String

25. Mappings at schema level Protein ID : D 1 ≡ PID : D U Accession Number AN : D 2 ≡ PID : D U Protein Sequence : D 1 ≡ AA Composition : D U AA Sequence : D 2 ≡ AA Composition : D U EC Number : D 1 ≡ GO Function : D U’ MIPS Funcat : D 2 ≡ GO Function : D U Protein ID: SwissProt ID Protein Name: String Protein Sequence: AA String Prosite Motifs: AA String EC Number: EC Hierarchy Accession No AN: MIPS ID Gene: Gene ID AA Sequence: AA String Length: Pos Integer MIPS Funcat: MIPS Hierarchy Pfam Motifs: Motifs D 1 D 2 PID: SwissProt ID Protein: AA String GO Function: GO Hierarchy D U Source: Species String

26. Mappings at ontology level D U D U D 1

27. Mappings at ontology level EC 2.7.1.126 : D 1 ≡ GO 0047696 : D U D U D 1

28. Mappings at ontology level D U EC 2.7.1 : D 1  GO 00047696 : D U D 1

29. Mappings at ontology level D 1 EC 2.7.1.126 : D 1  GO 0004672 : D U D U

30. INDUS: View Editor

31. INDUS: Mapping Editor

33. Query processing in Indus Query Formulation

34. INDUS: Query Editor

38. Summary

44. http://www.cs.iastate.edu/~dcaragea/indus.html