Abstract
We investigate logic-based query languages for sequence databases, that is, databases in which strings of symbols over a fixed alphabet can occur. We discuss different approaches to querying strings, including Prolog and Datalog with function symbols, and argue that all of them have important limitations. We then present the semantics of Sequence Datalog, a logic for querying sequence databases, and show how this language can be used to perform structural recursion over sequences.
The first author was partially supported by an operating grant from the Natural Sciences and Engineering Research Council of Canada (NSERC). The second author was partially supported by MURST and Consiglio Nazionale delle Ricerche (CNR).
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References
S. Abiteboul, R. Hull, and V. Vianu. Foundations of databases. Addison Wesley Publ. Co., Reading, Massachussetts, 1994.
S. Abiteboul and V. Vianu. Datalog extensions for database queries and updates. Journal of Computing and System Sciences, 43(1):62–124, August 1991.
K. Apt and M. H. Van Emden. Contributions to the theory of logic programming. Journal of the ACM, 29(3):841–862, 1982.
M. Atkinson, F. Bancilhon, D. DeWitt, K. Dittrich, D. Maier, and Z. Zdonik. The object-oriented database manifesto. In First Intern. Conference on Deductive and Object Oriented Databases (DOOD'89), Kyoto, Japan, pages 40–57, 1989.
P. Atzeni, editor. LOGIDATA+: Deductive Databases with Complex Objects, Lecture Notes in Computer Science 701. Springer-Verlag, 1993.
A. J. Bonner. Hypothetical Datalog: complexity and expressibility. Theoretical Computer Science, 76:3–51, 1990.
V. Breazu-Tannen, P. Buneman, and S. Naqvi. Structural recursion as a query language. In Third Intern. Workshop on Database Programming Languages (DB-PL'91), pages 9–19, 1991.
V. Breazu-Tannen, P. Buneman, and L. Wong. Naturally embedded query languages. In Fourth International Conference on Data Base Theory, (ICDT'92), Lecture Notes in Computer Science, pages 140–154, 1992.
S. Ceri, G. Gottlob, and L. Tanca. Logic Programming and Data Bases. Springer-Verlag, 1989.
S. Ceri, G. Gottlob, and L. Tanca. What you always wanted to know about Datalog (and never dared to ask). IEEE Transactions on Knowledge and Data Engineering, 1(1):146–166, March 1989.
A. K. Chandra and D. Harel. Computable queries for relational databases. Journal of Computing and System Sciences, 21:333–347, 1980.
W. Clocksin and C. Mellish. Programming in Prolog. Springer-Verlag, 1981.
L. S. Colby, E. L. Robertson, L. V. Saxton, and D. Van Gucht. A query language for list-based complex objects. In Thirteenth ACM SIGMOD Intern. Symposium on Principles of Database Systems (PODS'94), pages 179–189, 1994.
Communications of the ACM. Special issue on the Human Genome project. vol. 34(11), November 1991.
S. Ginsburg and X. Wang. Pattern matching by RS-operations: towards a unified approach to querying sequence data. In Eleventh ACM SIGACT SIGMOD SIGART Symp. on Principles of Database Systems (PODS'92), pages 293–300, 1992.
G. H. Gonnet. Text dominated databases: Theory, practice and experience. Tutorial presented at PODS, 1994.
G. Grahne, M. Nykanen, and E. Ukkonen. Reasoning about strings in databases. In Thirteenth ACM SIGMOD Intern. Symposium on Principles of Database Systems (PODS'94), pages 303–312, 1994.
S. Grumbach and T. Milo. An algebra for POMSETS. In Fifth International Conference on Data Base Theory, (ICDT'95), Prague, Lecture Notes in Computer Science, pages 191–207, 1995.
J. W. Lloyd. Foundations of Logic Programming. Springer-Verlag, second edition, 1987.
G. Mecca and A. J. Bonner. Finite query languages for sequence databases. In Fifth Intern. Workshop on Database Programming Languages (DBPL '95), Gubbio, Italy, 1995.
G. Mecca and A. J. Bonner. Sequences, Datalog and Transducers. In Fourteenth ACM SIGMOD Intern. Symposium on Principles of Database Systems (PODS'95), San Jose, California, pages 23–35, 1995.
G. Mecca and A. J. Bonner. Sequences, Datalog and Negation. In preparation, 1996.
C. Papadimitriou. Computational Complexity. Addison-Wesley, 1994.
J. Richardson. Supporting lists in a data model (a timely approach). In Eighteenth International Conference on Very Large Data Bases (VLDB'92), Vancouver, Canada, pages 127–138, 1992.
D. B. Searls. String Variable Grammars: a logic grammar formalism for dna sequences. Technical report, University of Pennsylvania, School of Medicine, 1993.
D. Stott Parker, E. Simon, and P. Valduriez. SVP — a model capturing sets, streams and parallelism. In Eighteenth International Conference on Very Large Data Bases (VLDB'92), Vancouver, Canada, pages 115–126, 1992.
X. Wang. Pattern matching by RS-operations: Towards a unified approach to querying sequence data. PhD thesis, University of Southern California, 1992.
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Bonner, A., Mecca, G. (1996). Sequence Datalog: Declarative string manipulation in databases. In: Pedreschi, D., Zaniolo, C. (eds) Logic in Databases. LID 1996. Lecture Notes in Computer Science, vol 1154. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0031753
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DOI: https://doi.org/10.1007/BFb0031753
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