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BioKleisli: A Digital Library for Biomedical Researchers
, 1996
"... Data of interest to biomedical researchers associated with the Human Genome Project (HGP) is stored all over the world in a number of different electronic data formats and accessible through a varietyof interfaces and retrieval languages. These data sources include conventional relational databases ..."
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Data of interest to biomedical researchers associated with the Human Genome Project (HGP) is stored all over the world in a number of different electronic data formats and accessible through a varietyof interfaces and retrieval languages. These data sources include conventional relational databases with SQL interfaces, formatted text files on top of which indexing is provided for efficient retrieval (ASN.1Entrez), and binary files that can be interpreted textually or graphically via special purpose interfaces (ACeDB). Researchers within the HGP wanttocombine data from these different data sources, add value through sophisticated data analysis techniques (such as the biosequence comparison software BLAST and FASTA), and view it using special purpose scientific visualization tools. However, currently there are no commercial tools for enabling such an integrated digital library, and a fundamental barrier to developing such tools appears to be one of language design and optimization: The data f...
Toward Routine Automatic Pathway Discovery from Online Scientific Text Abstracts
 Genome Informatics
, 1999
"... s SeeKiong Ng 1 Marie Wong 2 skng@krdl.org.sg marie@bic.nus.edu.sg 1 Kent Ridge Digital Labs, 21 Heng Mui Keng Terrace, Singapore 119613 2 NUS Bioinformatics Centre, National University of Singapore, Singapore 119260 Abstract We are entering a new era of research where the latest scienti ..."
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s SeeKiong Ng 1 Marie Wong 2 skng@krdl.org.sg marie@bic.nus.edu.sg 1 Kent Ridge Digital Labs, 21 Heng Mui Keng Terrace, Singapore 119613 2 NUS Bioinformatics Centre, National University of Singapore, Singapore 119260 Abstract We are entering a new era of research where the latest scientific discoveries are often first reported online and are readily accessible by scientists worldwide. This rapid electronic dissemination of research breakthroughs has greatly accelerated the current pace in genomics and proteomics research. The race to the discovery of a gene or a drug has now become increasingly dependent on how quickly a scientist can scan through voluminous amount of information available online to construct the relevant picture (such as proteinprotein interaction pathways) as it takes shape amongst the rapidly expanding pool of globally accessible biological data (e.g. GENBANK) and scientific literature (e.g. MEDLINE). We describe a prototype system for automatic...
On the Complexity of Nonrecursive XQuery and Functional Query Languages on Complex Values
 In Proc. PODS’05
"... This article studies the complexity of evaluating functional query languages for complex values such as monad algebra and the recursionfree fragment of XQuery. We show that monad algebra with equality restricted to atomic values is complete for the class TA[2O(n) , O(n)] of problems solvable in lin ..."
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This article studies the complexity of evaluating functional query languages for complex values such as monad algebra and the recursionfree fragment of XQuery. We show that monad algebra with equality restricted to atomic values is complete for the class TA[2O(n) , O(n)] of problems solvable in linear exponential time with a linear number of alternations. The monotone fragment of monad algebra with atomic value equality but without negation is complete for nondeterministic exponential time. For monad algebra with deep equality, we establish TA[2O(n) , O(n)] lower and exponentialspace upper bounds. We also study a fragment of XQuery, Core XQuery, that seems to incorporate all the features of a query language on complex values that are traditionally deemed essential. A close connection between monad algebra on lists and Core XQuery (with “child ” as the only axis) is exhibited, and it is shown that these languages are expressively equivalent up to representation issues. We show that Core XQuery is just as hard as monad algebra w.r.t. query and combined complexity, and that it is in TC0 if the query is assumed fixed. As Core XQuery is NEXPTIMEhard, it is commonly believed that any algorithm for evaluating Core XQuery has to require exponential amounts of working memory and doubly exponential time in the worst case. We present a property of queries – the lack of a certain form of composition – that virtually all realworld XQueries have and that allows for query evaluation in singly exponential time and polynomial space. Still, we are able to show for an important special case – Core XQuery with equality testing restricted to atomic values – that the compositionfree language is just as expressive as the language with composition. Thus, under widelyheld complexitytheoretic assumptions, the compositionfree language is an exponentially less succinct version of the language with composition.
Provenance as dependency analysis
 Proceedings of the 11th International Symposium on Database Programming Languages (DBPL 2007), number 4797 in LNCS
, 2007
"... Abstract. Provenance is information recording the source, derivation, or history of some information. Provenance tracking has been studied in a variety of settings; however, although many design points have been explored, the mathematical or semantic foundations of data provenance have received comp ..."
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Cited by 42 (16 self)
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Abstract. Provenance is information recording the source, derivation, or history of some information. Provenance tracking has been studied in a variety of settings; however, although many design points have been explored, the mathematical or semantic foundations of data provenance have received comparatively little attention. In this paper, we argue that dependency analysis techniques familiar from program analysis and program slicing provide a formal foundation for forms of provenance that are intended to show how (part of) the output of a query depends on (parts of) its input. We introduce a semantic characterization of such dependency provenance, show that this form of provenance is not computable, and provide dynamic and static approximation techniques. 1
Incremental Recomputation of Recursive Queries with Nested Sets and Aggregate Functions
, 1997
"... We examine the power of incremental evaluation systems that use an SQLlike language for maintaining recursivelydefined views. We show that recursive queries such as transitive closure, and "alternating paths" can be incrementally maintained in a nested relational language, when some a ..."
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We examine the power of incremental evaluation systems that use an SQLlike language for maintaining recursivelydefined views. We show that recursive queries such as transitive closure, and "alternating paths" can be incrementally maintained in a nested relational language, when some auxiliary relations are allowed. In the presence of aggregate functions, even more queries can be maintained, for example, the "same generation" query. In contrast, it is still an open problem whether such queries are maintainable in relational calculus. We then restrict the language so that no nested relations are involved (but wekeep the aggregate functions). Such a language captures the capability of most practical relational database systems. We prove that this restriction does not reduce the incremental computational power; that is, any query that can be maintained in a nested language with aggregates, is still maintainable using only flat relations. We also show that one does not need auxiliar...
Expressive Power of SQL
, 2001
"... It is a folk result in database theory that SQL cannot express recursive queries such as reachability; in fact, a new construct was added to SQL3 to overcome this limitation. However, the evidence for this claim is usually given in the form of a reference to a proof that relational algebra cannot ex ..."
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Cited by 16 (0 self)
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It is a folk result in database theory that SQL cannot express recursive queries such as reachability; in fact, a new construct was added to SQL3 to overcome this limitation. However, the evidence for this claim is usually given in the form of a reference to a proof that relational algebra cannot express such queries. SQL, on the other hand, in all its implementations has three features that fundamentally distinguish it from relational algebra: namely, grouping, arithmetic operations, and aggregation.
Typed Query Languages for Databases Containing Queries
 INFORMATION SYSTEMS
, 1999
"... This paper introduces and studies the relational meta algebra, a statically typed extension of the relational algebra to allow for meta programming in databases. In this meta algebra one can manipulate database relations involving not only stored data values (as in classical relational databases) ..."
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Cited by 14 (5 self)
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This paper introduces and studies the relational meta algebra, a statically typed extension of the relational algebra to allow for meta programming in databases. In this meta algebra one can manipulate database relations involving not only stored data values (as in classical relational databases) but also stored relational algebra expressions. Topics discussed include modeling of advanced database applications involving "procedural data"; desirability as well as limitations of a strict typing discipline in this context; equivalence with a firstorder calculus; and global expressive power and nonredundancy of the proposed formalism.
Bioinformatics Adventures in Database Research
 In Proceedings of the International Conference on Database Theory (ICDT) (2002), no. 2572 in Lecture Notes in Computer Science
, 2003
"... Informatics has helped launch molecular biology into the genomic era. It appears certain that informatics will remain a major contributor to molecular biology in the postgenome era. We discuss here data integration and datamining in bioinformatics, as well as the role that database theory played ..."
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Informatics has helped launch molecular biology into the genomic era. It appears certain that informatics will remain a major contributor to molecular biology in the postgenome era. We discuss here data integration and datamining in bioinformatics, as well as the role that database theory played in these topics.
Simulation of the Nested Relational Algebra By the Flat Relational Algebra, With an Application to the Complexity of Evaluating Powerset Algebra Expressions
, 1999
"... Paredaens and Van Gucht proved that the flat relational algebra has the same expressive power as the nested relational algebra, as far as queries over flat relations and with flat results are concerned. We provide a new, very direct proof of this fact using a simulation technique. Our technique is a ..."
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Cited by 3 (1 self)
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Paredaens and Van Gucht proved that the flat relational algebra has the same expressive power as the nested relational algebra, as far as queries over flat relations and with flat results are concerned. We provide a new, very direct proof of this fact using a simulation technique. Our technique is also applied to partially answer a question posed by Suciu and Paredaens regarding the complexity of evaluating powerset algebra expressions. Specifically, we show that when only unary flat relations are into play, any powerset algebra expression is either equivalent to a nested algebra expression, or its evaluation will produce intermediate results of exponential size.