Kyle Hart, Limsoon Wong, Chris Overton, and Peter Buneman. Using a query language to integrate biological data. In Abstracts of 1st Meeting on the Interconnection of Molecular Biology Databases, Stanford, August 1994. Available at http://www.cis.upenn.edu/cbil/mimbd94/mimbd94CPL.html.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....40 4 1 Introduction 1. 1 Introduction Kleisli is a system for querying heterogeneous data sources that are distributed over a wide area network and are not necessarily relational [5] It is being used to provide on demand integration of a number of databases in the Human Genome Project [13]. It is implemented in Concurrent ML [21] On top of Kleisli is a high level query language called CPL, for Collection Programming Language. Both CPL and much of the internal structure of Kleisli is based on the notion of monads [7, 6] In this report, the focus is on the optimizer of the ....

Kyle Hart, Limsoon Wong, Chris Overton, and Peter Buneman. Using a query language to integrate biological data. In Abstracts of 1st Meeting on the Interconnection of Molecular Biology Databases, Stanford, August 1994. Available at http://www.cis.upenn.edu/cbil/mimbd94/mimbd94CPL.html.

....across collection types. 3 Explicitly Typed Calculus As a basis for our language, we develop the explicitly typed calculus in this section. This calculus is based on the formalism of [2, 12, 26] which is recently being used as a query language for complex heterogenous genomic data sources [9]. The fragment dealing with sets is known [26] to be equivalent to several nested relational algebras [20, 17, 5, 15] The types used in the explicitly typed calculus are either eq types t or noneq types T . The eq types are those types where equality tests can be performed on their objects; the ....

K. Hart, L. Wong, C. Overton, and P. Buneman. Using a query language to integrate biological data. Talk given at the Meeting on the Interconnection of Molecular Biology Databases, Stanford, August 1994.

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Hart, K., Wong, L., Overton, C., & Buneman, P. (1994b). Using a query language to integrate biological data. Abstracts of 1st Meeting on the Interconnection of Molecular Biology Databases.

....(3) require information to be passed smoothly between the steps; 4) require increasing amount of computation; and (5) require increasing amount of visualization. Kleisli is designed to handle the first three requirements directly. In particular, Kleisli provides the high level query language CPL [5, 2] that can be used to express complicated transformation across multiple data sources in a clear and simple way. In addition, while Kleisli does not handle the last two requirements directly, it is capable of distributing computation to appropriate servers and initiating visualization programs. ....

Kyle Hart, Limsoon Wong, Chris Overton, and Peter Buneman. Using a query language to integrate biological data. In Abstracts of 1st Meeting on the Interconnection of Molecular Biology Databases, Stanford, August 1994. Available at http://www.cis.upenn.edu/¸cbil/mimbd94/mimbd94CPL.html.

....Few implement query languages allow function definition. We believe a functional account of database query languages is important here. At the university of Pennsylvania interfaces have been constructed between CPL Kleislli and several biological databases that are part of the Human Genome Project [64, 25, 24]. This language has provided biological researchers with a simple language for querying and integrating a number of biological data sources, something that could not be performed by existing query languages. These sources not only include standard (relational) databases, but also include data in a ....

K. Hart, L. Wong, C. Overton, P. Buneman, Using a query language to integrate biological data, in "Abstracts of Meeting on the Interconnection of Molecular Biology Databases," Stanford, August 1994. Available on WWW via http://www.cis.upenn.edu/ ~cbil/ mimbd94/ mimbd94CPL.html.

....such as Prolog [14] or CPL [4] in order to formulate more expressive queries. Therefore, we also present the embedding of our branch expression language into the Collection Programming Language (CPL) CPL is a language used for the retrieval and integration of heterogeneous distributed data [4, 10]. We describe optimizations within CPL that exploit the imported branch expression mechanism and provide a tight coupling between the two systems. This paper is organized in the following way. Section 2 provides an overview for path and branch expressions. In Section 3 we give a formal definition ....

....different size sets (1, 7, 12, etc. for testing. 6 Conclusions and Related Work Users of genetic data sources in both of our institutions (U. Penn. and I.S.S. have been frustrated by the lack of flexible tools for extracting information from these sources. We therefore embarked on a project [4, 8, 10] over a year ago to help solve some of their problems; the work in this paper is a part of that project. The main contributions here are: i) Branch expressions are introduced as a simple means for pruning complex data. ii) This mechanism has been applied in asncpl to access GenBank. iii) ....

K. Hart, L. Wong, C. Overton, and P. Buneman. Using a query language to integrate biological data, August 1994. In Abstracts of 1st Meeting on the Interconnection of Molecular Biology Databases, Stanford. Available at http://www.cis.upenn.edu/¸cbil/mimbd94/mimbd94CPL.html.

....(3) require information to be passed smoothly between the steps; 4) require increasing amount of computation; and (5) require increasing amount of visualization. Kleisli is designed to handle the first three requirements directly. In particular, Kleisli provides the high level query language CPL [10, 3] that can be used to express complicated transformation across multiple data sources in a clear and simple way. In addition, while Kleisli does not handle the last two requirements directly, it is capable of distributing computation to appropriate servers and initiating visualization programs. We ....

....c.#p, 1) A then modify #a of c to 1 c.#a else if string substring (s, c.#p, 1) C then modify #c of c to 1 c.#c else if string substring (s, c.#p, 1) G then modify #g of c to 1 c.#g else modify #t of c to 1 c. #t c S ] #p: p, #a: 0, #c: 0, #g: 0, #t: 0) p [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 ]] nr in [ #position: p, #consensus: mk consensus (C) #a pc: a pc, #c pc: c pc, #g pc: g pc, #t pc: t pc) q hist, a pc = mk pc (q.#a) c pc = mk pc (q.#c) g pc = mk pc (q.#g) t pc = mk pc (q.#t) C = #l: a , #c: a pc) #l: c , #c: c pc) #l: g , #c: g pc) #l: ....

Kyle Hart, Limsoon Wong, Chris Overton, and Peter Buneman. Using a query language to integrate biological data. In Abstracts of 1st Meeting on the Interconnection of Molecular Biology Databases, Stanford, August 1994. Available at http://www.cis.upenn.edu/¸cbil/mimbd94/mimbd94CPL.html.

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