Querying the File

Abiteboul, Serge; Cluet, Sophie; Milo, Tova

doi:10.1007/978-3-642-59623-0_53

Cited by 22 publications

(36 citation statements)

References 3 publications

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“…While we are aware of the fact that a native XML database or an SQL database with XML extensions might provide better performance, our setup corresponds to the way biosystematicists work with documents today. In addition, processing queries on files is an approach that the databaseresearch community has paid much attention to in the recent past (Abiteboul et al 1993(Abiteboul et al , 1995.…”

Section: Methodsmentioning

confidence: 99%

A Quantitative Comparison of XML Schemas for Taxonomic Publications

Sautter¹,

Böhm²,

Agosti³

2007

Biodiv. Inf.

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Abstract.-Large numbers of legacy taxonomic publications are currently being digitized to make them online available and ready for full text search. The documents are being marked up with XML for two purposes: To preserve the document structure, and to facilitate access via standard query languages like XQuery. With regard to the second aspect, the choice of an appropriate XML schema is crucial. It affects both query performance and the correctness of query results. Over the last few years, several different XML schemas have been proposed as markup standards for taxonomic publications. In this paper, we report on a thorough evaluation and comparison of these schemas. We have examined if they facilitate formulation and correct processing of queries that are common when it comes to taxonomic literature. We also compare the performance of these queries on documents that are marked up with the different schemas. Finally, we propose extensions to the schemas that enhance correctness of query results.Key words. -Heritage literature, quantiative analysis, systematics, taxonomy, TaxonX, xml schema At present, legacy taxonomic publications are being digitized in large numbers (e.g. Biodiversity Heritage Library 1 ). The intention is to store these documents in digital archives and to make them available online. The documents are marked up with XML for two purposes. The first one is to preserve the original document structure and publication-related in-formation like publisher, title and issue. The sec-ond one is to facilitate deployment of standard query languages like XPath (XPath) to access the document collection. In the recent past, several institutions and projects have proposed a variety of XML schemas for this purpose, such as ABCD (ABCD), SDD (SDD), TaxonX (TaxonX), and taXMLit (Weitzman & Lyall). In this paper, we compare these schemas and include some additional ones. Our comparison focuses on the second aspect mentioned above, relevant to the work of biologists. The queries typical for this domain are fine-grained (at the level of individual characters or distribution records), and their results are individual treatments, i.e., descriptions of a particular taxon. We have identified three basic types of criteria on which queries can be based: Taxonomic names, the collection locations, i.e., the locations 1 http://www.bhl.si.edu/ where specimens of a particular taxon have been collected, and the morphological feature concepts as the selection criterion. We investigate both the ease of formulation and the execution performance of these queries. Our results show that the four schemas mentioned above support queries over taxonomic names very well. The same is true for the collection locations. However, SDD is the only schema to allow formulating queries over morphological features at least to a certain degree, and they execute slowly in the environment investigated here. The other schemas do not provide any markup to identify individual concepts within morphologic descriptions. It is not possible to represent the r...

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Section: Methodsmentioning

confidence: 99%

A Quantitative Comparison of XML Schemas for Taxonomic Publications

Sautter¹,

Böhm²,

Agosti³

2007

Biodiv. Inf.

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“…Closer to XML2DB mappings are the notion of AIGs [2] and that of structural schema [1], which are also nontrivial extensions of attribute grammars. AIGs are specifications for schema-directed XML integration.…”

Section: Related Workmentioning

confidence: 99%

Selectively Storing XML Data in Relations

Fan

Ma²

2006

Lecture Notes in Computer Science

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Abstract. This paper presents a new framework for users to select relevant data from an XML document and store it in an existing relational database, as opposed to previous approaches that shred the entire XML document into a newly created database of a newly designed schema. The framework is based on a notion of XML2DB mappings. An XML2DB mapping extends a (possibly recursive) DTD by associating element types with semantic attributes and rules. It extracts either part or all of the data from an XML document, and generates SQL updates to increment an existing database using the XML data. We also provide an efficient technique to evaluate XML2DB mappings in parallel with SAX parsing. These yield a systematic method to store XML data selectively in an existing database.

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“…But there are still no adequate solution to ease the integration of files. Abiteboul et al (1993) show how to generate a parser that provides an object view of file data. But this parser must be manually enhanced with semantic actions that collect information in a structured way and build objects.…”

Section: Introductionmentioning

confidence: 99%

“…The wrapper is also responsible for writing data back into files after modifications ). This releases one from the tremendous task of building Yacc programs as it is necessary in Abiteboul et al (1993). A second generator produces an ODMG adapter for the relational database to be plugged in our federation approach ).…”

Section: Introductionmentioning

confidence: 99%

Plugging Files in Database Federations

Hohenstein¹,

Ebert²

2000

AJIS

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In order to use files in database federations, we propose to migrate file data into a relational database. Integrating the database in a federation is then well-understood. This procedure has the advantage that a ,/eal" database is handled supporting transactions and SQL; files obtain a high-level interface for free. This paper presents a specification-based approach to support the process of migrating file data into a relational database, and vice versa. A specification language provides powerful concepts to describe the contents of files and directories. In contrast to similar work, directory structures are taken into account, because they contain useful semantics. Given some descriptive specification of file contents, an adapter is generated moving data from several files into the database, and the other way round.

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Querying the File

Cited by 22 publications

References 3 publications

A Quantitative Comparison of XML Schemas for Taxonomic Publications

A Quantitative Comparison of XML Schemas for Taxonomic Publications

Selectively Storing XML Data in Relations

Plugging Files in Database Federations

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