Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases - PubMed (original) (raw)

Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases

L D Stein et al. Genome Res. 1998 Dec.

Abstract

Much of the world's genomic data are available to the community through networked databases that are accessed via Web interfaces. Although this paradigm provides browse-level access and has greatly facilitated linking between databases, it does not provide any convenient mechanism for programmatically fetching and integrating data from diverse databases. We have created a library and an application programming interface (API) named AcePerl that provides simple, direct access to ACEDB databases from the Perl programming language. With this library, programmers and computer-savvy biologists can write software to pose complex queries on local and remote ACEDB databases, retrieve the data, integrate the results, and move data objects from one database to another. In addition, a set of Web scripts running on top of AcePerl provides Web-based browsing of any local or remote ACEDB database. AcePerl and the AceBrowser Web browser run on Unix systems and are available under a license that allows for unrestricted use and redistribution. Both packages can be downloaded from URL. A Microsoft Windows port of AcePerl is in the planning stages.

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Figures

Figure 1

An ACEDB database object is a hierarchical set of tags and data values.

Box 1

This program fetches and displays information about a C. elegans genomic sequence and its predicted genes.

Figure 2

Graphical representation of the C01C4 Genome_Sequence object returned by the asGIF function.

Figure 3

The results of a text search for the word “pathogen” with the AceBrowser interface.

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References

1. 1. Anderson GW. Client/server database design with sybase: A high-performance and fine-tuning guide. New York, NY: McGraw-Hill; 1997.
2. 1. Barillot E, Guyon F, Cussat-Blanc C, Viara E, Vaysseix G. HuGeMap: A distributed and integrated Human Genome Map database. Nucleic Acids Res. 1998;26:106–1077. - PMC - PubMed
3. 1. Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BF. GenBank. Nucleic Acids Res. 1998;26:1–7. - PMC - PubMed
4. 1. Bigwood D. Databases at the National Agricultural Library. 1997. http://probe.nalusda.gov:8000/alldbs.html http://probe.nalusda.gov:8000/alldbs.html. .
5. 1. C. elegans sequencing consortium. 1998. Genome sequence of the nematode Caenorhabditis elegans: a platform for investigating biology. Science (in press). - PubMed

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