Name
Abstract | ||
|---|---|---|
As the eXtensible Markup Language (XML) becomes a popular or standard language for exchanging data over the Internet/Web, there are a growing number of genome Web sites that make their data available in XML format. Publishing genomic data in XML format alone would not be that useful if there is a lack of development of software applications that could take advantage of the XML technology to process these XML-formatted data. This paper illustrates the usefulness of XML in representing and interoperating genomic data between two different data sources (Snyder's laboratory at Yale and SGD at Stanford). In particular, we compare the locations of transposon insertions in the yeast DNA sequences that have been identified by BLAST searches with the chromosomal locations of the yeast open reading frames (ORFs) stored in SGD. Such a comparison allows us to characterize the transposon insertions by indicating whether they fall into any ORFs (which may potentially encode proteins that possess essential biological functions). To implement this XML-based interoperation, we used NCBI's "blastall" (which gives an XML output option) and SGD's yeast nucleotide sequence dataset to establish a local blast server. Also, we converted the SGD's ORF location data file (which is available in tab-delimited format) into an XML document based on the BIOML (BIOpolymer Markup Language) standard. |
Year | DOI | Venue |
|---|---|---|
2001 | 10.1109/BIBE.2001.974417 | BIBE |
Keywords | Field | DocType |
genomic data,xml-formatted data,transposon insertion,different data source,xml format,xml technology,xml output option,interoperating genomic data,xml application,orf location data,genomic data interoperation,xml document,genomics,bioinformatics,extensible markup language,internet,open reading frames,open reading frame,markup language,data exchange,nucleotide sequence,dna,genetics,xml,dna sequence,application software,publishing,sequences | XML framework,World Wide Web,Efficient XML Interchange,XML Schema (W3C),XML,Computer science,XML database,Simple API for XML,Bioinformatics,XML Catalog,XML Signature | Conference |
ISBN | Citations | PageRank |
0-7695-1423-5 | 0 | 0.34 |
References | Authors | |
5 | 6 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Kei-hoi Cheung | 1 | 664 | 60.65 |
| Yang Liu | 2 | 1 | 0.69 |
| Anuj Kumar | 3 | 23 | 11.02 |
| Michael Snyder | 4 | 138 | 26.15 |
| Mark Gerstein | 5 | 354 | 45.41 |
| Perry Miller | 6 | 7 | 1.69 |