Sarah Carrier
SILS/MRC
February 24, 2009
This document includes a very simple and informal example of metadata for
datasets associated with one publication that have been put into the structure of the
Dryad Application Profile, version 1.0. Some notes for discussion and lingering
issues are at the bottom. Some other notes are also included along with certain
elements.
DATASET 1
dryad:status: incomplete
PUBLICATION
dc:type: article
dc:creator: Arnar Palsson
dc:creator:Ann Rouse
dc:creator:Rebecca Riley-Berger
dc:creator:Ian Dworkin
dc:creator:Greg Gibson
dc:contributor: Greg Gibson (He is the corresponding author!)
dc:title: Nucleotide Variation in the EGFR Locus of Drosophila melanogaster
dcterms:issued: 2004
dc:publisher: The Genetics Society of America
dc:subject: (NO KEYWORDS ASSOCIATED WITH THIS JOURNAL)
dcterms:abstract: The Epidermal growth factor receptor is an essential gene with diverse
pleiotropic roles in development throughout the animal kingdom. Analysis of sequence
diversity in 10.9 kb covering the complete coding region and 6.4 kb of potential
regulatory regions in a sample of 250 alleles from three populations of Drosophila
melanogaster suggests that the intensity of different population genetic forces varies
along the locus. A total of 238 independent common SNPs and 20 indel polymorphisms
were detected, with just six common replacements affecting >1475 amino acids, four of
which are in the short alternate first exon. Sequence diversity is lowest in a 2-kb portion
of intron 2, which is also highly conserved in comparison with D. simulans and D.
pseudoobscura. Linkage disequilibrium decays to background levels within 500 bp of
most sites, so haplotypes are generally restricted to up to 5 polymorphisms. The two
North American samples from North Carolina and California have diverged in allele
frequency at a handful of individual SNPs, but a Kenyan sample is both more divergent
and more polymorphic. The effect of sample size on inference of the roles of population
structure, uneven recombination, and weak selection in patterning nucleotide variation in
the locus is discussed.
dcterms:temporal: (n/a)
dcterms:spatial: (n/a)
darwincore:Scientific Name: Drosophila melanogaster
darwincore:Scientific Name: D. simulans
darwincore:Scientific Name: D. pseudoobscura
dcterms:isPartOf: 1943-2361 (**this is the ONLINE ISSN, not print)
dc:identifier: 10.1534/genetics.104.026252
dcterms:bibliographicCitation: Palsson, Arnar, Rouse, Ann, Riley-Berger, Rebecca,
Dworkin, Ian, Gibson, Greg. Nucleotide Variation in the Egfr Locus of Drosophila
melanogaster Genetics 2004 167: 1199-1212
dcterms:hasPartOf: (handles for datasets here)
DATA OBJECT 1
dc:type: data
dc:creator: Arnar Palsson
dc:creator:Ann Rouse
dc:creator:Rebecca Riley-Berger
dc:creator:Ian Dworkin
dc:creator:Greg Gibson
dc:contributor: Greg Gibson (corresponding author)
dc:title: GenBank File 17571116 (Egfr Sequence)
dc:identifier: (Dryad handle)
dcterms:isPartOf: 10.1534/genetics.104.026252
DDI:depositr: Sarah Carrier
dcterms:available: 2/19/06
dcterms:issued: 2/19/06
dcterms:extent: (however big it is)
dcterms:format: Microsoft Word
dcterms:temporal: (n/a)
dcterms:spatial: (n/a)
darwincore:Scientific Name: Drosophila melanogaster
darwincore:Scientific Name: D. simulans
darwincore:Scientific Name: D. pseudoobscura
dc:subject: (keywords would be by default inherited from the article…NO KEYWORDS
ASSOCIATED WITH THIS JOURNAL)
dc:rights: (Dryad statement)
dc:description: (nothing immediately available to cut and paste into this field)
DATA OBJECT 2
dc:type: data
dc:creator: Arnar Palsson
dc:creator:Ann Rouse
dc:creator:Rebecca Riley-Berger
dc:creator:Ian Dworkin
dc:creator:Greg Gibson
dc:contributor: Greg Gibson (corresponding author)
dc:title: List of Amino Acid Replacement variants in DER
dc:identifier: (Dryad handle)
dcterms:isPartOf: 10.1534/genetics.104.026252
DDI:depositr: Sarah Carrier
dcterms:available: 2/19/06
dcterms:issued: 2/19/06
dcterms:extent: (however big it is)
dcterms:format: PDF
dcterms:temporal: (n/a)
dcterms:spatial: (n/a)
darwincore:Scientific Name: Drosophila melanogaster
darwincore:Scientific Name: D. simulans
darwincore:Scientific Name: D. pseudoobscura
dc:subject: (NO KEYWORDS ASSOCIATED WITH THIS JOURNAL)
dc:rights: (Dryad statement)
dc:description: (nothing immediately available to cut and paste into this field)
DATA OBJECT 3
dc:type: data
dc:creator: Arnar Palsson
dc:creator:Ann Rouse
dc:creator:Rebecca Riley-Berger
dc:creator:Ian Dworkin
dc:creator:Greg Gibson
dc:contributor: Greg Gibson (corresponding author)
dc:title: LD plot for all common polymorphisms
dc:identifier: (Dryad handle)
dcterms:isPartOf: 10.1534/genetics.104.026252
DDI:depositr: Sarah Carrier
dcterms:available: 2/19/06
dcterms:issued: 2/19/06
dcterms:extent: (however big it is)
dcterms:format: PDF
dcterms:temporal: (n/a)
dcterms:spatial: (n/a)
darwincore:Scientific Name: Drosophila melanogaster
darwincore:Scientific Name: D. simulans
darwincore:Scientific Name: D. pseudoobscura
dc:subject: (NO KEYWORDS ASSOCIATED WITH THIS JOURNAL)
dc:rights: (Dryad statement)
dc:description: (nothing immediately available to cut and paste into this field)
...etc. - there are many other files associated with this.
WHERE TO PUT THIS CONTACT INFORMATION?
--remember: DSpace cannot use hierarchical elements like DDI:contact...this is why we
have to drop this element.
Department of Genetics, North Carolina State University, Raleigh, North Carolina
27513-7614
Corresponding author: (GREG) Department of Genetics, Gardner Hall, North Carolina
State University, Raleigh, NC 27695-7614.
E-mail: ggibson@unity.ncsu.edu