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Standard URL
From GMOD
Revision as of 20:21, 12 September 2007 by Dongilbert (Talk | contribs)
In order to simplify the retrieval of common datasets, the
Generic Model Organisms Database (GMOD) community has recommended
a series of standard URLs. Each participating MOD has an index
page like the ones below, describing the species and datasets
that are available.
MOD Standard URL
MOD | Standard URL | Description |
---|---|---|
WormBase | http://www.wormbase.org/genome/ | Caenorhabditis elegans and related nematodes |
wFleaBase | http://wfleabase.org/genome/ | Daphnia pulex and related crustaceans |
DroSpeGe | http://insects.eugenes.org/genome/ | Twelve Drosophila insect species genomes |
About GMOD Standard URL
This standard specifies the following URLs (all located under http://yourmod.org/). Display this HTML-formatted index page that contains links to each of the species available through common URLs. See also Todd Harris' powerpoint presentation given at the Spring, 2005 GMOD meeting.
Standard URL | Description |
---|---|
/genome/Binomial_name | An index page for species "Binomial_name". This will be an HTML-format page containing links to each of the genome releases. |
/genome/Binomial_name/release | Leads to index for the named release. It should be an HTML-format page containing links to each of the data sets described below. |
/genome/Binomial_name/current | Leads to an index of the most current release, symbolic link style. |
/genome/Binomial_name/current/dna | Returns a FASTA file containing big DNA fragments (e.g. chromosomes). MIME type is application/x-fasta. |
/genome/Binomial_name/current/mrna | Returns a FASTA file containing spliced mRNA transcript sequences. MIME type is application/x-fasta. |
/genome/Binomial_name/current/ncrna | Returns a FASTA file containing non-coding RNA sequences. MIME type is application/x-fasta. |
/genome/Binomial_name/current/protein | Returns a FASTA file containing all the protein sequences known to be encoded by the genome. MIME type is application/x-fasta |
/genome/Binomial_name/current/feature | Returns a GFF3 file describing genome annotations. MIME type is application/x-gff3. |