Difference between revisions of "Standard URL"

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(MOD Standard URL)
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= See also =
 
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* http://gmod.cvs.sourceforge.net/gmod/standard-urls/
  
 
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[[Category:GMOD_Best_Practices]]
 
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[[Category:MOD_User_Interfaces]]

Revision as of 02:16, 20 July 2007


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

Genome datasets available through the GMOD commom 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.

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.

See also