Difference between revisions of "Standard URL"
(→MOD Non-Standard URL) |
Dongilbert (Talk | contribs) (→MOD Standard URL + common /genome pages) |
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|''Caenorhabditis elegans'' and related nematodes | |''Caenorhabditis elegans'' and related nematodes | ||
|- | |- | ||
− | |[http://wfleabase.org | + | |[http://wfleabase.org/ wFleaBase] |
|http://wfleabase.org/genome/ | |http://wfleabase.org/genome/ | ||
|''Daphnia pulex'' and related crustaceans | |''Daphnia pulex'' and related crustaceans | ||
Line 18: | Line 18: | ||
|http://insects.eugenes.org/genome/ | |http://insects.eugenes.org/genome/ | ||
|Twelve ''Drosophila'' insect species genomes | |Twelve ''Drosophila'' insect species genomes | ||
+ | |} | ||
+ | |||
+ | =Common /genome pages= | ||
+ | These projects provide data information at /genome/, if not yet in the common formats described below. | ||
+ | |||
+ | {| | ||
+ | |+ '''Common /genome/ data pages''' | ||
+ | !MOD!!Common URL!!Description | ||
+ | |-e | ||
+ | |[http://www.medicago.org/ Medicago] | ||
+ | |http://www.medicago.org/genome/ | ||
+ | |''Medicago truncatula'' plant genome | ||
+ | |- | ||
+ | |[http://www.maizegdb.org/ MaizeGDB] | ||
+ | |http://www.maizegdb.org/genome/ | ||
+ | |''Maize'' corn genome | ||
+ | |- | ||
+ | |[http://www.neurosporagenome.org/ Neurospora] | ||
+ | |http://www.neurosporagenome.org/genome/ | ||
+ | |''Neurospora crassa'' | ||
+ | |- | ||
+ | |[http://www.vectorbase.org/ Vectorbase] | ||
+ | |http://agambiae.vectorbase.org/Genome/<br>http://aaegypti.vectorbase.org/Genome/<br>http://iscapularis.vectorbase.org/Genome/<br>http://cpipiens.vectorbase.org/Genome/<br>http://phumanus.vectorbase.org/Genome/ | ||
+ | |Human vector insects genomes | ||
|} | |} | ||
Revision as of 14:18, 17 September 2007
In order to simplify the retrieval of common datasets, the Generic Model Organisms Database (GMOD) community has recommended a series of standard URLs, or a common download URL. Each participating MOD has an index page like the ones below, describing the species and datasets that are available.
Contents
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 |
Common /genome pages
These projects provide data information at /genome/, if not yet in the common formats described below.
MOD | Common URL | Description |
---|---|---|
Medicago | http://www.medicago.org/genome/ | Medicago truncatula plant genome |
MaizeGDB | http://www.maizegdb.org/genome/ | Maize corn genome |
Neurospora | http://www.neurosporagenome.org/genome/ | Neurospora crassa |
Vectorbase | http://agambiae.vectorbase.org/Genome/ http://aaegypti.vectorbase.org/Genome/ http://iscapularis.vectorbase.org/Genome/ http://cpipiens.vectorbase.org/Genome/ http://phumanus.vectorbase.org/Genome/ |
Human vector insects genomes |
MOD Non-Standard URL
For those genome projects that haven't yet standardized their URLs there is this site that lists what is available:
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. |
Other names for this: Common download URL, Common URL, Standard URL