[ensembl-dev] Dev Digest, Vol 24, Issue 45
Anne Parker
ap5 at sanger.ac.uk
Wed Jun 27 16:08:44 BST 2012
That is true - but I think it only applies to single-species databases e.g. not Ensembl Bacteria. Also, the SiteDefs module is specific to the web code and the information in it should not be used for direct API calls.
Cheers
Anne
On 27 Jun 2012, at 13:14, 陈岗 wrote:
> Hi Jonathan
>
> species name and abbreviation also can find in public-plugins/ensembl/conf/SiteDefs.pm
>
> Best
>
> Gang Chen
>
> 2012/6/27 <dev-request at ensembl.org>
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> 1. species names (jonathan myles)
> 2. Re: species names (Stephen Fitzgerald)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 Jun 2012 11:41:13 +0100
> From: jonathan myles <jonathanmyles1 at googlemail.com>
> Subject: [ensembl-dev] species names
> To: dev at ensembl.org
> Message-ID:
> <CAOXpw8LrWynbqB7du6gPH2h-9Gp41v2c0PfsQ2hLdTUirvZ9-g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi
>
> Sorry, this is such an elementary one that I'm really embarrassed
> that I can't find it in the documentation
>
> For a given species, eg mycosphaerella graminicola, how do I find the
> precise string which represents that species for querying the ENSEMBL
> or compara databases?
>
> Thank you
>
> Jonathan
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 27 Jun 2012 11:57:41 +0100 (BST)
> From: Stephen Fitzgerald <stephenf at ebi.ac.uk>
> Subject: Re: [ensembl-dev] species names
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <alpine.LRH.2.00.1206271150540.16190 at login-r6-1.ebi.ac.uk>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Hi Jonathan, running this on the command line should give you the species
> names in compara-67, which you can then pipe in to grep for your species
> of interest.
>
>
> mysql -uanonymous -hensembldb.ensembl.org -P5306 -Densembl_compara_67
> -e"select name from genome_db"
> +-------------------------------+
> | name |
> +-------------------------------+
> | ailuropoda_melanoleuca |
> | ancestral_sequences |
> | anolis_carolinensis |
> | bos_taurus |
> | caenorhabditis_elegans |
> | callithrix_jacchus |
> | canis_familiaris |
> | cavia_porcellus |
> | choloepus_hoffmanni |
> | ciona_intestinalis |
> | ciona_savignyi |
> | danio_rerio |
> | dasypus_novemcinctus |
> | dipodomys_ordii |
> | drosophila_melanogaster |
> | echinops_telfairi |
> | equus_caballus |
> | erinaceus_europaeus |
> | felis_catus |
> | gadus_morhua |
> | gallus_gallus |
> | gasterosteus_aculeatus |
> | gorilla_gorilla |
> | homo_sapiens |
> | latimeria_chalumnae |
> | loxodonta_africana |
> | macaca_mulatta |
> | macropus_eugenii |
> | meleagris_gallopavo |
> | microcebus_murinus |
> | monodelphis_domestica |
> | mus_musculus |
> | myotis_lucifugus |
> | nomascus_leucogenys |
> | ochotona_princeps |
> | oreochromis_niloticus |
> | ornithorhynchus_anatinus |
> | oryctolagus_cuniculus |
> | oryzias_latipes |
> | otolemur_garnettii |
> | pan_troglodytes |
> | petromyzon_marinus |
> | pongo_abelii |
> | procavia_capensis |
> | pteropus_vampyrus |
> | rattus_norvegicus |
> | saccharomyces_cerevisiae |
> | sarcophilus_harrisii |
> | sorex_araneus |
> | spermophilus_tridecemlineatus |
> | sus_scrofa |
> | taeniopygia_guttata |
> | takifugu_rubripes |
> | tarsius_syrichta |
> | tetraodon_nigroviridis |
> | tupaia_belangeri |
> | tursiops_truncatus |
> | vicugna_pacos |
> | xenopus_tropicalis |
> +-------------------------------+
>
>
> On Wed, 27 Jun 2012, jonathan myles wrote:
>
> > Hi
> >
> > Sorry, this is such an elementary one that I'm really embarrassed
> > that I can't find it in the documentation
> >
> > For a given species, eg mycosphaerella graminicola, how do I find the
> > precise string which represents that species for querying the ENSEMBL
> > or compara databases?
> >
> > Thank you
> >
> > Jonathan
> >
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org
> > List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
> >
>
>
>
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> End of Dev Digest, Vol 24, Issue 45
> ***********************************
>
>
>
> --
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, P.R.China
> Phone:（+86）512-82782588
>
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Anne Parker
Ensembl Web Production Manager
www.ensembl.org
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