[ensembl-dev] Inserting a new species in Ensembl
Diogo Costa
costa.h4evr at gmail.com
Thu Oct 27 20:52:57 BST 2011
Hi!
Yes, the meta table of the Drosophila_virilis_core_64_12 database has
multiple records, as shown below:
+---------+------------+------------------------+--------------------------------------------------------+
| meta_id | species_id | meta_key | meta_value
|
+---------+------------+------------------------+--------------------------------------------------------+
| 1 | NULL | schema_type | core
|
| 2 | NULL | schema_version | 64
|
| 3 | NULL | patch |
patch_63_64_a.sql|schema_version |
| 4 | NULL | patch |
patch_63_64_b.sql|add_operons |
| 5 | NULL | patch |
patch_63_64_c.sql|is_ref_added_to_alt_allele |
| 6 | NULL | patch |
patch_63_64_d.sql|linkage_type change in ontology_xref |
| 7 | 1 | species.taxonomy_id | 7244
|
| 8 | 1 | species.common_name | Drosophila virilis
Sturtevant, 1916 |
| 9 | 1 | species.classification | virilis
|
| 10 | 1 | species.classification | virilis group
|
| 11 | 1 | species.classification | Drosophila
|
| 12 | 1 | species.classification | Drosophiliti
|
| 13 | 1 | species.classification | Drosophilina
|
| 14 | 1 | species.classification | Drosophilini
|
| 15 | 1 | species.classification | Drosophilinae
|
| 16 | 1 | species.classification | Drosophilidae
|
| 17 | 1 | species.classification | Ephydroidea
|
| 18 | 1 | species.classification | Acalyptratae
|
| 19 | 1 | species.classification | Schizophora
|
| 20 | 1 | species.classification | Cyclorrhapha
|
| 21 | 1 | species.classification | Eremoneura
|
| 22 | 1 | species.classification | Muscomorpha
|
| 23 | 1 | species.classification | Brachycera
|
| 24 | 1 | species.classification | Diptera
|
| 25 | 1 | species.classification | Endopterygota
|
| 26 | 1 | species.classification | Neoptera
|
| 27 | 1 | species.classification | Pterygota
|
| 28 | 1 | species.classification | Dicondylia
|
| 29 | 1 | species.classification | Insecta
|
| 30 | 1 | species.classification | Hexapoda
|
| 31 | 1 | species.classification | Pancrustacea
|
| 32 | 1 | species.classification | Mandibulata
|
| 33 | 1 | species.classification | Arthropoda
|
| 34 | 1 | species.classification | Panarthropoda
|
| 35 | 1 | species.classification | Protostomia
|
| 36 | 1 | species.classification | Coelomata
|
| 37 | 1 | species.classification | Bilateria
|
| 38 | 1 | species.classification | Eumetazoa
|
| 39 | 1 | species.classification | Metazoa
|
| 40 | 1 | species.classification | Opisthokonta
|
| 41 | 1 | species.classification | Eukaryota
|
| 42 | 1 | species.classification | cellular organisms
|
| 43 | 1 | assembly.default | v1
|
| 44 | 1 | assembly.mapping | supercontig:v1|chunk:v1
|
+---------+------------+------------------------+--------------------------------------------------------+
On Thursday, October 27, 2011, Anne Parker wrote:
> Hi Diogo
>
> Did you load the Drosophila taxonomy into the meta table? That's what's
> used by the webcode to sort the species in the dropdown list - if there are
> no entries, or the entries are wrong, the species will be ignored.
>
> Cheers
>
> Anne
>
>
> On 27 Oct 2011, at 10:38, Diogo Costa wrote:
>
> > Hello!
> >
> > In the process of my masters dissertation I created a mirror of Ensembl
> web site in a local server. It is up and running except for BLAST and search
> functionality.
> >
> > I've been trying to insert a new species (Drosophila virilis, from
> FlyBase), but have been unsuccessful so I was wondering if someone could
> give some pointers!
> >
> > I've tried to follow the instructions on these two sites:
> >
> > - Ensembl doc:
> >
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-doc/loading_sequence_into_ensembl.txt?revision=1.5&root=ensembl&pathrev=MAIN
> >
> > - Loading an Ensembl species database from scratch
> > http://www.warelab.org/blog/?p=218
> >
> > I have the genome sequences by scaffold and chromossomes and the CDS in
> FASTA format. Following the "Loading chromosome sequences and faking the
> assembly" section of the second link, I adjusted the script given to suit my
> data. I've managed to insert the data into the MySQL database.
> >
> > Then, I followed the instructions on
> http://www.ensembl.org/info/docs/webcode/species/index.html to make the
> specie information available from the website.
> >
> > However, the specie doesn't show up in the list of species (yes, I have
> deleted config/packed/* and config/config.packed and restarted the server).
> > When accessing the URL manually (http://..../Drosophila_virilis/Info/Index)
> I don't get any error in the log file.
> >
> > The server is running on top of Fedora 14, if it makes any difference..
> >
> > I don't really know what I can do, or what other information I need to
> give to Ensembl.
> >
> > Is this not the way to go?
> >
> > Sorry for the long email,
> > Diogo Costa
> > Portugal
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org <javascript:;>
> > List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
>
> Anne Parker
> Ensembl Web Production Manager
> http://www.ensembl.org
>
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
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