[ensembl-dev] CellBase, new project based on Ensembl released

[Nacho]

Hi Ensembl developers,

I would like to announce the second release of a homemade project based
mainly on Ensembl called CellBase. I think this project may be of interest
to many Ensembl user and developers. CellBase has been recently published
at NAR:
http://nar.oxfordjournals.org/content/early/2012/06/12/nar.gks575.short


*Goals*
The aim of CellBase is to integrate different data sources and make easy
many of the daily biological queries. CellBase is based on Ensembl (v2 is
based on Ensembl 67) and takes genome sequence, core features and
variations from it. We have also integrate Uniprot, Cosmic, Intact,
Biogrid, miRNAs, Reactome and many other biological sources. All these
sources have been integrated together in a SQL schema.

Notice that CellBase do not pretend to be a replacement form Ensembl or any
other data source, we just try to put together different sources and make
the access to data easier to the bioinformatic community. We make a
exhaustive use of Ensembl API for our projects. But in some cases or
scenarios it can be hard for some users to use Ensembl API or to have
enough hardware capabilities to install database.


*RESTful Web Services API*
To make data accessible to users a RESTful Web Services API has been
developed. This is a young project and many more web services are being
added every week. Much effort was made to make the URL sensible and easy to
users, the basic structure is:

*ws.bioinfo.cipf.es/cellbase/rest/ {version} / {species} / {category}
/ {subcategory} / id / {resource} ? {filters}*

*
*
Where *category* could be 'genomic' or 'feature', and *subcategory* specify
the type of the *id*, finally, *resource* defines what info we want to
retrieve. Eleven species are available right now. Below and in the
documentation and paper you can find many more info and examples. If
'of=json' added at the end then the result is returned in JSON format.

Some examples:

To get the transcripts from a gene:

http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA2/transcript

Or the SNPs or miRNA targets from a region:

http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/genomic/region/16:3618105-3701105/snp

http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/genomic/region/1:2201105-2319315/mirna_target

COSMIC mutations from a gene:

http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA2/mutation

Uniprot features from a transcript/protein:

http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/transcript/BRCA2/protein_feature

Or SNP phenotype:

http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/snp/rs3934834/phenotype


many many more at:
http://docs.bioinfo.cipf.es/projects/cellbase/wiki#Categories-and-subcategories



*Some applications using it*
Some applications form our lab are successfully using CellBase, so we think
it's enough mature ans usable project right now, some apps using it:
 1) Genome Maps: a HTML5 genome browsers (tuned for Google Chrome), visit:
http://genomemaps.org/
 2) VARIANT: cloud-based solution for predict the consequence type of
variants in NGS: http://docs.bioinfo.cipf.es/projects/variant/wiki, the
tool at: http://variant.bioinfo.cipf.es/. Recently published in NAR:
http://nar.oxfordjournals.org/content/early/2012/06/11/nar.gks572.abstract
 3) RENATO: also in NAR:
http://nar.oxfordjournals.org/content/40/W1/W168.short


You can find more information at:
http://docs.bioinfo.cipf.es/projects/cellbase/wiki

I hope CellBase can be useful for you and fell free to contact me if some
WS are needed or some bugs are found.

Best regards,

Nacho

-----------------------------------------------------------
Ignacio Medina Castello
Head of the Computational Biology Unit
Bioinformatics & Genomics Department
Prince Felipe Research Centre (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(Junto Oceanografico)
46012 Valencia, Spain.

Tfn: +34 96 328 96 80 ext: 1016 (+34 96 328 96 81 1016)
Fax: +34 96 328 97 01
Web : http://bioinfo.cipf.es
-----------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120724/52e0d0a0/attachment.html>