Question: Recommended data warehouse tools for bioinformatics search?
2
gravatar for billzt
3.8 years ago by
billzt20
Australia
billzt20 wrote:

I'm a bioinformatician with some Perl programming skills. However other members in my lab didn't know much about bioinformatics. Sometimes they need to search for some specific gene IDs and obtain their sequences, structures (GFF) and GO annations. As the organisms are non-model species, public servers such as Ensembl or Phytozome are not sufficient. I want to do a web interface with simple data search function and using SQL database as backends. I tried building local InterMine server but it was too complex. Any other good open source tools?

sequence gene genome • 1.3k views
ADD COMMENTlink modified 3.8 years ago by Jean-Karim Heriche20k • written 3.8 years ago by billzt20
1
gravatar for Darked89
3.8 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:
Unless you need something really extraordinary in terms of presenting the genomic data, abandon the idea of writing such system from scratch, especially as a first step. Use Jbrowse, collect opinions, and if end users really need more, then rather invest your time into installing a local copy if ENSEMBL than reproduce maybe 30% of functionality in X weeks. And give the users/institute hard to maintain, one in a world solution, which will die once you change the job.
ADD COMMENTlink written 3.8 years ago by Darked894.2k
0
gravatar for billzt
3.8 years ago by
billzt20
Australia
billzt20 wrote:

All the data had been stored on local server, in FASTA, GFF, or tab delimited files. They could be dumped into databases. We want to implement data search frontends like the "key word search" and "gene page" of Phytozome or Metazome.

ADD COMMENTlink written 3.8 years ago by billzt20
0
gravatar for Jean-Karim Heriche
3.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

See if genoverse fits your needs. It doesn't need any database back-end and can work with many file formats. Otherwise, you could turn tab-delimited files into SQLite tables and write simple cgi scripts to access the data.

ADD COMMENTlink written 3.8 years ago by Jean-Karim Heriche20k
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