[Bioperl-l] Strain/Plasmid database

[Paolo Romano]

Dear Jing,

I'm not proficient with perl, and I cannot support your effort, or even 
judge it, anyway.
But I'm in charge since many years of the CABRI network services.

This is the final achievement of a EU funded project for a Common Access 
to Biological Resources and Information , hence CABRI.
It currently includes 28 catalogues of European biological resource 
centers, preserving with high quality procedures such resources as 
bacteria, archae,
filamentous fungi, yeasts, plasmids, phages, and more.

CABRI has developed a standard for the databases.
This includes a minimum data set (MDS), a recommended data set (RDS) and 
a full data set (FDS) for each of these resource types.
This standard leverage from the MINE project, and has been later used by 
OECD for the definition of its standards.
Finally, the newly funded Microbial Resource Research Infrastructure 
(MIRRI), which is being built as a research infrastructure for Europe,
is currently examining CABRI standard in view of the definition of a 
Minimum  Information about Biological Resources (MIaBRe) paper.

You may find some information on line at:
CABRI web site: www.cabri.org
MIRRI web site: www.mirri.org

and the following paper:
Romano, P., Kracht, M., Manniello, M.A., Stehehuis, G., Fritze, D.
The role of informatics in the coordinated management of biological 
resources collections.
Appl Bioinformatics 2005, 4(3):175-186.
doi: 10.2165/00822942-200594030-00002

I'm wondering whether you took these standards into account when 
developing your system.
If not, I would be pleased to support your work in this direction since 
I really think that a shared perl library for the management of these data,
that is based on a shared data model, is of extreme interest and can be 
very useful.

I'm looking forward to hearing from you.

All the best . Paolo Romano

On 10/03/2014 11:57, Jing Yu wrote:
> Hi all,
>
> I've been developing lab Strain/Plasmid database using Perl Dancer2 as web interface and MySQL as the actual database. The idea is to centralise strain/plasmid data onto one server, and everyone in the lab (or local network, to be precise) can query the database from their own or any computer in the same network. I'm only a beginner in perl, and know almost nothing about HTML/CSS/Javascript, and this is primary why the web interface looks rubbish. But I assume (or I rather hope) people working on biology don't have a taste on graphics...
>
> This is my github page: https://github.com/logust79/Strain-Plasmid-database
>
> If you have any suggestions/advice or even criticisms, feel free to throw them at me. Any help is warmly welcome!
>
> Regards,
> Jing
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>    


-- 
Paolo Romano
Bioinformatics Lab, Biopolimers and Proteomics Service
IRCCS AOU San Martino IST, Genova, Italy
Email: paolo.dm.romano at gmail.com