Question: Integrative Arabidopsis Database - A Superdatabase Of Arabidopsis Databases
2
gravatar for Lo Sauer
8.3 years ago by
Lo Sauer160
Lo Sauer160 wrote:

Is there an integrative database for Arabidopsis Thaliana or plant data out there. Similar to the efforts of SRI and the many *Cyc e.g. Biocyc, Plantcyc or Aracyc databases and the Openhouse server.

In particularly I am looking for a database which integrates tables from other DBs including e.g. IUBMB enzyme information, but also localization of the various gene products in particular of functional proteins. Such tables should be integrated in an relational manner.

I have been working on this on and off for the past couple of months of Arabidopsis data, and don't acidentially want to find out that this work has already been done.

So far I only found this project, with a strong genomic bias:

  • ATIDB : The Arabidopsis thaliana Integrated Database

(PS: I've lost my account, so I am posting as a new user)

data database interaction • 2.9k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 8.3 years ago by Lo Sauer160
2
gravatar for Qdjm
8.3 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

First check to see if Ensembl Plants has what you need:

Besides that there's two other web portals besides TAIR that might be useful:

I know BAR has content that Ensembl doesn't have but I'm not sure if either of BAR or iPlant provide a relational database or web services. Nick Provart, who runs BAR, is very helpful so email him if you have trouble getting data out of BAR.

I heard that TAIR lost its funding, so it's not clear how much you can rely on them in the future.

ADD COMMENTlink written 8.3 years ago by Qdjm1.9k
1

The TAIR website states funding will be lost effective 1 Sep 2013.

ADD REPLYlink written 8.3 years ago by Larry_Parnell16k

Any idea what happens after that?

ADD REPLYlink written 8.3 years ago by Qdjm1.9k

In roughly two years. TAIR will likely realign itself and submit new funding proposals. You can contact arabidopsisinformatics§gmail§com for more information or if you want to be on the discussion panel.

ADD REPLYlink written 8.3 years ago by Lo Sauer160

@qdjm's post: thanks for the resources. very helpful

ADD REPLYlink written 8.3 years ago by Lo Sauer160
1
gravatar for Larry_Parnell
8.3 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Is what is presented, collected and planned at TAIR (The Arabidopsis Information Resource) of any use or present an overlap?

TAIR (from the website): The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.

ADD COMMENTlink written 8.3 years ago by Larry_Parnell16k
1

The TAIR data is crucial for the project I am working on. highly recommended. I've uploaded some of the tsv data as SQL to my datasets https://github.com/lsauer/Data-Hub/tree/master/databases/metabolic

ADD REPLYlink modified 3 months ago by RamRS25k • written 8.3 years ago by Lo Sauer160
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