MaizeGDB: A Next- Generation Maize Database. 2 What Is MaizeGDB? MaizeGDB is a central repository for public maize information

MaizeGDB: A Next-Generation Maize Database

http://www.maizegdb.org 2

What Is MaizeGDB? MaizeGDB is a central repository for public maize

information. MaizeGDB incorporates data from various public

resources, including GenBank, as well as curated data. MaizeGDB features a new web interface with the goal of

making it as easy as possible for visitors to find the data they need.

MaizeGDB provides tools to allow users to dig into the data quickly and efficiently.


MaizeGDB’s Mission Our mission is simple: to create a useable and useful

maize community database. To achieve this mission, we have three main principles

that we follow: Respond efficiently and effectively to feedback at all times. It is

the community’s database, and thus the community’s input is vital.

Develop tools that are easy to use, but at the same time are useful for complex data extraction.

Continue to seek new data and new initiatives to make the site useful to all.


Some Features of MaizeGDB

Consistent interface throughout site; each page has identical tools at top and bottom to reduce confusion:

The top of every page includes links to essential pages, a shortcut menu to reach data pages and important tools, and a search tool that lets you search for the data you need.


Some Features of MaizeGDB (2) Other features include:

Integrated help throughout the site, including tutorial

BLAST tool which provides map locations of hits

Easy-to-use advanced searches

Tab-delimited search results which you can download to your own analysis programs

Tools integrated into retrieved records.

Extensive linking to other resources.

Picture shows output from BLAST run at MaizeGDB website. Results include summary, links to other sites, map locations,

and detailed alignments.


A Quick Tour – Sequences, Maps, and Genes

Let’s say we have a sequence on hand and we want to find out information about genes and map locations that are known for strong matches for this sequence.

We would start by running a blastn…

The BLAST tool at MaizeGDB lets you choose blastn, blastx, or tblastn; set your evalue cutoffs, and choose

among several sequence data sets.



… and then looking at the blast results, we find two good matches, both of which have map locations.

From here, we can look at the map…

The blast results provide links to the matching sequences at MaizeGDB, EMBL, DDBJ, and GenBank;

describe the map locations of various hits; gives the alignment of matches; and summarizes the data at the

top.



… which features that gene, pop1, highlighted for us already on the map.

We can also look at the gene itself…

Map results provide color coding of the loci so you can tell whether they are genes or not and their detection methods. You can also compare the maps with other

maps or view the map with associated sequences.



The record for pop1 includes a great deal of information on the gene, including details on the region surrounding it and references.

Locus records provide map locations and the nearby regions on high density maps among other data types;

with just a click, you can also search other databases for this loci or get a general view of the region in which this

locus lies.


A Quick Tour – Phenotypes and Stocks

Now, let’s say you’ve observed a particular phenotype, but you have no other information other than what it looks like, but you’d like to find more.

The image browser tool will help! Typing in a one-word description will provide images of different phenotypes and links to their respective records.

The phenotype image browser lets you filter through our image database, selecting for the phenotypes you’re

interested in. This allows for quick visual verification of what you’re looking for.



After looking at the images, we decide that colorless aleurone is the phenotype we’re looking for.

Visiting that record reveals a great deal of genetic information, as well as the ability to see stocks that express that phenotype.

The phenotype record shows genotypic information as well as stocks that express the phenotype. Stocks listed

in bold are easily orderable from our website!.



Choosing a stock takes us to the stock page, which provides detailed information on that stock.

From here, we can make a final visual verification that we’ve found an appropriate stock…

The stock record shows genotypic and phenotypic information about the stock, as well as the ability to see

images of the stock and a stock ordering tool.



Clicking on the “see images” link lets us get a visual review of the phenotype.

Since we’re satisfied that we’ve found an appropriate stock, we go back to the stock record and order…

This tool, integrated into the stock record, shows images of all of the variations that are present in that stock. The

images and descriptions provide a visual overview of what you can expect from the stock.



Clicking on the “Order this stock” link adds the stock to our stock “shopping cart.”

We can now browse for more stocks to order or go ahead and order this stock.

The integrated stock ordering tool lets you fill a “shopping cart” with the stocks you’re interested in while

you browse. When you’re finished, you can click to order the stocks or empty out your cart to start over.


Future Plans For MaizeGDB Addition of a postdoc to oversee biological integrity of

data Continued development of interface and curation tools Investigation into new data sources which can be

integrated into the MaizeGDB system (microarray data, GRIN germplasm data)

Involvement in cross-species and cross-community collaborative projects to improve data for all (gene ontology, plant ontology, data sharing mechanisms such as XML and Moby)


AcknowledgementsMaizeGDB Team

Volker Brendel (PI)

Sanford Baran

Darwin Campbell

Trent Seigfried

ZmDB Team

Mike Brekke

Qunfeng Dong

MaizeDB Team

Mary Polacco

Ed Coe

Denis Hancock

National Steering Committee

Ed Buckler

Vicki Chandler

Mike Freeling

Sarah Hake

Mary Polacco

Marty Sachs

Tom Slezak

Cari Soderlund

Lincoln Stein

Virginia Walbot

Doreen Ware

Heike Kross

USDA/ARS

NSF

Maize Research Community

Documents

MaizeGDB: A Next- Generation Maize Database. 2 What Is MaizeGDB? MaizeGDB is a central repository for public maize information