Download An Introduction to MaizeGDB

MaizeGDB: A NextGeneration Maize
Database
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.
http://www.maizegdb.org
2
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.
http://www.maizegdb.org
3
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.
http://www.maizegdb.org
4
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.
http://www.maizegdb.org
5
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.
http://www.maizegdb.org
6
A Quick Tour – Sequences, Maps, and Genes


… 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.
7
http://www.maizegdb.org
A Quick Tour – Sequences, Maps, and Genes


… 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.
http://www.maizegdb.org
8
A Quick Tour – Sequences, Maps, and Genes

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.
9
http://www.maizegdb.org
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.
http://www.maizegdb.org
10
A Quick Tour – Phenotypes and Stocks


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!.
http://www.maizegdb.org
11
A Quick Tour – Phenotypes and Stocks


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.
http://www.maizegdb.org
12
A Quick Tour – Phenotypes and Stocks


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.
http://www.maizegdb.org
13
A Quick Tour – Phenotypes and Stocks


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.
http://www.maizegdb.org
14
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)
http://www.maizegdb.org
15
Acknowledgements
MaizeGDB 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
http://www.maizegdb.org
Heike Kross
USDA/ARS
NSF
Maize Research
Community
16