MaizeGDB: A Next-Generation Maize Database

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MaizeGDB A Next-Generation Maize Database
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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.

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MaizeGDBs 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 communitys database,
  and thus the communitys 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.

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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.

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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.
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A Quick Tour Sequences, Maps, and Genes

• Lets 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.
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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.
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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.
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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.
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A Quick Tour Phenotypes and Stocks

• Now, lets say youve observed a particular
  phenotype, but you have no other information
  other than what it looks like, but youd 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 youre interested in. This allows for
quick visual verification of what youre looking
for.
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A Quick Tour Phenotypes and Stocks

• After looking at the images, we decide that
  colorless aleurone is the phenotype were 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!.
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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 weve 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.
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A Quick Tour Phenotypes and Stocks

• Clicking on the see images link lets us get a
  visual review of the phenotype.
• Since were satisfied that weve 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.
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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 youre
interested in while you browse. When youre
finished, you can click to order the stocks or
empty out your cart to start over.
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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)

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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
Heike Kross USDA/ARS NSF Maize Research
Community