An overview of the MaizeGDB project and web interface, etc. Carolyn J. Lawrence [email protected] 15 September 2005 (Write this down)

An overview of the MaizeGDB project and web interface, etc.

Carolyn J. Lawrence

[email protected]

15 September 2005

(Write this down)

MaizeGDB 101

• MaizeGDB aims to:– Provide a central repository for public maize

information– Present the data in a way that creates intuitive

biological connections for the researcher with minimal effort

– Enable the community to become involved in the evolution of the data and interface

• MaizeGDB is funded by USDA-ARS.

Who are the gremlinsworking behind scenes?

MaizeGDB Data

• MaizeGDB includes a number of data types, all available from the front page.

• Data types available:– Probes (BACs, overgos, SSRs, etc.) – Gene Products – Locus/Loci – Maps – Metabolic Pathways – People/Organizations – Phenotypes – QTL – References – Sequences– Stocks – Variations

Basic Utility of MaizeGDB-Top-

• Each page at MaizeGDB offers a set of consistent tools for users, from searching to access to popular pages…

• These tools are found along the top of each page.

Basic Utility of MaizeGDB-Bottom-

• Search bar (duplicate)

• Feedback is key to getting what you want!

From the front page

Search Pages: Overgo

• Type here

From the front page

References• There are too many maize publications for us to curate

each and every one (especially given our staff size!)• Stellar publications are chosen by our Editorial Board

Editorial Board

New! Raw Data• QTL data (MapMaker Infiles accessible through the QTL Data Center)

• RN maps (from Map Data Center)

All About Searching

• From any page, just choose your data type, type in a term, and hit “Go!”

• For example, let’s say we observed a purple colored phenotype, and we wanted to find out more…

Purple Plant Phenotype

• We choose the purple plant phenotype record, which you can see at right

• Note: stocks available, images available, genetic info, printer friendly version, tools…

Does this phenotype look like *our* purple plant?

A Stock with Purple Plant

• Clicking on the purple plant link for a stock, we see a stock record

• Note: phenotype details, images of the stock, interlaced GRIN info (GRIN is just a click away!), and with one click you can order the stock from the Stock Center or from the Plant Introduction Station.

Purple Plant Gene

• We choose the purple plant gene, as we are interested in the gene controlling the phenotype…

• Note: research tools, images, domain experts, map coordinates, and more… (next slide)

Purple Plant Gene, Cont.

• The purple plant gene is well-annotated…

• Note: primers & enzymes, variations, phenotypes, nearby loci on multiple maps…

Purple Plant Gene, Cont.

• The purple plant gene is very well-annotated…

• Note: sequences (also downloadable), related loci, and gel patterns

• There is even more available that you don’t see here: map scores, comments, recombination data, references, etc.

Purple Plant On A Map

• If we want to see the approximate location of purple plant on a map, we just click on a map name…

• Note: different locus types are highlighted with different colors, the locus of interest is highlighted, etc.

• There is even more available that you don’t see here: comments, mapping panels, references, etc.

Purple Plant On A Map, Cont.

• If the map is available in another database, it’s just a click away to see the map at other sites (Gramene and NCBI).

• You’ve also got all kinds of alternate map perspectives available with just a click: a sequence view (sequenced loci highlighted), primer view (loci with available primers highlighted), comparisons to other maps, etc.

Sequence of Purple Plant

• Clicking on one of the sequences on the purple plant gene record takes us to a sequence record…

• Note: sequence, available tools, associated detailed annotations (genes, maps, etc.)

• Additional data include stocks, gel patterns, etc.

• MaizeGDB is *not* the best place to find every single sequence similar to a sequence of interest, but does have it’s uses!

MaizeGDB’s BLAST Tool

• Clicking on the MaizeGDB BLAST link automatically inserts the sequence into our BLAST tool…

• Note: multiple databases available, simple options and explanations

• Let’s run the BLAST and…

BLAST (cont.)

• We get one mapped hit that isn’t our query! It’s on another chromosome and may be a member of a gene family!

• Note: detailed BLAST alignments, statistical scores, and map locations of results

It’s All Interconnected!

• The big idea is that all of this data is interconnected, and using our search tools, you can easily jump into the data flow at any point of interest.

• This enables plant breeders to start from the phenotype perspective, bioinformaticists to jump in with a sequence, or geneticists to dive in starting with a particular gene

Integrated Searching

• But let’s say you’re not sure what data type to search in.

• We handle that, too, by including sensible search redirection and alternate search results.

• For example, if you were to search the references for “Walbot,” not only would you get references with “Walbot” in the summary, but the site would automatically suggest visiting Virginia Walbot’s MaizeGDB bibliography and provide you with a citation count.

Community Relations

Success of Feedback

• At MaizeGDB we have received hundreds of messages via the integrated feedback mechanism.

• Beyond this, additional discussion directly with maize researchers has yielded more than 1000 additional messages.

• The feedback mechanism that we use appears to be something people use!

Example Interaction:Bill Sheridan

Bill Sheridan is a maize researcher at the University of North Dakota.

Bill phoned MaizeGDB on August 6, 2004, asking for help with a research issue.

What Did Bill Want?

Bill was having difficulty easily figuring out which SSRs detected BACs and were associated with markers that were genetically mapped.

During his conversation with Trent, it became clear that Bill could find this information, but that it was not available to him in a quick summary fashion.

How Can MaizeGDB Help?

Over the phone, Bill outlined the general concept of a table of information that would help him, with approximate map locations for markers, the SSRs for these markers, and BACs detected by these SSRs.

Once Trent had this information, he was able to design a tool to help Bill out.

MaizeGDB’s Solution

Trent designed an automatically generated table meeting Bill’s description and made links to generate each table available on the SSR page, a mere click away from the main index page (or from any other page using the Useful Pages tool). This meets the stressed requirement of “easy to find and use” that Bill stressed on the phone.

The table contained the exact data specified by Bill, thus from the ground up, design was led by real-world research needs.

What Did Bill Think?

When Trent emailed Bill about the solution on August 9, here’s what he responded with:

Thank you for your excellent work in compiling the new table of data containing anchored SSRs. It will be very helpful.

How can I add data to the database?

How do I cite MaizeGDB?

Exercises! Questions?

• Exercise 1• Exercise 2• Exercise 3 (optional)

Answers to the exercises will be given orally using the live site and the dry erase board