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WHERE DOES THE DATA STORED AT MAIZEGDB COME FROM?

Much of the data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects.

MaizeGDB's sequence data comes from GenBank.

Other data are generally added to the database in bulk by members of the MaizeGDB Team, and are contributed by community members directly.


HOW CAN COMMUNITY MEMBERS CONTRIBUTE DATA?

Tracks for the MaizeGDB Genome Browser can be created for sequence-based datasets using ZeAlign.

Notes can be added to records at MaizeGDB by researchers directly (like the one contributed by John Fowler that is shown toward the bottom of this page). To add a note, you should log in to the site using the login/register link displayed at the top of any MaizeGDB page. Once logged in, click the link to "Add your own annotation to this record" shown at the top of virtually all data displays - it's that easy! (Note that this link is not displayed unless you are logged in to the site.)

Small datasets can be added directly to the database using a set of Java-based community curation tools that are currently available for general use. Datatypes accessible through these tools include: Clone Library, Gel Pattern, Gene Product, Linkage Group, Locus, Map, Map Scores, Panel Of Stocks, Person, Phenotype, Primer/Enzyme, Probe, Recombination Data, Reference, Species, Stock, Term, Variation, and QTL. By creating data records, researchers become Community Curators who own the records they create and retain the ability to edit owned records directly.

A workshop demonstrating the use of the Community Curation Tools was taught at Iowa State University in August of 2004, another took place in January of 2005 at the Plant and Animal Genome Conference in San Diego, California. MaizeGDB staff members regularly attend the Plant and Animal Genome Conference in San Diego, California the Annual Maize Genetics Conference to demonstrate the tools. To gain access to the Community Curation Tools, follow the link at the top of the page marked "login/register" and check the box to become a Community Curator when you fill out the form to "Create an Annotation Account". To schedule an on-site training session for your research group, use the feedback form at the bottom of this page to contact the MaizeGDB team.

Large datasets can be made available through MaizeGDB by special arrangement. Use the feedback form at the bottom of this page to contact the MaizeGDB team to find out what arrangements can be made to accommodate your data. If possible, it is best to contact the MaizeGDB Team before you begin to generate large datasets so that a standardized format can be agreed upon and so that a customized pipeline can be created for importing your data in a timely and efficient manner.


WHEN CAN I EXPECT DATA I GENERATED TO 'APPEAR' AT MAIZEGDB?

MaizeGDB is minimally staffed at present, so we seldom go out looking for datasets to add to the database! Unless you have contacted us to make specific arrangements to accommodate your data, you shouldn't expect it to appear at the MaizeGDB site. Check out which data types are the focus of our work each month, and use the feedback form at the bottom of this page to contact the MaizeGDB team to find out what arrangements can be made to make your important data become available through MaizeGDB!


THE AGENCIES THAT FUND OUR RESEARCH HAVE ENCOURAGED ME TO CONTRIBUTE DATA TO MAIZEGDB. WHAT CAN I DO TO ENSURE THAT MAIZEGDB WILL TAKE MY DATA?

If you wish to contribute a large dataset, you should contact the MaizeGDB team using the feedback form at the bottom of this page to make special arrangements for its inclusion at MaizeGDB. Note that contacting MaizeGDB personnel well in advance and committing funds from your grants to cover the cost of personnel to curate your data into MaizeGDB are the best ways of ensuring that MaizeGDB can accommodate your requests for data storage.

In general, if the data you are generating have historically been stored at MaizeGDB (e.g., your project is planning to generate genetic maps using a new set of probes), it is very easy for us to commit to including your data in the database. However, if you are proposing to create data of a type that is not currently stored at MaizeGDB (e.g., if you were planning to generate a set of antibodies that recognize specific cellular components in maize and would like to make those antibodies available for general use), more work would be required of the staff at MaizeGDB (i.e., it would be necessary to make new tables in which to store your data and new data displays would be needed for the website).

Unless you have contacted the MaizeGDB team, please do not assume that we can accommodate your data. We are happy to make special arrangements to create new tables and data displays (e.g., we currently collaborate with the FSU Cytogenetic Map of Maize Project to make their cytological images and data available).

In summary, we encourage you to contact us prior to reporting to the funding agencies that we will take any and all maize data your project plans to generate.


ARE YOU PLANNING TO ASSEMBLE AND/OR ANNOTATE THE MAIZE GENOME?

From community surveys by the Maize Genetics Executive Committee and community discussions at the 2010 Maize Meeting, the maize community desires, as top priorities, to have the maize B73 DNA sequence assembly improved and annotated. MaizeGDB accepts updates to the B73 Reference Genome Assembly (currently B73 RefGen_v2) and is committed to working with members of the community to release new assemblies annually. In addition, MaizeGDB works with various groups that are involved in both structural and functional genome annotation. Click here to read the MaizeGDB Assembly and Annotation Manifesto!


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Last updated 1:43 pm, Dec 03, 2014.

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