If your research is identifying new genes, providing evidence of gene function, and/or linking gene loci to gene models, it would be very helpful to MaizeGDB and the maize community, as well as increasing visibility of your research if you submit this information directly to MaizeGDB rather than relying on the MaizeGDB curators reading your paper and extracting this information to load into the database. The number of maize papers published each month is much greater than the number of papers that can be curated. Send your paper to a MaizeGDB curator to have your gene function information loaded into the MaizeGDB database.

Notes can be added directly to records at MaizeGDB by researchers. To add a note, you will need a community curation account. Log in to the site using the login/register link displayed at the top of any MaizeGDB page. Once logged in, click "Add free text annotation" in the annotation section of most data record displays.

When your genomic data is hosted at MaizeGDB, it increases the visibility and usability of your data. Depending on the level of hosting, genomic datasets are presented as downloads and BLAST targets, and via a variety of visualizations and browsers. Selected genomic datasets are also included in pan-Zea analyses, and linked to other data hosted by MaizeGDB.

Preparing a genome assembly for hosting at MaizeGDB is a lengthy process. Satr by contacting a MaizeGDB sequence curator to receive identifiers for your assembly and annotations and for additional instructions before submitting your assembly to Genbank or other INSDC database . The MaizeGDB metadata template contains information required by GenBank (also ENA and DDBJ) for genome assembly submissions, along with additional information required by MaizeGDB for hosting genomes.

Requirements for hosting genomic dataset at MaizeGDB at any hosting level:

1. Must follow the maize nomenclature rules
2. Chromosome names should be prefaced with "chr", for example, chr1, chr2, et cetera. Unplaced scaffolds should be named individually, NOT be combined into one. That is, there should be no "chr0" or "chrUnplaced".
3. Must be deposited in an INSDC database (Genbank, EBI, or DDBJ)
4. Include a completed metadata spreadsheet.
5. If possible, sibling seed and pedigree should be deposited at GRIN.
6. A contact person from your team/consortium should be assigned to coordinate with MaizeGDB staff.

To submit your data to EBI's ENA, see instructions here. Note that ENA submission requires command line skills as there is no longer a web portal for submitting genome assemblies. Additional tutorials for submiting data to ENA are available:
To submit your data to GenBank, see these tutorials. Note that NCBI checks for vector/primer contamination so you may need to warn in advance about known chloroplast sequence in the maize nuclear genome.

Level 1:

1. Web page describing the dataset (from the metadata spreadsheet).
2. Downloads of the assembly FASTA, annotation GFF, annotation CDS and protein files. Additional download files will be considered if available.
3. Public BLAST targets.
4. Will be tagged as a pre-release under Toronto if requested.

Level 2:
To qualify for Level 2 hosting, the assembly must be of reference quality, the dataset must include gene model annotation and at least two additional datasets aligned on the assembly, and the data must be published, at least as a preprint, and therefore, not under Toronto agreement.

Level 2 hosting includes everything from Level 1 and:

5. A genome browser.
6. Inclusion in Zea pan-gene analyses.
7. If part of a larger sequencing project, a page describing the project.

Level 3:
To qualify for Level 3 hosting, the dataset will need to meet all requirements above and, the cultivar or accession must be considered to be of significant importance by the community.

Level 3 hosting includes everything from Levels 1 and 2, and:

8. Browser enhancements, e.g. gene models from other assemblies lifted.
9. Individual gene model pages that link gene models to other data held by MaizeGDB.
10. Inclusion in PanEffect Tool, possibly other tools.

Revisions
When a genome assembly is updated, the latest version only is used in the Zea pan-gene analysis. The exception is the representative maize genome, B73 and the commonly-used Mo17, where all versions are included. Downloads, BLAST targets, and (depending on hosting level) browsers are maintained for the earlier version as well.

New assembly by a different group
If a cultivar or accession is reassembled by another group, if one is significantly improved over the other, only the more improved dataset is used in Zea pan-gene analyses. Downloads, BLAST targets, and (depending on hosting level) browsers are maintained for both versions.

• The original data was inherited from the MaizeDB and ZmDB projects.
• Sequence data comes from GenBank, genome assembly and annotation groups, and other research groups that are producing genomic, transcriptomic, and proteomic sequence data for maize.
• Other types of bulk data are contributed by community members, usually in standard file formats like GFF, VCF, BED and are added to the database by members of the MaizeGDB Team.
• Pubic data from published literature are hand curated and entered record-by-record by MaizeGDB and community curators.

To create a community annotator account, follow the link at the top of the page marked "login/register" and check the box to become labeled "I am interested in being a MaizeGDB curator" when you fill out the form to "Create an Annotation Account". You will be contacted via e-mail when your account is activated.

MaizeGDB staff members regularly attend the Plant and Animal Genome Conference in San Diego, California and the Annual Maize Genetics Conference. To schedule a meeting at any of these conferences, use the feedback form at the top of this page to contact the MaizeGDB team, or you can contact a specific MaizeGDB member.

Contact MaizeGDB directly with a request to host your data, using the feedback button at the top of the page or contact a specific MaizeGDB member.

Notes can be added directly to records at MaizeGDB by researchers. To add a note, you will need a community curation account. Log in to the site using the login/register link displayed at the top of any MaizeGDB page. Once logged in, click "Add free text annotation" in the annotation section of most data record displays.

Although researchers are encouraged to use a standard long-term repository that is appropriate for the type of data, large datasets can be made available through MaizeGDB by special arrangement. Use the feedback form at the top of this page to contact the MaizeGDB team or contact a specific MaizeGDB member 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.

The MaizeGDB database is typically updated the first Tuesday of each month.

Unless you have contacted us to make specific arrangements to accommodate your data, you shouldn't expect it to appear at the MaizeGDB site unless our data curators have curated your paper, usually because it was recommended by the Editorial Board. Use the feedback form at the top 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.

If you wish to contribute a large dataset, you should contact the MaizeGDB team 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, more work would be required of the staff at MaizeGDB (e.g., it may 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 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.

It is strongly advised that you contact a MaizeGDB sequence curator well in advance of producing any data. See the guidelines for genome assemblies and annotations above.