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How to Contribute Data to MaizeGDB
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MaizeGDB accepts data that adheres to the
FAIR data principles
and which has been published and licensed as public data
(See https://creativecommons.org/licenses/).
Click here for MaizeGDB's recommendations on FAIR
data practices for maize researchers. Comprehensive metadata (information
about your dataset) is also required for all data accepted by MaizeGDB.
To request an exception, contact us.
MaizeGDB is not a permanent repository for primary data. In many cases we may
request that your data also be submitted to long-term repository that is
appropriate for the type of your research and data.
We can help you find the proper repository for your data.
MaizeGDB will happily accept data directly from researchers. Some types of
data must also be deposited at standard repositories. The MaizeGDB team can
advise on the correct repository and help with the submission, if needed.
It is particularly important that all sequence data be submitted to either
NCBI's GenBank (US),
EBI's ENA (Europe),
or the
DDBJ (Japan).
These repositories share all of their data on a daily basis, so data
submitted by any of these will be visible at all three.
Members of the maize community are also encouraged to become
community curators
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NEW GENES, GENE FUNCTION, AND GENE TO GENE MODEL ASSOCIATIONS
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 extractng 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.
Download and fill in [this template - link] then send it to the
MaizeGDB curators to have your gene function
information loaded into the MaizeGDB database.
GENOME ASSEMBLIES
Preparing a genome assembly for archival and hosting at MaizeGDB is a
lengthy process. Genome assemblies must be submitted to
GenBank
before they can be hosted at MaizeGDB. Genomes may also be submitted
to EBI.
GenBank (US), EBI (European), and DDBJ (Japan) share all data on a
daily basis, so data can be submitted to any of the three.
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- The first and most important step is to
contact the MaizeGDB staff
before before your assembly is complete and ready
for submission and hosting.
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Collect metadata describing your genome.
Contact the MaizeGDB team to
request a data template. This metadata will be needed for
both MaizeGDB and GenBank. Work with the MaizeGDB sequence
curator to ensure the data is complete and correct.
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Submit your genome to
GenBank
or EBI ENA.
This will involve creating
BioSample,
BioProject,
and WGS
records.
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Depending on your hosting agreement with MaizeGDB, you may
need to send additional data, such as annotation, and
additional datasets that have been aligned to your genome
assembly.
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ANNOTATIONS
Genome annotations (gene models) can be hosted at MaizeGDB in the
form of browser tracks and/or downloads of GFF or FASTA files.
Contact a MaizeGDB team member for more
information.
OTHER NUCLEOTIDE SEQUENCES, INCLUDING INDIVIDUAL GENES
Non-genome nucleotide sequences should also be submitted to
GenBank,
EBI's ENA
or the
DDBJ.
GenBank (US), EBI (Europe), and DDBJ (Japan) share sequence data on a
daily basis, so data can be submitted to any of the three.
Data sets that can be aligned to one or more reference genomes hosted
by MaizeGDB can also be added to genome browsers.
Contact the MaizeGDB curators for more
information.
PROTEIN SEQUENCES
NEXT GENERATION SEQUENCE READS
MAPPED SEQUENCE READS AND OTHER EXPRESSION DATA
Gene expresion data should be submitted to GenBank's
Gene
Expression Omnibus (GEO).
MaizeGDB can also host gene expression tracks on genome browsers.
Contact a MaizeGDB team member for more
information.
NON-HUMAN SNPS
GenBank dbSNP no longer accepts non-human SNPs. Maize SNPS should
be submitted to
EBI's
EVA.
It is important to submit SNPs to EVA because EVA will provide
permanent identifiers for each SNP, and because it will collapse
identical SNPs into one record, maintaining the original submission
identifier as well as a consensus identifier.
MaizeGDB will also host tracks of aligned SNPs on the genome browsers.
Note that MaizeGDB does not have sufficient personnel to do the
alignments. Contact a MaizeGDB team for more
information.
GENOTYPE AND PHENOTYPE DATA
The MaizeGDB team is still working on the problem of long-term storage
of genotype and/or phenotype data in a form that enables integrating
the data with other important data, exploration of datasets, and
comparison with data from related studies. For now, consider using
a generic long-term data repository like
Data Dryad for your genotype and
phenotype data.
The SNPversity tool developed by MaizeGDB permits
browsing and extracting blocks of genotype type data.
Contact a MaizeGDB team member if you have
genotype and/or phenotype data.
MAPS
METABALOMICS, IONOMICS AND OTHER DATA TYPES
Contact the MaizeGDB team if you have a dataset
you would like hosted at MaizeGDB which is not listed here. We will
work with you to see if and how your data can be hosted.
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FAQs
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WHERE DOES THE DATA STORED AT MAIZEGDB COME FROM?
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The original data was inherited from the MaizeDB and ZmDB projects.
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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.
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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.
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Pubic data from published literature are hand curated and entered
record-by-record by MaizeGDB and community curators.
BECOME A COMMUNITY CURATOR
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.
HOW CAN COMMUNITY MEMBERS CONTRIBUTE DATA?
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.
WHEN CAN I EXPECT DATA I GENERATED TO APPEAR AT MAIZEGDB?
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.
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, 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.
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