User:Maxglycine/sandbox

SoyBase
Content
Description	SoyBase the USDA-ARS soybean genetics and genomic database
Data types; captured	Nucleic Acid, Protein, Expression, Metabolism, Epigenetics
Organisms	Glycine max, Glycine soja (soy, soya, soybean)
Contact
Research center	USDA Agricultural Research Service
Laboratory	Corn Insects and Crop Genetics Research Unit
Primary citation	PMID 20008513
Access
Data format	Various
Website	soybase.org
Miscellaneous
License	Public domain-US Government
Versioning	None
Data release; frequency	Continuously
Curation policy	Professionally curated

History

SoyBase^[1] was instituted in the early 1990's by the United States Department of Agriculture Agricultural Research Service in the Corn Insects and Corn Genetics Research Unit (CICGRU) in Ames, IA as a central repository for the soybean genetics community's published information. Originally the database concentrated on genetic information such as genetic linkage maps and other Mendalian genetics information. The SoyBase genetic maps are a manually curated composite of all published mapping and QTL studies and thus provide a species level view of markers and QTL.

Since the 2010^[2] release of the soybean genome sequence, it along with gene models and many other types of genome annotations have been integrated in to SoyBase. SoyBase genetic linkage maps were integral to the assembly of the soybean genomic sequence.

Currently (2018-2019) the database receives approximately 63,000 page requests from 2,600 users per month from 130 countries. Users from about 40 U.S. and 82 foreign educational institutions access SoyBase yearly. SoyBase also supplies data to a number of U.S. and foreign government organizations and corporate entities.

Data Submission and Release Policy

Data submission is accepted from the original source generators only. Users that independently identify data for inclusion into the database can contact SoyBase directly. A number of Excel-based spreadsheet templates are available to facilitate the inclusion of data into Soybase.

All data in SoyBase are freely available without restrictions. A number of data sub-setting and download tools are provided, and when needed ad hoc subsets of the data can be requested from the SoyBase Curator.

Tools

The SoyBase Database Search Tool uses a single text entry box for querying the entire database Results are returned as both text and as displays of using word-based searches for data as well as displays of soybean genetic and genomic data using a number of Generic Model Organism Database (GMOD) open-source software. In addition to SoyBase objects identified by exact lexical matches to the query term, the tool also uses a soybean-specific ontology to identify biologically related SoyBase objects.

Some SoyBase sequence data and annotations are also available through an InterMine instance (SoyMine), which is a collaboration with the Legume Information System^[3] Project

Graphical Displays

Genetic maps at SoyBase contain information on markers (Simple Sequence Repeat-SSR, Restriction Fragment Length Polymorphism-RFLP, Single Nucleotide Polymorphism-SNP, etc.), genes, and biparental and Genome Wide Association Study (GWAS) Quantitative Trait Loci(QTL). Soybean genetic maps are displayed using the CMap comparative genetic map viewer. Soybean genomic sequence and gene model data are displayed using the GBrowse sequence viewer. Other geneome annotations in this viewer include epigenetic data such as DNA methylation and gene expression data of various soybean strains subjected to different treatments and from different soybean tissues or cultivars. Metabolic data and biochemical pathway information is displayed using PathwayTools. Soybean metabolic pathway information (SoyCyc) was inferred by the Plant Metabolic Network^[4] project and was used to populate PathwayTools displays.

External Links

References

^ Grant, David; Nelson, Rex T.; Cannon, Steven B.; Shoemaker, Randy C. (2010). "SoyBase, the USDA-ARS soybean genetics and genomics database". Nucleic Acids Research. 38 (Suppl 1): D843–D846. doi:10.1093/nar/gkp798. PMID 20008513.
^ Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica; et al. (2010). "Genome sequence of the palaeopolyploid soybean". Nature. 463: 178–183. doi:10.1038/nature08670. PMID 20075913. {{cite journal}}: Explicit use of et al. in: |last4= (help)
^ Dash, S.; Campbell, J.D.; Cannon, E.K.; et al. (2016). "Legume information system (LegumeInfo. org): a key component of a set of federated data resources for the legume family". Nucleic Acids Research (44): D1181–D1188. doi:10.1093/nar/gkv1159. {{cite journal}}: Explicit use of et al. in: |last4= (help)
^ Schlapfer, P.; Zhang, P.; Wang, C.; et al. (2010). "Genome-Wide Prediction of Metabolic Enzymes, and Gene Clusters in Plants". Plant Physiology. 173 (4): 2041–2059. doi:10.1140/99.16.01942. {{cite journal}}: Explicit use of et al. in: |last4= (help)

[[Category:Biological databases]] [[Category:Model organism databases]]

[1] Grant, David; Nelson, Rex T.; Cannon, Steven B.; Shoemaker, Randy C. (2010). "SoyBase, the USDA-ARS soybean genetics and genomics database". Nucleic Acids Research. 38 (Suppl 1): D843–D846. doi:10.1093/nar/gkp798. PMID 20008513.

[2] Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica; et al. (2010). "Genome sequence of the palaeopolyploid soybean". Nature. 463: 178–183. doi:10.1038/nature08670. PMID 20075913. {{cite journal}}: Explicit use of et al. in: |last4= (help)

[3] Dash, S.; Campbell, J.D.; Cannon, E.K.; et al. (2016). "Legume information system (LegumeInfo. org): a key component of a set of federated data resources for the legume family". Nucleic Acids Research (44): D1181–D1188. doi:10.1093/nar/gkv1159. {{cite journal}}: Explicit use of et al. in: |last4= (help)

[4] Schlapfer, P.; Zhang, P.; Wang, C.; et al. (2010). "Genome-Wide Prediction of Metabolic Enzymes, and Gene Clusters in Plants". Plant Physiology. 173 (4): 2041–2059. doi:10.1140/99.16.01942. {{cite journal}}: Explicit use of et al. in: |last4= (help)

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