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Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics.

Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D - BMC Genomics (2012)

Bottom Line: It allows users of certain levels to share their expertise by adding comments to the data.It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers.SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of Missouri, Columbia, MO 65211, USA.

ABSTRACT

Background: Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs).

Methods: SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers of registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers.

Conclusions: SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/.

Show MeSH
Protein 3D structure viewer. Visualization of predicted protein 3D structure for gene Glyma16g01990.1 showing alpha-helices in purple and beta-sheets in yellow.
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Figure 7: Protein 3D structure viewer. Visualization of predicted protein 3D structure for gene Glyma16g01990.1 showing alpha-helices in purple and beta-sheets in yellow.

Mentions: Protein 3D structural models for all proteins have been predicted using MULTICOM [24] and incorporated on the gene card page using Jmol [25]. Figure 7 shows an example of the protein 3D structure for gene Glyma16g01990.1.


Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics.

Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D - BMC Genomics (2012)

Protein 3D structure viewer. Visualization of predicted protein 3D structure for gene Glyma16g01990.1 showing alpha-helices in purple and beta-sheets in yellow.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3303740&req=5

Figure 7: Protein 3D structure viewer. Visualization of predicted protein 3D structure for gene Glyma16g01990.1 showing alpha-helices in purple and beta-sheets in yellow.
Mentions: Protein 3D structural models for all proteins have been predicted using MULTICOM [24] and incorporated on the gene card page using Jmol [25]. Figure 7 shows an example of the protein 3D structure for gene Glyma16g01990.1.

Bottom Line: It allows users of certain levels to share their expertise by adding comments to the data.It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers.SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of Missouri, Columbia, MO 65211, USA.

ABSTRACT

Background: Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs).

Methods: SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers of registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers.

Conclusions: SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/.

Show MeSH