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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
Querying the database for gene, miRNA, metabolite and SNP entities. SoyKB has various options for querying (a) gene; (b) miRNA; (c) metabolite and (d) SNP.
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Figure 5: Querying the database for gene, miRNA, metabolite and SNP entities. SoyKB has various options for querying (a) gene; (b) miRNA; (c) metabolite and (d) SNP.

Mentions: The data in SoyKB can be queried is multiple ways. Searches can be made based on a single gene, miRNA, metabolite or SNP using the "Search" menu on the top bar or the "Quick Search" tabonthe homepage. All queries support partial fuzzy search without an exact or complete keyword match. For the genes, entity search can be made using partial or complete gene names, keywords, domain IDs from Pfam/Panther/KOG, gene family names or by specifying a location using nucleotide coordinates on a particular chromosome as shown in Figure 5a. The miRNA entity can be searched using the miRNA ID or simply by clicking on the "Search all miRNA IDs" tab to obtain all miRNAs in the database (Figure 5b). Metabolite entities in the database can be accessed via a metabolite keyword search or by utilizing the link to browse all metabolites in the database. Users can also search metabolites based on a combination of experiment types, tissue types, experimental conditions and polarity to narrow the search down to specific lists of metabolites as in Figure 5c. The SNPs data can be accessed using SNP number or selecting a genomic location using a range of nucleotide positions and a chromosome number (Figure 5d). SoyKB also allows users to query multiple genes or metabolites in a single query and combine the search results.


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)

Querying the database for gene, miRNA, metabolite and SNP entities. SoyKB has various options for querying (a) gene; (b) miRNA; (c) metabolite and (d) SNP.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Querying the database for gene, miRNA, metabolite and SNP entities. SoyKB has various options for querying (a) gene; (b) miRNA; (c) metabolite and (d) SNP.
Mentions: The data in SoyKB can be queried is multiple ways. Searches can be made based on a single gene, miRNA, metabolite or SNP using the "Search" menu on the top bar or the "Quick Search" tabonthe homepage. All queries support partial fuzzy search without an exact or complete keyword match. For the genes, entity search can be made using partial or complete gene names, keywords, domain IDs from Pfam/Panther/KOG, gene family names or by specifying a location using nucleotide coordinates on a particular chromosome as shown in Figure 5a. The miRNA entity can be searched using the miRNA ID or simply by clicking on the "Search all miRNA IDs" tab to obtain all miRNAs in the database (Figure 5b). Metabolite entities in the database can be accessed via a metabolite keyword search or by utilizing the link to browse all metabolites in the database. Users can also search metabolites based on a combination of experiment types, tissue types, experimental conditions and polarity to narrow the search down to specific lists of metabolites as in Figure 5c. The SNPs data can be accessed using SNP number or selecting a genomic location using a range of nucleotide positions and a chromosome number (Figure 5d). SoyKB also allows users to query multiple genes or metabolites in a single query and combine the search results.

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