Community News | ||
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New genomes added to SoyBase Posted on Wednesday, April 26th, 2023 3 new G. soja genomes have been added to the SoyBase download page. The GRIN accessions PI 549046, PI 562565 and PI 578357 genomes, CDS and protein sequences are now available for download. | ||
4 Glycine max genomes added to the SoyBase download page Posted on Tuesday, April 18th, 2023 Now you can have access to the genome, CDS and protein sequences from Cv. Lee.a2, Cv. ZH13.a1(Zhonghuang 13) and Cv. FiskebyIII (Fiskeby III, PI 438471) and the second assembly of Williams 82 ISU_01 (Wm82_ISU_01.a2). | ||
Registration for Soy2023 is open Posted on Tuesday, March 28th, 2023 | ||
Soybean Breeders Workshop Favorite Tool Posted on Monday, March 13th, 2023 | ||
Job announcements posted on SoyBase Posted on Sunday, February 26th, 2023 | ||
Seed Micro-Dissection Data Added to SoyBase Expression Explorer Posted on Friday, February 3rd, 2023 | ||
Summer 2023 Research and Extension Experiences for Undergraduates Posted on Wednesday, January 25th, 2023 |
Upcoming Events | |
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World Soybean Research Conference 11 From: 6-18-2023 To: 6-23-2023 | |
ASPB Plant Biology 2023 From: 8-5-2023 To: 8-9-2023 | |
National Association of Plant Breeders 2023 From: 7-16-2023 To: 7-19-2023 | |
Soy2023: Biennial Cellular and Molecular Biology of the Soybean Conference From: 8-10-2023 To: 8-13-2023 |
Results of a search at SoyBase are presented in two complementary ways.
The user-submitted search term is used to find exact lexical matches to the name or description of data objects in SoyBase (QTL, genes, etc.). If an exact match is not found, and when the search term was two or more words, then a further search is done using the individual words. These text-based matches are reported in the Text column of the results table.
The goal of the ontology search is to identify data objects in SoyBase that are related to the search term but which might not have the exact search word(s) in their name or description. Data in SoyBase are tagged using a soybean-specific ontology termed a SOYnumber (SOY#). The user-submitted search term is used to search this SoyBase ontology for an exact match. If an exact match is not found, and when the search term was two or more words, the individual words are used in an additional search. Once a match is found its SOY# is used to traverse the ontology tree to identify related terms. These terms are then used to find SoyBase objects that are related to those directly identified by the search term. These ontology-based matches are reported in the Ontology column of the results table.
Occasionally unrelated SoyBase data objects will be reported in the Ontology-based results along with the correctly identified ones. This is an unavoidable consequence of the the way we have structured the underlying trait, structure and development ontologies at SoyBase. For example a search for 'protein' also returns 'oil'-related objects since both are seed components.
Data Category | Search Was Performed Against |
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Genetic Marker | Genetic Markers (SNPs, SSRs, etc.). |
Gene | Gene records (ex. Glyma.15g026400, Fad2-1). |
QTL | Bi-Parental QTL and GWAS QTL collections. |
Germplasm Collections | The Induced Mutant and Uniform Field Trial records. |
Publications | Paper records and abstracts held within the Soybase data set. |
Sitemap, News & Tutorials | SoyBase Sitemap, News archive, Upcoming meetings and Tutorials. |
As an example of how these two searching capabilities can be helpful, a search for 'oil' will return those QTL that contain the word 'oil' in their name ('Seed oil', 'Seed oil to protein ratio', etc.) in the QTL line of the Text column. The Ontology column will contain these QTL along with the related QTL 'Seed palmitate', 'Seed oleic', etc.
Note: Because of the idiosyncratic ways that authors name phenotypic and developmental traits it is always advisable to look through the Ontology-based results, even when the submitted search term seems unambiguous. This can reveal additional SoyBase objects that might have been missed using exact text matching.
Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA | ||