Community News | ||
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USDA-ARS Job Announcement Posted on Tuesday, April 16th, 2024 National Program Leader for USDA-ARS National Plant Germplasm System, comprising plant genetic resource management, genetic enhancement and applied research programs related to plant genetic resource conservation and sustainable use of 200+ crops from 16,000+ species. Apply by April 26, 2024. | ||
New parentage information added to the Soybean Parentage Database Posted on Wednesday, March 20th, 2024 621 new strain parentage information added to the SoyBase Soybean Parentage Datanbase. The strains were testing in the 2023 Northern Soybean Uniform Test (NUST). Parentage information was provided by the NUST cooperators. | ||
Save the Date for the 2025 Bi-annual Soybean Conference Posted on Friday, March 15th, 2024 | ||
AG2PI Scientific Computing & Data Analytics Virtual Workshop Posted on Wednesday, March 13th, 2024 | ||
CROPS Conference 2024 Posted on Sunday, March 10th, 2024 | ||
2024 Soybean Breeders Workshop fast approaching Posted on Sunday, January 28th, 2024 | ||
Save the Date for the 2024 Soybean Breeders Workshop Posted on Tuesday, November 7th, 2023 |
Upcoming Events | |
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CROPS 2024: Improving Agriculture Through Genomics From: 6-3-2024 To: 6-6-2024 | |
Annual Meeting of the National Association of Plant Breeders From: 7-21-2024 To: 7-25-2024 | |
11th International Conference on Legume Genetics and Genomics (ICLGG) From: 9-20-2024 To: 10-3-2024 | |
2025 Soybean Breeders Workshop From: 2-17-2025 To: 2-19-2025 | |
Molecular and Cellular Biology of Soybean (SOY2025) From: 7-23-2025 To: 7-25-2025 | |
International Plant and Animal Genome Conference From: 1-10-2025 To: 1-15-2025 |
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 | ||