SoyBase
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Integrating Genetics and Genomics to Advance Soybean Research
SoyBase
Follow us on Twitter @SoyBaseDatabase
| Community News | ||
|---|---|---|
| Soybean Pangenome Search Page Available Posted on Tuesday, July 30th, 2019 From the Pangenome search page you can compare your sequence or sequences of interest to a number of other De Novo sequenced soybean cultivars (G. max or G. soja). This type of analysis will allow users the ability to see how sequences evolved (were eliminated or were retained) in the various soybean cultivars. | ||
| Expression Study GSE42550 available in the SoyBase Genome Viewer Posted on Tuesday, June 18th, 2019 GSE42550 "Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling" is now browsable on the SoyBase Genome Viewer. This experiment profiles gene expression in cotyledons at 7 developmental stages. The experiment can be browsed HERE under the label of "Expression profiling Williams cotyledon development". | ||
| Expression data from GSE42871 added to the SoyBase Genome Viewer Posted on Wednesday, June 12th, 2019 | ||
| Paretage of 2018 Southern Uniform Soybean tests added to parentage database Posted on Wednesday, June 12th, 2019 | ||
| Precision Genomics and Soybean Mutant Finder Day 2019 deadline Posted on Monday, June 10th, 2019 | ||
| David Grant Retirement Posted on Wednesday, May 29th, 2019 | ||
| Research Geneticist position open in Raleigh, NC Posted on Tuesday, May 28th, 2019 | ||
| Expression study of control and defective seed coats available in the SoyBase Genome Viewer Posted on Monday, May 20th, 2019 | ||
| Expression data from GSE89126 added to the SoyBase Genome Browser Posted on Wednesday, May 15th, 2019 | ||
| Pedigrees added to SoyBase Pedigree Database Posted on Wednesday, May 8th, 2019 | ||
| Upcoming Events | |
|---|---|
| World Soybean Research Conference XI From: 9-6-2020 To: 9-11-2020 | |
| 2020 Soybean Breeders' Workshop From: 2-10-2020 To: 2-12-2020 | |
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 |
|---|---|
| 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.
