SGD Video Tutorials: YeastMine

YeastMine is a data search and retrieval tool that incorporates the many different types of data present in SGD and allows users to query that data in different combinations, facilitating analysis. Datatypes that can be queried in YeastMine include chromosomal features, sequences, protein features, GO annotations, phenotypes, interaction data, expression data, and curated literature. SGD has provided a variety of pre-defined queries, termed "Templates," to help you access different types of data. The results of a query can be saved as a "List" that can be organized into suitable tables, edited, exported, and even combined, subtracted, or intersected with other Lists of the same datatype.

Because YeastMine allows flexible searching, you can also modify existing Templates to create a new query, or design custom Templates using the "QueryBuilder" tool. QueryBuilder allows you to construct a query from scratch by displaying an interactive browser, within YeastMine, to selectively apply constraints and specify your desired output.

Lastly, creating a personal "MyMine" account allows you to permanently save your Lists, Queries, and Templates for future use. The following tutorials demonstrate how YeastMine can be used for data acquisition and analysis, and highlight the many uses of this tool.

Contents

  1. Overviews & Navigation
  2. Data Types
  3. Templates (Search forms)
  4. Lists
  5. MyMine
  6. Analysis Tools
  7. Webinars & Scenarios

Overviews & Navigation

A quick sampling of 3 cool features in YeastMine. (1:07; created 1/29/14)
An overview of YeastMine's major features. (3:21; created 7/17/14)

Data Types

Search the OMIM-based human-to-fungal or fungal-to-human homologs in YeastMine. (2:28; created 3/5/14)
Fungal Homolog data for 25 different fungal species has been loaded into YeastMine. (2:13; created 9/15/14)
 

Templates (Search forms)

Learn how to perform searches for different types of data using our pre-defined search templates. (1:09; created 5/2/14)
Modify a pre-defined template to add or remove datatypes from that search. (2:12; created 8/25/14)
Additional ways you can customize searches to get the data you need. (2:52; created 9/15/14)

Lists

Create a list of gene names (or another datatype) to use in YeastMine searches. (3:00; created 4/29/14)
Save search results as lists for use in subsequent searches. (1:53; created 5/19/14)
Use a list you've made to perform a search. (1:47; created 9/25/14)
Combine and manipulate saved lists to create a new list for analysis or export. (2:16; created 10/6/14)
Add or remove individual entries from a list. (2:19; created 11/3/14)
 

MyMine

Create your own account in YeastMine to permanently save lists and queries for future use. (2:20; created 12/4/14)
Make your own search templates and save them for future use. (1:52; created 12/5/14)
 

Analysis Tools

Use YeastMine to find shared GO terms among the genes in a list. (2:13; created 1/7/15)
   

Webinars & Scenarios

Use YeastMine to find potentially undiscovered subunits of the mitochondria. (6:29; created 3/17/16)
SGD's second webinar demonstrates the use of YeastMine in a cancer therapy application. (16:49; created 5/5/16)
 

 

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