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

Overviews & Navigation


An overview of new features in YeastMine version 1.1 - new format for template results, new homolog data, an improved GO display, list sharing (2 minutes, 22 seconds; posted 05/31/13)

An overview of YeastMine's major features. For more detailed information on any one of these features, see the tutorials below. (3 minutes, 21 seconds; posted 09/16/11)

A quick sampling of 3 cool features in YeastMine. (1 minute, 7 seconds; revised 01/30/14)
 

 


Data Types


OMIM data has been loaded into SGD's YeastMine. Learn how to search for the human or fungal homolog(s) of your favorite yeast gene, or start with a human gene or disease and find its S. cerevisiae counterparts (2 minutes, 29 seconds; posted 03/04/14)

Fungal Homolog data for 25 different fungal species has been loaded into YeastMine. Learn how to search for the fungal homolog(s) of your favorite S. cerevisiae gene (2 minutes, 03 seconds; posted 09/15/14)
 

 

Templates (Search forms)

 
Learn how to perform searches for different types of data using our pre-defined search templates. (1 minute, 9 seconds; revised 05/02/14)

Modify a pre-defined template to add or remove datatypes from that search. (2 minutes, 12 seconds; revised 08/25/14)

Additional ways you can customize searches to get the data you need. (2 minutes, 52 seconds; revised 09/15/14)

 

Lists


Create a list of gene names (or another datatype) to use in YeastMine searches. (3 minutes; revised 04/29/14)

 


Save search results as lists for use in subsequent searches. (1 minute, 53 seconds; revised 05/19/14)

 


Use a list you've made to perform a search. (1 minute, 47 seconds; revised 09/25/14)

 


Combine and manipulate saved lists to create a new list for analysis or export. (2 minutes, 17 seconds; revised 10/06/14)

Add or remove individual entries from a list. (2 minutes, 20 seconds; posted 11/04/14)
 

 

MyMine


Create your own account in YeastMine to permanently save lists and queries for future use. (2 minutes, 20 seconds; posted 12/04/14)

Make your own search templates and save them for future use. (1 minute, 52 seconds; posted 12/05/14)
 

 

Analysis Tools


Use YeastMine to find shared GO terms among the genes in a list. (2 minutes, 20 seconds; posted 09/13/11

 

   

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