ThaleMine User Guide

  1. Welcome to ThaleMine
  2. Search
  3. Data Sources
  4. Template Queries
  5. Results Page
  6. Regions
  7. Lists
  8. Query Builder
  9. MyMine
  10. Thalemine Data Statistics 


Welcome to ThaleMine 

ThaleMine is an instance of InterMine, offering quick and easy searching and browsing
of data found in Araport. This user guide will introduce you to some basic features.

Search: Available at the top of all pages, type an identifier or keyword to see a report page.

Templates: Preset search forms that allow you to query different data types.

Lists: Act on entire lists of data at once. Upload your own list, save one from a results tables or use one of our pre-computed lists.

QueryBuilder: Create custom queries or modify existing templates.

Regions: Find features that overlap a list of genome coordinates you enter or upload.

MyMine: Create an account to save your own lists, templates and queries.


Search 

A search box is found on the homepage as well as the header of every page.

search



Search results can be filtered by Categories.

categories



Once a Category is selected you can save the results directly to a List.

categories_list



Clicking on a feature brings you to a Report Page containing many data-types and pre-computed Template Queries.

results



Data Sources 

ThaleMine integrates data from a large number of sources into a single data warehouse. This section lists the data that are
included in the current release. Many more data sets will be added in future releases, please contact us if there are any
particular data you would like to see included.

Data Sources



Template Queries 

These preset search forms have been created to perform common tasks. If you think we are missing any important
Templates just let us know.

templates



You can find a Template of interest by filtering for keyword or category.

templates-filter



This particular template takes a Gene as input and returns all Proteins for that Gene. Enter an idenifier, symbol or synonym
and ThaleMine will try to find the right gene. Templates can also search Lists.

templates-form



Results Page 

Results tables provide a range of ways to view, filter and download data. This particular result comes from the Template
Sample Property --> Expressions. Columns can be sorted, re-arranged, added, hidden or summarized using the Manage
Columns button and Icons at the top of Columns. Filters can be applied through Manage Columns, Filters or with
the Summarize Column Icon. You can create a new List with your results or add them to an existing List.

results-page



The Download button enables you to retrieve your results in a number of formats and save them to your computer, send
them to Galaxy, or upload them to your Genomespace account.

download-formatsdownload-download



Regions 

The Regions Search enables exploration of features contained within a genomic interval or set of regions.

regions-toolbar



You can specify the types of features to search for. All features are selected by default. Deselect any features you are not
interested in or un-check Select Feature Types to turn off all features and re-select those that are relevant.

regions-select



You can either type, cut and paste or upload the genomic regions from a file. Each region should be on a new line and the
following formats are accepted:

  • chromosome:start..end, e.g. Chr1:29733..37349
  • chromosome:start-end, e.g. Chr2:393758-394189
  • tab delimited, e.g. Chr4 1495567 1503324


regions-format



Finally, you can choose to extend your regions by any specified length.

regions-extend



Search results are reported in table format with results displayed separately for each interval. You can export results in a
range of formats, or create Lists of any particular feature type. Exports and Lists can be performed either per region or for
the entire set. Clicking a Feature will take you to its Report Page.

regions-results



Lists 

We have already seen that ThaleMine provides a number of ways to create Lists of data. You can save Lists from results pages
or create them by uploading identifiers.

Identifiers can be uploaded from the home page

lists-analyse



or in the Lists tab.

lists-toolbar



Query Builder 

The QueryBuilder allows you to construct your own custom searches, modify your previous searches and edit Templates.
It can be accessed through its tab in the menu bar

querybuilder-toolbar



or from the Edit Query button on each template form. The QueryBuilder is aimed at advanced users but editing a
Template to change the output or add a filter is relatively easy and a good place to start.

querybuilder-template



The QueryBuilder is composed of 4 distinct areas.

  1. The Model Browser pane is a view of the data model starting at the Probe class. ThaleMine uses an object based
    model - biological types are termed 'classes' and individual entries are termed 'objects'. For example the PISTILLATA
    and AGAMOUS genes are both objects in the class Gene.
  2. The Query Overview pane shows a summary of the query. Fields selected to be in the results are in boxes and
    the constraints are shown in purple.
  3. The Constraint Editor allows you to modify the logic of your constraints.
  4. In Fields Selected for Output you can quickly arrange, sort and remove Columns from the Results Table.


querybuilder-overview



Building or editing a query involves three main steps:

  • Navigating the data model to find the classes and fields of data you are interested in --> you can click '+' to open related
    classes and see their attributes.
  • Selecting the data you wish to see in your results --> use the 'show' buttons to add fields to the results output
    and 'x' to remove fields.
  • Refining the query with a set of constraints or filters --> use the 'constrain' buttons to refine your search,
    click 'edit' to edit current Constraints or 'x' to remove them.



MyMine 

A MyMine account allows you to permanently save all Lists and Queries you run. Creating your own account is quick
and easy, just provide an email address and password to generate an account. No other information is
required and your data is always private.

Log in



You can access your Lists, Templates and Queries from the MyMine tab.

MyMine



While signed into your account, you can filter Templates by your favorites or by Templates you have created and saved.

MyMine_templates


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Araport Workshop Hands-on (for UMD2014)