Difference between revisions of "UserGuide:WormMine"

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== Lists ==
 
== Lists ==
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WormMine can operate on custom lists of data. You can save lists from results pages or create them by uploading lists of identifiers. Lists can be used when running template queries and analyzed by a series of widgets on a list analysis page. You can merge, subtract and find common members if you have more than one list.
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WormMine includes a set of 'Public' lists (marked with 'PL') that we think might be useful for our users. Some of these originate from external data sources.
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All lists, public ones as well as personal ones (if you are logged in) can be viewed on the Lists page, where you can search them and do operations on them.
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To create a new list yourself, click on 'Lists', and then on 'Upload' in the toolbar on any WormMine page:
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WormMine's list creation tool helps you upload a list of identifiers, the list can contain a mix of identifier types.
  
 
== QueryBuilder ==
 
== QueryBuilder ==

Revision as of 22:35, 30 May 2013

(modified from FlyMine tour)

WormMine is an integrated search tool of WormBase data built with the Intermine data warehouse platform.


Search: type in an identifier or keyword and GO.

Templates: 'canned' queries that others have found useful. The easiest way to learn WormMine query is to modify and customize existing templates. You can create and save your own templates after logging in.

Lists: operate on whole lists of data at once. You can upload lists or save them from results tables. Useful public lists are provided.

QueryBuilder: create custom queries and edit existing templates. QuiryBuilder is very powerful but may demand some learning.

MyMine: create an account to save your own queries, bags and templates, as well as marking public templates as favorites.


Template Query

WormMine provides a library of public template queries - predefined queries designed to perform a particular task. Each one has a description and a form to fill in. For example, there are templates to find genes annotated with a specific GO (GeneOntology) term, genes expressed in a specific tissue (anatomy term).

You can find all WormMine templates on the templates page, accessible via the toolbar on any page. Here you can search the titles and descriptions of all templates.

Anyone can add private (for-your-eyes-only) templates. To create a template:

* Log in
* Construct a query using Query Builder
* Must include at least one constrain condition (e.g. restrict the format of the identifier)
* "Start building a template query"
* Fill in Name, Title and Description, and optionally comment
* Make necessary adjustments, then "Save template"

Lists

WormMine can operate on custom lists of data. You can save lists from results pages or create them by uploading lists of identifiers. Lists can be used when running template queries and analyzed by a series of widgets on a list analysis page. You can merge, subtract and find common members if you have more than one list.

WormMine includes a set of 'Public' lists (marked with 'PL') that we think might be useful for our users. Some of these originate from external data sources.

All lists, public ones as well as personal ones (if you are logged in) can be viewed on the Lists page, where you can search them and do operations on them.

To create a new list yourself, click on 'Lists', and then on 'Upload' in the toolbar on any WormMine page:

WormMine's list creation tool helps you upload a list of identifiers, the list can contain a mix of identifier types.

QueryBuilder

MyMine