Difference between revisions of "GMOD Malaysia 2014/Intermine Tutorial"

Revision as of 18:22, 27 February 2014

The Web Interface

This section focusses on the features of the graphical web interface.

All these tasks will look at FlyMine.

Search

The most basic search interface - the "quick-search" allows unstructured access to data in the system. Information is provided about what type of data is returned, to help narrow the search.

Tasks:

• How many hits are returned for "eve", "alzheimer"?
• Which fly genes match "alzheimer"?

ID Resolution

A more specialised search interface is the ID resolution mechanism that lies at the heart of list uploads. This is critically important for dealing with the kinds of messy identifier lists people often have, and turning them into clean sets of items.

Tasks:

• Upload a set of gene identifiers

Templates

Templates provide a more targeted search, which can be more powerful once you know what you are looking for.

Tasks:

• Find the templates section
• What genes are associates with "Homeo-" domains?
• How many templates are good matches for "protein domain"?
• Can you find the protein domains for the gene "mad"?
• Can you find the protein domains for genes expressed in the Fly ovary? How many are there?

nes.

Templates are frequently used to query against lists of items - choose one from the list of available public lists:

• Which genes have a particularly large number of interactions with your set of genes? What if you are only interested in “suppression” interactions?
• Which orthologue data set has the most orthologues for genes in your list? What if you only look at the orthologues in mosquito?

Using the Report Pages

Report pages allow you to get an overview of the diverse data available for individual items.

Using the Results Tables

The results tables allow you to start exploring once you have begun to query the data.

Using Lists

Lists allow you to store and re-use sets of items.