About tagging

Tagging is act of associating arbitrary keywords with bits of data.

http://en.wikipedia.org/wiki/Folksonomy

User tagging

It's hoped that tagging will be a useful feature for general users. Users will be able to tag objects arbitrarily within an InterMine database and use the tags for organising objects, navigating the data warehouse and for referring to objects in queries. A FlyMine folksonomy (public tagging) would be an interesting experiment.

Configuration tags

Tagging is immediately useful for configuration. Configuration tags always contain a colon character, for example "aspect:Disease". Currently tagging is used to associate elements within the web application with aspects. Things that are currently taggable:

• Classes
  displayed as "starting points" on aspect pages
• Global template queries
  displayed on aspect pages and on object details pages under particular aspect headings
• References and collections
  displayed under particular aspect headings on the object details pages

Tagging is performed by the administrator from within the running InterMine web application. Only the administrator can apply/view/edit tags. The tag data is stored in the user-profile database.

Tagging template queries

Log in to the webapp with the administrator account.

On the History page, go to the "Saved template queries" tab.

Enter the tag "aspect:AspectName" where "AspectName?" is an aspect name and hit Enter/Return or the "Add" button. This will associate the template with the given aspects so that the template appears on the aspect page and in the section of the object details page for that aspect.

Note that you need to match the case and any spaces in aspect title.

Reload any aspect or object details pages you have open to see changes.

Special tags

im:public

The superuser can make his lists and templates available to all users by tagging them with "im:public".

im:frontpage

The superuser can make templates and lists visible on the front page by using the "im:frontpage" tag.

NOTE: they need to also have the "im:public" tag.

im:converter

If the template is tagged with "im:converter", the template can be used by the bag upload page to converter between types. An example is: the user pastes in a protein identifier, but chooses "Gene" from the type drop down menu. A converter template can be used to look up the Gene corresponding to the given Protein.

To work as a converter the template must follow the following pattern:

• the top-level class in the query must be the class we wish to convert from (eg. Gene)
• there must be exactly one editable constraint - the id field of the top level class (eg. Gene.id)
• the fields selected for output must be Gene.id and the id field of the class to convert to

Note that normally the id field isn't shown in the query builder and probably isn't useful in other queries. Only the administrator user can create queries using the id field.

im:preferredBagType

Tags a class to show up first and in bold on the class chooser page.

Tagging classes

You can associate a class with an aspect with an "aspect:AspectName" tag. Apply tags to classes from the "Browse model" page.

Log in as the administrator.

Go to New Query -> Browse model.

Enter the tag, hit the Return/Enter key or the "Add" button.

Refresh aspect pages to see changes.

Tagging collections and references

Log in as the administrator user.

You can assign references and collections to one of more aspects. They will then display under a sub-section for that aspect on object details pages along with template queries and displayers assigned to that aspect.

Choose the class for which you want to tag collections and references. Go to an object details page for an instance that class. Find the collection or reference. It will be listed under the "Miscellaneous" section at the bottom of the page if it has not been tagged.

Remember to refresh the page to see the changes applied.