Tagging

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. Currently taggable:

• Classes - displayed as "starting points" on aspect pages
• Template queries - displayed on aspect and report pages under particular aspect headings
• References and collections - displayed under particular aspect headings on the report 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.

Special tags

im:public - The superuser can make lists and templates available to all users by tagging them with the im:public tag.

im:frontpage - The superuser can make templates and lists visible on the front page by using the im:frontpage tag. NOTE: templates must also be tagged as im:public to appear on the front page.

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.

placement:summary - Tags a field to appear in the summary section of the report page.

Tagging template queries

Log in to the webapp with the administrator account and navigate to the "Saved template queries" tab in MyMine.

Enter the tag aspect:AspectName where AspectName is an aspect name and then click 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 the aspect title is case sensitive.

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.