This document describes what you have to do to see your calhoun database features in argo.
If you need further help, bug this person.
You have to log on to the database as annotdbo to do the things described in this document.
Have a new subtype you'd like to look at in Argo? Register the subtype in the table: ap_feature_subtype.
FYI: "subtype" is calhounese for "track." From now on, I'll use the term "track" in this document unless I am referring to a specific database entity.
If your new track is similar to an existing track, creating an entry here may be all you need to do. The decisive question is: can one of the existing views display features of your track? If not, you'll have to create a new view.
Argo will have to be restarted to pick up the new track.
You can use the web ui to view and edit existing track information.
To figure out which values to put in view and component view, find a similar exisiting track and use those. Examples: If your feature is a transcript, then 'AP_GENERIC_TRANSCRIPT_VIEW' and 'AP_GENERIC_EXON_VIEW'. If your feature is an alignment, then 'AP_ALIGNMENTSPAN_VIEW' and 'AP_ALIGNMENTSEGMENT_VIEW'.
Your new view will have to have the following fields:
ap_feature_id
, ap_label
, ap_name
, ap_start
, ap_stop
, ap_strand
, ap_sequence_id
, ap_subtype
, ap_length
, ap_sortkey
See ap_generic_feature view for a minimal view that will load in argo.
Argo will display any additonal features as properties/ user settable filtering criteria.
IMPORTANT! Once you have created your view, you will have to create a public synonym so users besides annotdbo can see it. Here is some sample sql for how to do that.
create public synonym AP_CPG_ISLAND_VIEW for annotdbo.AP_CPG_ISLAND_VIEW; grant select on AP_CPG_ISLAND_VIEW to ANNOTATOR; grant select on AP_CPG_ISLAND_VIEW to ANNOTDEV;
Contact: Reinhard Engels argo-support@broad.mit.edu 617-452-2650 320 Charles, Room 2164