Difference between revisions of "Main Page"

The "GO" links in the right-hand column of the association view page popup a window on geneontology.org pointing to the GO entry for each association (generally via their unique gene id). These links are exclusively generated by db entries in the dbxref table. To create GO links in the "Associated to" column for any particular association, look up that association's individual dbxref entry and set cols exist_in_go = 1 and go_id = (the value of the xref_key).
This data is not loaded manually, however. There are perl and shell scripts (written by Shuly) in /data/www/plantontology/*_amigo/database/link2go for the purpose of downloading GO associations from DB2GO, creating a mapped list of GO and PO associations, and populating this data into the dbxref tbl as described above. We just have to add the appropriate data source entries in the shell scripts once the folks at GO have verified that they have associations for the data in question.

Formats for the Ontology and Annotation Files

Ontology file format
If your database/project would like to submit annotations to the PO database, please consult the suggested file format: Annotation Association File Format
For more information about how to use column 16: PO_Annotation_Extensions_(column_16)#Specific_suggestions_for_column_16
See also Google docs spread sheet with specific suggestions of what terms and relations to put in column 16.

Other

Calendar (POC outreach schedule)

@@ Line 133: / Line 133: @@
 * [http://palea.cgrb.oregonstate.edu/viewsvn/plantontology/html/docs/dbxref/PO_DBXref.txt?view=markup Database cross reference file on the SVN- current]
 * Custom references maintained by PO, for items without a url. See [[PO references]]
+'''Adding "Associated to" links to GO (final table column in the association view):'''
+* The "GO" links in the right-hand column of the association view page popup a window on geneontology.org pointing to the GO entry for each association (generally via their unique gene id). These links are exclusively generated by db entries in the dbxref table. To create GO links in the "Associated to" column for any particular association, look up that association's individual dbxref entry and set cols '''exist_in_go''' = 1 and '''go_id''' = (the value of the xref_key).
+* This data is not loaded manually, however. There are perl and shell scripts (written by Shuly) in /data/www/plantontology/*_amigo/database/'''link2go''' for the purpose of downloading GO associations from DB2GO, creating a mapped list of GO and PO associations, and populating this data into the dbxref tbl as described above. We just have to add the appropriate data source entries in the shell scripts once the folks at GO have verified that they have associations for the data in question.
 ''' Formats for the Ontology and Annotation Files '''