Talk:Chado New Users

From GMOD

[edit] Meeting Notes

[edit] 20070405

• Tried to work through some of the Central Dogma stuff in Chado Best Practices. Zheng ran the sample query, which hung his laptop.
• Jim created the Problems template Template:Problems for adding notes to documentation pages in the wiki.

[edit] 20070329

Jim was out of town and everyone else attended the Systems Biology meeting

[edit] 20070322

Lincoln was able to attend today. We looked at Chado tables using a combination of phpPgAdmin and command line. To do direct SQL queries in phpPgAdmin, click at the schema level.

Example query:

select f.name, d.*, fd.* from dbxref as  d, feature_dbxref as fd, feature as f where d.dbxref_id = fd.dbxref_id and f.feature_id = fd.feature_id and accession !='SGD'

Gives:

name  | dbxref_id | db_id | accession | version | description | feature_dbxref_id | feature_id | dbxref_id | is_current 
-------+-----------+-------+-----------+---------+-------------+-------------------+------------+-----------+------------
COX2  |     42435 |     2 | landmark  | 1       |             |             16241 |      16241 |     42435 | t
COB   |     42435 |     2 | landmark  | 1       |             |             16176 |      16176 |     42435 | t
COX1  |     42435 |     2 | landmark  | 1       |             |             16129 |      16129 |     42435 | t
RPC40 |     42435 |     2 | landmark  | 1       |             |             15800 |      15800 |     42435 | t
HTS1  |     42435 |     2 | landmark  | 1       |             |             15623 |      15623 |     42435 | t
ERG10 |     42435 |     2 | landmark  | 1       |             |             15474 |      15474 |     42435 | t
PEP4  |     42435 |     2 | landmark  | 1       |             |             15173 |      15173 |     42435 | t
TPK2  |     42435 |     2 | landmark  | 1       |             |             15058 |      15058 |     42435 | t
GAL4  |     42435 |     2 | landmark  | 1       |             |             14960 |      14960 |     42435 | t
RAD17 |     42435 |     2 | landmark  | 1       |             |             14775 |      14775 |     42435 | t

Note that all have the same dbxref_id.

Conclusions

• bulk loaded sample yeast gff3 may not create canonical chado data.
  • features all have dbxref = NULL
    • feature.dbxref_id is nullable; the original design was to have the dbxref_id that appears in the feature table to be the 'primary' dbxref_id. A fairly recent addition was to add a command line flag to the bulk loader to allow the user to specify what (if anything) should be used as feature.dbxref_id. All others go in feature_dbxref.
  • feature_dbxref acts strange (see example above)
    • Not strange at all :-) In typical installations, db_id=2 is the GFF_source that comes from the GFF3 file. If you take a look at the GFF3 that SGD produces, most have a source of 'SGD', but a few have a source of 'landmark', which is used by SGD to put a few gene features in the overview in a GBrowse display.
      • OK, it was a little strange--the GFF bulk loader (and the underlying bioperl module, Bio::FeatureIO::gff) didn't recognize attribute tags of 'dbxref' as dbxref tags (the standard is to use 'Dbxref'. I've modified bioperl and the bulk loader to allow the lowercase, non-standard dbxref now.
  • other?
• should get XML from a known Chado db and import via XORT or other.
  • talk to Pei Li and Eric Just