Missing features in Gramene release 19 data

[Gregory Brown]

Hi,

It appears to me that all Rice "BAC", and "Gene Model" data  and some  
"Interpolated Gene", "mmp-unigene", "Maize EST" data is missing from  
both the mysqldump and tabbed data files for CMap release 19. Doing a  
search for all features that are 'bacs' or 'gene-model' from the CMap  
UI returns 0 entries when the same search at Gramene.org Map page  
returns 3438 and 3915 features repectively.  Looking in the Mysql  
database directly there are no entries that correspond to features  
that are 'bac' oe 'int-phen'and then searching either the  
cmap19.mysqldump or tabbed data files (cmap19-txt) show that there  
are no data fields for those feature types.


Would it be possible to re-export the CMap data either completely, or  
just the cmap_feature table?  Thanks.


mysql> SELECT * FROM cmap_feature WHERE feature_type_acc="gene-model"  
OR feature_type_acc = "bac";
Empty set (2.92 sec)

mysql> SELECT count(*) FROM cmap_feature WHERE feature_type_acc =  
"int-phen";
+----------+
| count(*) |
+----------+
|      710 |  There should be 3915 features of this type.
+----------+

mysql> SELECT count(*) FROM cmap_feature WHERE feature_type_acc =  
"mmp-unigene";
+----------+
| count(*) |
+----------+
|    32256 |  There are 39150 mmp-unigene features at Gramene.org
+----------+

mysql> SELECT count(*) FROM cmap_feature WHERE feature_type_acc =  
"maize-est";
+----------+
| count(*) |
+----------+
|     5052 |  There are 191,819 Maize EST features at Gramene.org
+----------+


< 47 > awk '{print $9}' cmap_feature.txt | egrep -c "^bac"
0
< 49 > awk '{print $9}' cmap_feature.txt | egrep -c "gene-model"
0

Greg Brown