[Genome] data inconsistence from table browser and mysql server

[Kayla Smith]

Hello Tao,

The two databases you are accessing in your question are not necessarily 
kept in sync with each other.   When you use any of the genbank tables, 
you should stay within one instance of a database.

To illustrate that the author is consistent between the two methods you 
mentioned below, let me paste some queries:

 From the mysql server:

mysql> select id, name from author where id = 173413;
+--------+-----------------------------------------------------------------------------------------------------------------------------------+
| id     | name 
      |
+--------+-----------------------------------------------------------------------------------------------------------------------------------+
| 173413 | Tsuritani,K., Irie,T., Yamashita,R., Sakakibara,Y., 
Wakaguri,H., Kanai,A., Mizushima-Sugano,J., Sugano,S., Nakai,K. and 
Suzuki,Y. |
+--------+-----------------------------------------------------------------------------------------------------------------------------------+
1 row in set (0.11 sec)


And from the Table Browser:

Clade: Vertebrate, Genome: Human, Assembly: May 2004, grlup: All Tables, 
database: hg17, table: author

Paste list:  173412

#id	name	crc
173412	Tsuritani,K., Irie,T., Yamashita,R., Sakakibara,Y., Wakaguri,H., 
Kanai,A., Mizushima-Sugano,J., Sugano,S., Nakai,K. and Suzuki,Y.	2746902304

You can see from this that the data in the authors table agree.

I hope this is helpful for understand the data.  Please don't hesitate 
to contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Tao Peng wrote:
> Dear colleague,
> 
> I want to retrieve cDNA information from UCSC genome browser. To do this, I
> tried two methods. One is by table browser and the other is by querying
> directly with mysql server. But I found some results with these two methods
> are inconsistent.
> 
> For example, I query the EST BP870449 in both table browser and mysql
> server.
> 
> 1) By table browser:
> Clade: Vertebrate Genome: Human  assembly: May 2004
> group: mRNA and EST Tracks          track: Human ESTs
> table: gbCdnaInfo
> Paste list:  BP870449
> result:
> #id    acc    version    moddate    type    direction    source
> organism    library    mrnaClone    sex    tissue   development    cell
> cds    keyword    description    geneName    productName    author    gi
> mol
> 13582040    BP870449    1    2007-06-17    EST    5    293    292
> 18113     9788246    0    6731    0    866    0  42740    0    0    0
> 173412    50713749    mRNA
> 
> 2) By mysql server:            mysql --user=genome --host=
> genome-mysql.cse.ucsc.edu -A
> use hg17;
> select * from gbCdnaInfo where or acc='BP870449'
> result:
> +----------+----------+---------+------------+------+-----------+--------+----------+---------+-----------+-----+--------+-------------+------+-----+---------+-------------+----------+-------------+--------+----------+------+
> | id       | acc      | version | moddate    | type | direction | source |
> organism | library | mrnaClone | sex | tissue | development | cell | cds |
> keyword | description | geneName | productName | author | gi       | mol  |
> +----------+----------+---------+------------+------+-----------+--------+----------+---------+-----------+-----+--------+-------------+------+-----+---------+-------------+----------+-------------+--------+----------+------+
> | 13582040 | BP870449 |       1 | 2007-06-17 | EST  | 5         |    293
> |      292 |   18113 |   9788246 |   0 |   6731 |           0 |  866 |   0
> |   42740 |           0 |        0 |           0 | 173413 | 50713749 | mRNA
> |
> +----------+----------+---------+------------+------+-----------+--------+----------+---------+-----------+-----+--------+-------------+------+-----+---------+-------------+----------+-------------+--------+----------+------+
> 
> You can see that the 'author' field in table browser result is 173412, while
> in mysql server result, it's 173413.
> 
> I'm not sure whether there are other inconsistence. Could anyone tell my
> why?
> 
> Thank you very much!
> 
> 
>