[Genome] go term level

[Kayla Smith]

Hello Pete,

If I understand correctly, you're looking to retrieve data in the form 
of a gene and its highest level ontology.

There are three main term_types in the term table, as shown in this query:

mysql> SELECT DISTINCT term_type, COUNT(*) AS number FROM term GROUP BY 
term_type;
+-----------------------+--------+
| term_type             | number |
+-----------------------+--------+
| association_qualifier |      4 |
| biological_process    |  12905 |
| cellular_component    |   1977 |
| gene_ontology         |      1 |
| molecular_function    |   8050 |
| relationship          |      1 |
| sequence              |      5 |
| subset                |      5 |
| synonym_type          |      5 |
| universal             |      1 |
+-----------------------+--------+

Notice that the main term_types are:  biological_process, 
cellular_component and molecular_function.

Now, let's use your example:

mysql> select * from goaPart where dbObjectId like "O00139";
+------------+----------------+-------+------------+--------+
| dbObjectId | dbObjectSymbol | notId | goId       | aspect |
+------------+----------------+-------+------------+--------+
| O00139     | KIF2A_HUMAN    |       | GO:0000166 | F      |
| O00139     | KIF2A_HUMAN    |       | GO:0003774 | F      |
| O00139     | KIF2A_HUMAN    |       | GO:0003777 | F      |
| O00139     | KIF2A_HUMAN    |       | GO:0005524 | F      |
| O00139     | KIF2A_HUMAN    |       | GO:0005856 | C      |
| O00139     | KIF2A_HUMAN    |       | GO:0005874 | C      |
| O00139     | KIF2A_HUMAN    |       | GO:0005875 | C      |
| O00139     | KIF2A_HUMAN    |       | GO:0007018 | P      |
+------------+----------------+-------+------------+--------+
8 rows in set (0.01 sec)

The goaPart.aspect column is just symbols representing the 3 main 
term_types above.

F = Molecular Function
C = Cellular Component
P = Biological Process

You can see that the gene you are interested in is part of all three of 
the goaPart.aspect values.

Note that in the data you pasted in your email, you already have this 
information displayed.

I hope this information is helpful to you.  If I misunderstood your 
question, or you require further assistance, please don't hesitate to 
contact us again.

Kayla Smith
UCSC Genome Bioinformatics Group


Pete Shepard wrote:
> Good Morning Browser Folks,
> 
> I am using the Table Browser to extract GO terms for a number of genes from
> go.goaPart table and joining this with the go.term field. I am hoping to get
> the level of each term in the ontology. For example, if I enter a single
> Trembleid=dbObjectId (O00139) I get the following output for the cellular
> component ontology:
> 
> #go.goaPart.dbObjectId	go.goaPart.dbObjectSymbol	go.goaPart.aspect	go.term.name	go.term.term_type	go.term.acc
> O00139	KIF2A_HUMAN	C	cytoskeleton	cellular_component	GO:0005856
> O00139	KIF2A_HUMAN	C	microtubule	cellular_component	GO:0005874
> O00139	KIF2A_HUMAN	C	microtubule associated
> complex	cellular_component	GO:0005875
> 
> 
> 
> I am hoping to get the term at the highest level for each ontology. Is
> there a way to accomplish this such as a number associated with each
> term.
> 
> Thank you.
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome