Question: Gene Ontology Database Heirarchy
0
gravatar for Deepak Tanwar
4.8 years ago by
Deepak Tanwar4.1k
ETH Z├╝rich, Switzerland
Deepak Tanwar4.1k wrote:

I am looking for GO hierarchy relationship file.

A file similar to Reactome Pathways Relationship file for GO.

go pathway • 1.2k views
ADD COMMENTlink modified 4.8 years ago by LLTommy1.2k • written 4.8 years ago by Deepak Tanwar4.1k

Expand your question? What is it exactly what you are looking for? All potential relationships in all of GO? The relationships of a specific term? And what for do you need it? There might be easier ways than what Pierre posted, depending on what you are actually looking for.

ADD REPLYlink written 4.8 years ago by LLTommy1.2k
0
gravatar for Pierre Lindenbaum
4.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

using mysql

$ mysql -h  ensembldb.ensembl.org -u anonymous  -A


mysql> select T2.accession,T2.name,T.name,T1.accession,T1.name from term as T1,term as T2, ontology as ONT , relation as R,relation_type as T where ONT.ontology_id=T1.ontology_id and ONT.name="GO" and R.parent_term_id= T1.term_id and R.child_term_id=T2.term_id and T.relation_type_id=R.relation_type_id limit 10;
+-------------+------------------------------------------------+---------+------------+----------------------------------+
| accession   | name                                           | name    | accession  | name                             |
+-------------+------------------------------------------------+---------+------------+----------------------------------+
| GO:0032042  | mitochondrial DNA metabolic process            | part_of | GO:0000002 | mitochondrial genome maintenance |
| GO:0033955  | mitochondrial DNA inheritance                  | is_a    | GO:0000002 | mitochondrial genome maintenance |
| GO:0003006  | developmental process involved in reproduction | part_of | GO:0000003 | reproduction                     |
| GO:0019953  | sexual reproduction                            | is_a    | GO:0000003 | reproduction                     |
| GO:0019954  | asexual reproduction                           | is_a    | GO:0000003 | reproduction                     |
| GO:0022414  | reproductive process                           | part_of | GO:0000003 | reproduction                     |
| GO:0032504  | multicellular organism reproduction            | is_a    | GO:0000003 | reproduction                     |
| GO:0032505  | reproduction of a single-celled organism       | is_a    | GO:0000003 | reproduction                     |
| GO:0051321  | meiotic cell cycle                             | part_of | GO:0000003 | reproduction                     |
| EFO:0002950 | pregnancy                                      | is_a    | GO:0000003 | reproduction                     |
+-------------+------------------------------------------------+---------+------------+----------------------------------+
10 rows in set (0.04 sec)

ADD COMMENTlink written 4.8 years ago by Pierre Lindenbaum133k
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