Gene Ontology Database Heirarchy

Question

[Deepak Tanwar]

I am looking for GO hierarchy relationship file.

A file similar to Reactome Pathways Relationship file for GO.

[LLTommy]

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.

Answer 1

[Pierre Lindenbaum]

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)