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TreeFam
TreeFam
- James Estill
Owned by James Estill
TreeFam: http://www.treefam.org/#introduction
I could not find an overview of the TreeFam schema by google searching. so I did .
$mysql -uanonymous -P3308 -hdb.treefam.org
mysql> show databases;
+--------------------+
| Database |
+--------------------+
| information_schema |
| treefam_3 |
| treefam_4 |
| treefam_5 |
| treefam_6 |
| treefam_7 |
| treefam_8 |
| treefam_test |
| treefamweb_2 |
+--------------------+
mysql>use treefam_8;
mysql>show tables;
+------------------------+
| Tables_in_treefam_8 |
+------------------------+
| aa_full_align |
| aa_seed_align |
| aa_seq |
| core_species |
| cur_comment |
| ens_ext_db |
| ens_xref |
| exp_map |
| famB2A |
| fam_cluster |
| fam_genes |
| fam_hmm |
| familyA |
| familyB |
| familyC |
| genes |
| hmmer |
| hmmer_matches |
| map |
| misc_feat |
| misc_key |
| nt_seq |
| ortholog |
| pfam |
| phigs |
| spec_names |
| spec_nodes |
| species |
| statistics |
| tf_gnfAtlas2 |
| tf_gnfAtlas2MedianExps |
| tff_fam |
| tff_node_info |
| tff_topology |
| trees |
+------------------------+
mysql> show columns from trees;
+-------+-------------------------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------+-------------------------------------+------+-----+---------+-------+
| AC | char(8) | NO | PRI | | |
| TYPE | enum('SEED','FULL','WHOLE','CLEAN') | NO | PRI | SEED | |
| TREE | mediumtext | NO | | | |
+-------+-------------------------------------+------+-----+---------+-------+
3 rows in set (0.18 sec)
mysql> show columns from species;
+---------+-----------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+---------+-----------------------+------+-----+---------+-------+
| TAX_ID | int(10) unsigned | NO | PRI | 0 | |
| TAXNAME | varchar(45) | NO | MUL | | |
| SWCODE | varchar(5) | NO | UNI | | |
| KINGDOM | enum('E','V','A','B') | NO | | E | |
| FLAG | tinyint(3) unsigned | NO | | 0 | |
| COMMON | varchar(45) | NO | | | |
| SYNONYM | varchar(45) | NO | | | |
+---------+-----------------------+------+-----+---------+-------+
7 rows in set (0.12 sec)
mysql> show columns from spec_nodes;
+-------------+------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------------+------------------+------+-----+---------+-------+
| taxon_id | int(10) unsigned | NO | PRI | 0 | |
| parent_id | int(10) unsigned | NO | MUL | 0 | |
| name | varchar(255) | YES | MUL | NULL | |
| rank | char(32) | NO | | | |
| genbankflag | tinyint(1) | NO | | 0 | |
+-------------+------------------+------+-----+---------+-------+
5 rows in set (0.11 sec)
mysql> show columns from spec_names;
+------------+------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+------------+------------------+------+-----+---------+-------+
| taxon_id | int(10) unsigned | NO | MUL | 0 | |
| name | varchar(255) | YES | MUL | NULL | |
| name_class | varchar(50) | YES | MUL | NULL | |
| swcode | varchar(10) | YES | MUL | NULL | |
+------------+------------------+------+-----+---------+-------+
4 rows in set (0.12 sec)
mysql> show columns from ortholog;
+-----------+----------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------+----------------------+------+-----+---------+-------+
| idx1 | int(11) | NO | PRI | 0 | |
| idx2 | int(11) | NO | PRI | 0 | |
| taxon_id | int(10) unsigned | NO | | 0 | |
| bootstrap | smallint(5) unsigned | NO | | 0 | |
+-----------+----------------------+------+-----+---------+-------+
4 rows in set (0.12 sec)
mysql> show columns from tff_fam;
+-----------+----------------------------------------------+------+-----+----------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------+----------------------------------------------+------+-----+----------+-------+
| tree_id | int(10) unsigned | NO | PRI | 0 | |
| ac | char(8) | NO | MUL | TF000000 | |
| tree_type | enum('ASEED','SEED','FULL','CLEAN','CCLEAN') | NO | | ASEED | |
+-----------+----------------------------------------------+------+-----+----------+-------+
3 rows in set (0.12 sec)
mysql> show columns from tff_topology;
+------------+----------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+------------+----------------------+------+-----+---------+-------+
| tree_id | int(10) unsigned | NO | PRI | 0 | |
| node_id | smallint(5) unsigned | NO | PRI | 0 | |
| parent_id | smallint(5) unsigned | NO | MUL | 0 | |
| branch_len | float | NO | | 0 | |
+------------+----------------------+------+-----+---------+-------+
4 rows in set (0.12 sec)
mysql> show columns from tff_node_info;
+----------+----------------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+----------+----------------------+------+-----+---------+-------+
| tree_id | int(10) unsigned | NO | PRI | 0 | |
| node_id | smallint(5) unsigned | NO | PRI | 0 | |
| node_key | varchar(31) | NO | PRI | | |
| node_val | varchar(255) | NO | | | |
+----------+----------------------+------+-----+---------+-------+
4 rows in set (0.11 sec)
mysql> show columns from pfam;
+-----------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------+-------------+------+-----+---------+-------+
| ID | varchar(64) | NO | PRI | | |
| PFAM_ID | varchar(7) | NO | PRI | | |
| SEQ_START | int(11) | NO | PRI | 0 | |
| SEQ_END | int(11) | NO | PRI | 0 | |
| PF_START | int(11) | NO | | 0 | |
| PF_END | int(11) | NO | | 0 | |
| EVALUE | double | NO | | 0 | |
+-----------+-------------+------+-----+---------+-------+
7 rows in set (0.13 sec)