MySQL Table Formats¶
schema¶
all_mappings¶
'dbprimary_acc' varchar(512) DEFAULT NULL: primary accession number of
gene from db_name
'display_label' varchar(512) DEFAULT NULL: additional label for gene
used on Ensembl website
'db_name' varchar(100) NOT NULL: name of database where gene
id is taken from
'priority' int(11) NOT NULL: Ensembl priority placed on
db_name
'db_display_name' varchar(255) DEFAULT NULL: additional label for
database
'stable_id' varchar(128) DEFAULT NULL: Ensembl stable gene id that
corresponds to the primary
accession number
'species' varchar(255) DEFAULT NULL: species that gene belongs to
edge¶
'n1_id' varchar(64) NOT NULL: node 1 mapped identifier
'n2_id' varchar(64) NOT NULL: node 2 mapped identifier
'et_name' varchar(80) NOT NULL: name edge type
'weight' float NOT NULL: score for edge type
'edge_hash' varchar(40) NOT NULL: md5 checksum of mapped edge
PRIMARY KEY ('n1_id', 'n2_id', 'et_name')
KEY 'n2_id' ('n2_id')
KEY 'et_name' ('et_name')
edge2line¶
'edge_hash' varchar(40) NOT NULL: md5 checksum of mapped edge
'line_hash' varchar(40) NOT NULL: md5 checksum of original line string
from source
PRIMARY KEY ('edge_hash', 'line_hash')
edge_meta¶
'line_hash' varchar(40) NOT NULL: md5 checksum of original line string
from source
'info_type' varchar(80) NOT NULL: type of metadate ('reference',
'experiment', etc)
'info_desc' varchar(255) NOT NULL: description string of metadata
PRIMARY KEY ('line_hash','info_type','info_desc')
edge_type¶
'et_name' varchar(80) NOT NULL: name of edge type
'n1_type' varchar(12) NOT NULL: type of node 1 ('Gene', 'Property')
'n2_type' varchar(12) NOT NULL: type of node 2 ('Gene', 'Property')
'bidir' tinyint(1) NOT NULL: boolean indicating bidirectionality of
edge
'et_desc' text: description of edge type
'sc_desc' text: description of edge score
'sc_best' float DEFAULT NULL: highest edge score
'sc_worst' float DEFAULT NULL: lowest edge score
PRIMARY KEY ('et_name')
KEY ('n1_type')
KEY ('n2_type')
node¶
'node_id' varchar(64) NOT NULL: node identifier
'n_alias' varchar(512) DEFAULT NULL: alternate name for node
'n_type' varchar(12) DEFAULT NULL: type of node ('Gene', 'Property')
PRIMARY KEY ('node_id')
node_meta¶
'node_id' varchar(64) NOT NULL: mapped node identifier
'info_type' varchar(80) NOT NULL: type of metadata ('alt_alias', 'link',
etc)
'info_desc' varchar(255) NOT NULL: description string of metadata
PRIMARY KEY ('node_id','info_type','info_desc')
node_species¶
'node_id' varchar(64) NOT NULL: mapped node identifier
'taxon' int(11) NOT NULL: taxon id of node species, 0 if property
PRIMARY KEY ('node_id','taxon')
KEY 'taxon' ('taxon')
node_type¶
'n_type' varchar(12) NOT NULL: type of node ('Gene', 'Property')
'n_type_desc' text: description of node type
PRIMARY KEY ('n_type')
raw_file¶
'file_id' varchar(80) NOT NULL: processed name of downloaded
file (source.alias)
'remote_url' varchar(255) NOT NULL: url of file on the remote source
'remote_date' varchar(40) DEFAULT NULL: modification date of file on the
remote source
'remote_version' varchar(40) DEFAULT NULL: release version of the remote
source
'remote_size' bigint(11) DEFAULT NULL: size of file on the remote source
'source_url' varchar(255) DEFAULT NULL: url of the homepage of the source
'image' varchar(255) DEFAULT NULL: url of an image for the source
'reference' varchar(512) DEFAULT NULL: reference for the source
'date_downloaded' datetime NOT NULL: date source was last downloaded
'local_filename' varchar(255) NOT NULL: name of the downloaded file on
local disk
'checksum' varchar(80) DEFAULT NULL: md5 checksum of the downloaded
file
PRIMARY KEY ('file_id')
raw_line¶
'line_hash' varchar(40) NOT NULL: md5 checksum of rawline field
'line num' int(11) NOT NULL: line number in downloaded file
'file_id' varchar(80) NOT NULL: processed name of downloaded file
(source.alias)
'line_str' text NOT NULL: original line string from downloaded source
species¶
'taxon' int(11) NOT NULL: taxon id of organism species
'sp_abbrev' varchar(8) DEFAULT NULL: abbreviated name of species
'sp_sciname' varchar(255) NOT NULL: species scientific name
'representative' varchar(255) DEFAULT NULL: representative species
scientific name
PRIMARY KEY ('taxon')
status¶
'table_hash' varchar(40) NOT NULL: md5 checksum of raw edge generated
from source line
'n1_id' varchar(64) NOT NULL: node 1 mapped identifier
'n2_id' varchar(64) NOT NULL: node 2 mapped identifier
'et_name' varchar(80) NOT NULL: name edge type
'weight' float NOT NULL: score for edge type
'edge_hash' varchar(40) NOT NULL: md5 checksum of mapped edge
'line_hash' varchar(40) NOT NULL: md5 checksum of original line string
from source
'status' varchar(80) NOT NULL: "production" if both nodes mapped
and "unmapped" otherwise
'status_desc' varchar(255) NOT NULL: description of reason for status
label
PRIMARY KEY ('table_hash')
KEY ('status_desc')
KEY ('et_name')