anopheles.

from the meta table (the meta_key 'species.alias').

    Script to populate the meta table with species aliases.

    The script reads the already existing aliases from the
    meta table (meta_key 'species.alias') and adds to this
    aliases computed from the species name.  It also uses the
    information stored for the meta_keys species.taxonomy_id,
    species.common_name, species.ensembl_common_name, and
    species.ensembl_alias_name as aliases.

    If the -n or --dryrun options are *not* specified, the existing
    list of aliases is deleted from the meta table and the new list
    is inserted.  In any case, the list of aliases will be displayed
    on the console.

    If the -d or --dbname options are *not* used, the script will
    iterate over all Core databases.  If the -d or --dbname option
    *is* used, only that Core database will be examined.

    This script assumes that the database is a single-species
    database.

    This script does not check for alias duplications between
    species.


Usage:
        ./add_species_aliases.pl        [-n] -h dbhost [-P dbport] \
                                        -u dbuser [-p dbpass] \
                                        [-d dbname]

        ./add_species_aliases.pl        -?

Arguments:
        -n/--dryrun             Dry run, don't write to database
        -h/--host dbhost        Database server host name
        -P/--port dbport        Database server port (optional)
        -u/--user dbuser        Database user name
        -p/--pass dbpass        User password (optional)
        -d/--name dbname        Database name (optional)
        -?/--help               Displays this information

# Some aliases are added programatically.
# 1) The "species_name"
# 2) The "species name"
# 3) The "sname" (1+last part)
# 4) The "snam" (1+3 letters)
# 5) The "spenam" (3+3 letters)

# Others are read from the meta table.
# 6) Any species.alias
# 7) The species.taxonomy_id
# 8) The assembly.name
# 9) The species.common_name (if it exists)

Remove hardcoded aliases (these are now in Core meta tables).

Convert tabs to spaces.

Include meta data for patches patch_55_56_[a-d].sql

#
# Title: Add an index to the splicing_event_feature table
#
# Description:
# With an index on transcript_id in splicing_event_feature, the
# generation of biomarts will be sped up.

table.sql updated too.

get_all_Exons( '-constitutive' => 1 ).

db_display_name to "GOSlim GOA".

as well as about how to build the latter.

The script adds one table by subset previously added to the database and
maps all terms to the closest term within that subset.  The tables are
named "aux_XX_YY_map" where "XX" is the ontology ("GO" or "SO"), and
"YY" is the subset name (e.g., "goslim_goa").

The schema for each of the subset map tables is simply as follows:

  +----------------+------------------+------+-----+---------+-------+
  | Field          | Type             | Null | Key | Default | Extra |
  +----------------+------------------+------+-----+---------+-------+
  | term_id        | int(10) unsigned | NO   | PRI | NULL    |       |
  | subset_term_id | int(10) unsigned | NO   | PRI | NULL    |       |
  +----------------+------------------+------+-----+---------+-------+

... where both fields refers into the 'term' table.

http://www.ebi.ac.uk/GOA/rat_release.html.