diff --git a/misc-scripts/external_db/README b/misc-scripts/external_db/README
index 8433c54489f23567396bf7a0a0cfad2d8927c5a8..a1b0fa6924b245fa842af0a57896cebde51445d0 100644
--- a/misc-scripts/external_db/README
+++ b/misc-scripts/external_db/README
@@ -23,18 +23,37 @@ The master list of external databases is stored in the file:
${ENSEMBL_HOME}/ensembl/misc-scripts/external_db/external_dbs.txt
This file contains a tab-seperated list of values which are loaded into
-the external_db tables. In order the columns are 'external_db_id', 'db_name',
-'release', 'status'. The release column is currently not used by the
-software and is always set to 1. The status must be one of 'XREF', 'KNOWNXREF',
-'KNOWN', 'PRED', 'ORTH', 'PSEUDO'. This is used by the webcode to determine
-which genes/transcripts can be considered to be known or unknown etc.
-
-90 UMCU_Hsapiens_19Kv1 1 XREF
-100 AFFY_HG_U133 1 XREF
-110 AFFY_HG_U95 1 XREF
-120 AFFY_MG_U74 1 XREF
-130 AFFY_MG_U74v2 1 XREF
-140 AFFY_Mu11Ksub 1 XREF
+the external_db tables. In order the columns are:
+ 'external_db_id', 'db_name', 'release', 'status',
+'db_primary_acc_linkable', 'display_label_linkable', 'priority',
+'db_display_name', 'type', 'secondary_db_name', 'secondary_db_table',
+'description'
+
+- external_db_id -- internal identifier for this entry, primary key
+- release -- is currently not used by the software and is always set to 1
+- status -- must be one of 'KNOWNXREF','KNOWN', 'XREF', 'PRED', 'ORTH', 'PSEUDO'.
+This is used by the webcode to determine which genes/transcripts can be considered
+to be known or unknown etc.
+- dbprimary_acc_linkable -- used by the webcode to indicate if the linkable
+element is the internal name in the database (e.g. HGNC_curated_gene)
+- display_label_linkable -- used by the webcode to indicate if the linkable
+element is the name of the database (e.g. WikiGene )
+- priority -- used for the website to indicate priority of display in page
+( the higher the number, the closer to the top of the page)
+- db_display_name -- name to be displayed in the website might be different
+to name of database (e.g. HGNC Symbol rather than HGNC)
+- type -- indicates kind of information the xref database offers (e.g. ALT_GENE
+is used in OTTG to indicate that this external database produces alternative gene from Vega)
+- secondary_db_name --
+- secondary_db_table --
+- description -- free column to describe the external database
+
+...
+12300 HGNC_curated_gene 1 KNOWNXREF 1 0 5 HGNC (curated) MISC \N \N
+12305 HGNC_automatic_gene 1 KNOWNXREF 1 0 5 HGNC (automatic) MISC \N \N
+12310 Clone_based_vega_gene 1 KNOWNXREF 1 0 5 Clone-based (Vega) MISC \N \N
+12315 Clone_based_ensembl_gene 1 XREF 1 0 5 Clone-based (Ensembl) MISC \N \N
+12400 HGNC_curated_transcript 1 KNOWNXREF 1 0 5 HGNC (curated) MISC \N \N
...
@@ -42,65 +61,53 @@ UPDATE PROCEDURE
----------------
The following describes the steps necessary to update the external_db table
-and how to load new mart/GKB xrefs.
+
(1) Add new external database(s) if the appropriate database(s) are not in the
master list:
(a) Add a row to the external_dbs.txt file. The columns must be tab
seperated and the external_db identifier must be unique. The
- release should be set to 1 and the status should reflect the
+ db_release should be set to 1 and the status should reflect the
how xrefs from this external database are used by web.
- For example a new external_db 'AFFY_HG_U101' could be added as the
+ For example a new external_db 'Celera_gene' could be added as the
following:
- 115 AFFY_HG_U101 1 XREF
+
+ 400 Celera_Gene 1 PRED 1 0 5 Celera gene MISC \N \N
(b) Commit the external_dbs.txt file using cvs commit. This is to
ensure that nobody else who may also be updating the file will use
- the same identifier that you chose (in the example ID 115).
-
- (c) Propagate the contents of the file to all of the release databases.
- If not all of the databases have yet arrived on the mysql instance
- then you will have to re-run the propogation script when they get there.
-
- The changes to the list can be applied to all of the databases by
- running the script:
- ${ENSEMBL_HOME}/ensembl/misc-scripts/external_db/update_external_dbs.pl
-
- To update all of the core databases for release 14 (note that vega
- may have to be applied seperately):
-
- perl update_external_dbs.pl -host ecs2d -file external_dbs.txt \
- -user ensadmin -pass secret -release 14
-
- To update the homo_sapiens_core_13_31 and mus_musculus_core_14_30
- databases:
+ the same identifier that you chose (in the example ID 400).
- perl update_external_dbs.pl -host ecs2d -file external_dbs.txt \
- -user ensadmin -pass secret -release 14
- Upon executing the script it will display a list of dbs that the updates
- will be applied and you will have to type 'yes' at a confirmation.
- If the databases to be updated contain rows that are not in the file,
- a warning will be given and the database in question skipped.
+(2) Propagate the contents of the file to all of the core style databases
+(core|cdna|vega|otherfeatures). To update all of the core style databases
+for release 56:
-(2) Add new mart or GKB xrefs. This can be done using the following scripts
- and the appropriate input files from Damian / Imre. It is important to
- ensure that any new external databases have been added as described in
- step 1.
+perl update_external_dbs.pl -host ens-staging -file external_dbs.txt \
+ -user ensadmin -pass secret -release 56
- ${ENSEMBL_HOME}/ensembl/misc-scripts/external_db/load_additional_human_affy_xrefs.pl
-
- ${ENSEMBL_HOME}/ensembl/misc-scripts/external_db/load_additional_human_gkb_xrefs.pl
+To update the human core database:
- These scripts take database connection args for a single db and a filename.
+perl update_external_dbs.pl -host ens-staging -file external_dbs.txt \
+ -user ensadmin -pass secret -dbnames homo_sapiens_core_56_37a
- To load affy xrefs for the homo_sapiens db:
+Upon executing the script it will display a list of dbs that the updates
+will be applied and you will have to type 'yes' at a confirmation.
- perl load_additional_human_affy_xrefs.pl -host ecs2d -user ensadmin \
- -pass secret -port 3306 -dbname homo_sapiens_core_14_31 -file affy.txt
+If the databases to be updated contain rows that are not in the file,
+a warning will be given and the database in question skipped.
+The flag -nonreleasemode it is used when we we want to load the master
+database (use in combination with -master): e.g. we want to create a new
+database with all the external_db from the file
+The flag -force is used to update the databases even there is a difference
+between the master file and the databases. This should only be used when
+we are sure the data in the database is wrong/not necessary and we want to
+overwrite it with the information in the external_db.txt file.
+In Ensembl, the release coordinator is responsible for running this script
+during the release process.