From 96276d3414f2a2a55798e814a71f4acc7f25bcfc Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 23 Jul 2012 15:06:51 +0000
Subject: [PATCH] updated instructions on producing the ontology database
---
misc-scripts/ontology/README | 22 ++++++++++++++++------
1 file changed, 16 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/ontology/README b/misc-scripts/ontology/README
index e23fd41b86..a67643f9cb 100644
--- a/misc-scripts/ontology/README
+++ b/misc-scripts/ontology/README
@@ -258,21 +258,31 @@
for help on usage, it is simple). The script lives in
ensembl/misc-scripts/ontology/scripts/
- e.g.: perl load_OBO_file.pl -h ens-staging1 -u ensadmin -p ensembl -d ensembl_ontology_67 -f GO.obo -o GO
+ e.g.: perl load_OBO_file.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67 -f GO.obo -o GO
- 6. Compute the transitive closure (the 'closure' table in the
+
+ 6. Delete the 'UNKNOWN' ontology row from the ontology table.
+ Once you're finished loading all the ontology files run the load_OBO_file.pl script
+ with option -delete_unknown:
+ e.g.: perl load_OBO_file.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67 -delete_unknown
+
+ The script will delete the dummy ontology if none of the loaded terms are still linked to it.
+ It will report a problem in case it finds any terms linked to the UNKNOWN ontology.
+ This may indicate that you haven't loaded all the files as definitions for some terms are missing.
+
+ 7. Compute the transitive closure (the 'closure' table in the
database) by running the 'compute_closure.pl' in almost the same
way as in step 4. This step may take some time.
- e.g.: perl compute_closure.pl -h ens-staging1 -u ensadmin -p ensembl -d ensembl_ontology_67
+ e.g.: perl compute_closure.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67
- 7. Add the auxiliary map tables by running 'add_subset_maps.pl'
+ 8. Add the auxiliary map tables by running 'add_subset_maps.pl'
with the same arguments that you used for the script in the
previous step.
- e.g.: perl add_subset_maps.pl -h ens-staging1 -u ensadmin -p ensembl -d ensembl_ontology_67
+ e.g.: perl add_subset_maps.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67
- 8. Copy the newly created database to ens-staging2 using ensembl/misc-srcipts/CopyDBOverServer.pl script.
+ 9. Copy the newly created database to ens-staging2 using ensembl/misc-srcipts/CopyDBOverServer.pl script.
$Id$
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