Difference between revisions of "Populating OBS database"

From NCBO Wiki
Jump to navigation Jump to search
(New page: = Population of the OBS database = The OBS database contains the data used by the OBA/OBR workflow. It contains the concepts and terms used for direct annotations as well as the relations...)
 
 
(One intermediate revision by the same user not shown)
Line 5: Line 5:
  
 
To populate an OBS DB used the Populate.java or PopulateObsTablesTest.java programs.
 
To populate an OBS DB used the Populate.java or PopulateObsTablesTest.java programs.
 +
 +
Optra & Clement are working on a instruction document to be posted here soon.
 +
Image Resource: [[Image:PopulationOBStables.png|thumb|Population of OBS tables workflow]]
 +
Image Resource: [[Image:AccessNewOntologies.png|thumb|Access new ontologies]]
 +
Image Resource: [[Image:PopulateAllTables.png|thumb|Populate all tables]]
 +
 +
= OBS workflow execution logs =
 +
 +
Text file resource: [[Image:PopulateOBSv1_update_sept2009.txt.doc]]
 +
 +
Text file resource: [[Image:PopulateOBSv1_update_may2009.txt.doc]]

Latest revision as of 09:27, 18 September 2009

Population of the OBS database

The OBS database contains the data used by the OBA/OBR workflow. It contains the concepts and terms used for direct annotations as well as the relations between concepts used during the semantic expansion step. The OBS DB is populated using 3 access tools (ObsUmlsAccessTool, ObsBioPortalAccessTool and ObsJaxAccessTool) that implement a common interface (ObsOntologyAccess). The OBS DB is accessed using a tool called ObsOntologiesAccessTool that implements also the same interface. cf. http://obs.bioontology.org/docs/model/EARoot/EA3/EA67.htm

To populate an OBS DB used the Populate.java or PopulateObsTablesTest.java programs.

Optra & Clement are working on a instruction document to be posted here soon.

Image Resource:

Error creating thumbnail: /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 61: ulimit: cpu time: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 84: ulimit: virtual memory: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 90: ulimit: file size: cannot modify limit: Permission denied /bin/bash: /usr/bin/convert: No such file or directory Error code: 127
Population of OBS tables workflow

Image Resource:

Error creating thumbnail: /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 61: ulimit: cpu time: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 84: ulimit: virtual memory: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 90: ulimit: file size: cannot modify limit: Permission denied /bin/bash: /usr/bin/convert: No such file or directory Error code: 127
Access new ontologies

Image Resource:

Error creating thumbnail: /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 61: ulimit: cpu time: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 84: ulimit: virtual memory: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 90: ulimit: file size: cannot modify limit: Permission denied /bin/bash: /usr/bin/convert: No such file or directory Error code: 127
Populate all tables

OBS workflow execution logs

Text file resource: File:PopulateOBSv1 update sept2009.txt.doc

Text file resource: File:PopulateOBSv1 update may2009.txt.doc

Retrieved from "https://www.bioontology.org//mediawiki/index.php?title=Populating_OBS_database&oldid=9192"