Difference between revisions of "Resource Index Dataset Workflow Howto"

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== Introduction ==
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As of Virtual Appliance v2.2, populating the Resource Index Dataset is no longer supported. A separate Resource Index Virtual Appliance may be released at some point.
 
 
The Resource Index is a system for automated ontology-based annotation and indexing of biomedical data. The application processes the textual metadata of diverse elements of biomedical resources, such as gene expression data sets, descriptions of radiology images, clinical-trial reports, and PubMed abstracts, to annotate and index them with terms from ontologies. The workflow that computes the annotations and indices is run from the shell using a provided shell script.
 
 
 
 
 
== Running the Resource Index Workflow ==
 
 
 
=== Configuring Resources to Process ===
 
By default there are no resources configured to be processed in the Resource Index workflow. Some of the resources are very time-intensive to process, so you should test them to see which ones are appropriate for your use case and feasible to process given your resources.
 
 
 
To configure the resources to be processed by the workflow, do the following:
 
* Login to the NCBO Appliance with the root user.
 
* <code>cd /ncbo/sources/resource_index/workflow/2000</code> - this directory contains the Resource Index workflow code.
 
* Edit the <code>build.properties</code> file.
 
* The last line on the file contains a property called <code>obr.resource.ids</code>. Change this line to include a comma-separated list of the resource identifiers. Possible identifiers are included on the line above in the same file.
 
* <code>cd /ncbo/sources/resource_index/svn/tags/2001</code> - this directory contains the Resource Index client code.
 
* Edit the <code>build.properties</code> file to match the changes
 
* Stop the Tomcat service.
 
* Run <code>ant clean deploywar</code>.
 
* Start the Tomcat service.
 
* Continue with the workflow execution below.
 
 
 
To see a list of resources that NCBO uses, you can visit http://rest.bioontology.org/resource_index/resources
 
 
 
=== Executing the Workflow ===
 
 
 
Execute the following shell commands to build and execute resource index workflow:<br>
 
<pre>
 
[root@example ~]# cd /ncbo/sources/resource_index/workflow/2000/
 
[root@example 2000]# sh ./all.sh
 
</pre>
 
* The script will build the resource index workflow project and create execution environment in the /ncbo/sources/resource_index/workflow/2000/dist/ folder and execute script run.sh
 
* Logs files location:
 
<pre>
 
/ncbo/sources/resource_index/workflow/2000/dist/files/logs/branch1.0/localhost/resource_index
 
</pre>
 
 
 
The application will display its progress in the console as it is running. While it is running, or after it is finished, you can look at the resource_index database to validate that data is actually being processed and written.
 
 
 
=== Database Structure ===
 
The Resource Index Database contains many tables, with a common set of six per processed resource. These resource-specific tables are named with the resource acronym as a prefix. For example, for the WikiPathways resource these are the tables that are populated:
 
* obr_wp_aggregation
 
* obr_wp_annotation
 
* obr_wp_concept_frequency
 
* obr_wp_element
 
* obr_wp_isa_annotation
 
* obr_wp_map_annotation
 
 
 
There is also a common set of tables that are not resource-specific. These include obr_resource, obr_context, obr_dictionary, obr_execution and obr_statistics.
 
 
 
== Initial Population, Ontology Update Population, Resource Update Population ==
 
 
 
The Resource Index can be configured to run the data population in a variety of modes in order to save on processing time. The following are descriptions of the various modes and the flags that need to be set in the build.properties file before running the workflow.
 
 
 
=== Initial Population ===
 
The first time you run the Resource Index workflow, it contains no data about any of the ontologies, terms, or resources that you want to process. Therefore, it is necessary to run the entire workflow just to achieve a minimum state in which the API will function. This type of workflow execution will gather all of the ontology data that's available in OBS/Annotator (ontologies with status 28) and will then process all of the resources configured in the build.properties file.
 
    obs.slave.populate=true
 
    obr.table.index.disabled=true
 
    obr.resources.process=true
 
    obr.update.resource=true
 
    obr.dictionary.complete=true
 
 
 
=== Ontology Update ===
 
When Annotator has processed new ontologies, the resource index must be updated to match. Running this workflow type will update the ontology data to match Annotator and then annotate all of the resources currently present in the database using the newer ontology data.
 
    obs.slave.populate=true
 
    obr.table.index.disabled=true
 
    obr.resources.process=true
 
    obr.update.resource=false
 
    obr.dictionary.complete=false
 
    obs.slave.ontology.remove=true
 
 
 
=== Resource Update ===
 
From time to time the resources used with in the Resource Index will make new information available. Running this workflow type will update the resources that have been configured in the build.properties file. After the resources have been updated, new elements are annotated using the existing ontology data. None of the ontology-related data will be modified.
 
    obs.slave.populate=false
 
    obr.table.index.disabled=false
 
    obr.resources.process=true
 
    obr.update.resource=true
 
    obr.dictionary.complete=true
 
 
 
 
 
== Troubleshooting ==
 
* The shell script may not have execution permissions by default. If this is the case, you will get a permissions error and will have to run the following command to change the permissions: <code>chmod +x ./all.sh</code>
 
* Newly-added ontologies may not appear in the Resource Index API until you restart Tomcat, which can be done by running <code>ncborestart</code>
 
 
 
[[Category:NCBO Virtual Appliance]]
 

Latest revision as of 17:07, 14 January 2015

As of Virtual Appliance v2.2, populating the Resource Index Dataset is no longer supported. A separate Resource Index Virtual Appliance may be released at some point.