ontologies_api provides a RESTful interface for accessing BioPortal (an open repository of biomedical ontologies). Supported services include downloads, search, access to terms and concepts, text annotation, and much more.
To configure Solr for ontologies_api usage, modify the example project included with Solr by doing the following:
cd $SOLR_HOME
cp example ncbo
cd $SOLR_HOME/ncbo/solr
mv collection1 core1
cd $SOLR_HOME/ncbo/solr/core1/conf
# Copy NCBO-specific configuration files
cp `bundle show ontologies_linked_data`/config/solr/solrconfig.xml ./
cp `bundle show ontologies_linked_data`/config/solr/schema.xml ./
cd $SOLR_HOME/ncbo/solr
cp -R core1 core2
cp `bundle show ontologies_linked_data`/config/solr/solr.xml ./
# Edit $SOLR_HOME/ncbo/solr/solr.xml
# Find the following lines:
# <core name="NCBO1" config="solrconfig.xml" instanceDir="core1" schema="schema.xml" dataDir="data"/>
# <core name="NCBO2" config="solrconfig.xml" instanceDir="core2" schema="schema.xml" dataDir="data"/>
# Replace the value of `dataDir` in each line with:
# /<your own path to data dir>/core1
# /<your own path to data dir>/core2
# Start solr
java -Dsolr.solr.home=solr -jar start.jar
# Edit the ontologieS_api/config/environments/{env}.rb file to point to your running instance:
# http://localhost:8983/solr/NCBO1
$ git clone git@github.com:ncbo/ontologies_api.git
$ cd ontologies_api
$ bundle install
$ cp config/environments/config.rb.sample config/environments/development.rb
config.rb.sample can be copied and renamed to match whatever environment you're running, e.g.:
production.rb
development.rb
test.rb
Requires a configuration file for the test environment:
$ cp config/environments/config.rb.sample config/environments/test.rb
Execute the suite of tests from the command line:
$ bundle exec rake test
$ bundle exec rackup --port 9393
Once started, the application will be available at localhost:9393.
We encourage contributions! Please check out the contributing guide for guidelines on how to proceed.
The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund under grant U54-HG004028.