DDBJ Ontologies

DDBJ Ontologies is designed for the conversion of DDBJ-related ontologies and publishing them on the web site. http://ddbj.nig.ac.jp/ontologies/

Generate taxonomy ontology

1. Clone the source code

$ git clone --recursive https://github.com/ddbj/ddbj-ontologies.git

2. Set environment variables(if necessary)

$ cp template.env .env

DDBJ_ONTOLOGIES_CONVERTOR_CONTAINER_NAME

If the container name conflicts with another container, change it. The default value is 'ddbj_ontologies_convertor'

DDBJ_ONTOLOGIES_CONVERTOR_IMAGE_NAME

If the image name conflicts with another image, change it. The default value is 'ddbj_ontologies_convertor'

3. Build a image

$ docker-compose build

4. Download (or copy) the 'taxdump.tar.gz'

$ curl -o data/taxdump/taxdump.tar.gz ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz

If you have a specific version of 'taxdump.tar.gz', coyp it in 'data/taxdump' directory. File names other than 'taxdump.tar.gz' will be ignored.

5. Generate taxonomy ontology via this image

$ docker-compose run --rm convertor /usr/src/app/bin/generate_ontologies_taxonomy_ttl.sh

A turtle file 'taxonomy.ttl' will be generated in the directory 'data/taxonomy/'.

Generate contents file for web site

1. Convert taxonomy turtle file to RDF/XML format

$ docker run --rm -v `pwd`/data/taxonomy:/data ddbj_ontologies_raptor -i turtle -o rdfxml-abbrev /data/taxonomy.ttl > ./data/taxonomy/taxonomy.rdf 2>> ./logs/OwlConverter.log

2. Output static html file

$ docker-compose run --rm convertor /usr/src/app/bin/generate_ontologies_contents.sh

HTML static files will be generated in the directory 'data/contents/'.

Start the web server

1. Set environment variables(if necessary)

$ cp template.env .env

DDBJ_ONTOLOGIES_APP_CONTAINER_NAME

If the container name conflicts with another container, change it. The default value is 'ddbj_ontologies_app'

DDBJ_ONTOLOGIES_APP_IMAGE_NAME

If the image name conflicts with another image, change it. The default value is 'ddbj_ontologies_app'

DDBJ_ONTOLOGIES_APP_ROOT_DIR

The application root directory. If you want to run the application without a container, change it.

DDBJ_ONTOLOGIES_APP_DATA_DIR

The html contents root directory. If you want to run the application without a container, change it.

DDBJ_ONTOLOGIES_APP_PORT

web server port on host

2. Start this container

start with 'docker-compose_web.yml' compose file.

$ docker-compose -f docker-compose_web.yml up -d