Bioportal Importer

Some ruby code to import metadata of ontologies and submissions from bioontology.org into a local SQLite Database.

Requirements

You need Ruby 2.0 and sqlite3

Installation

git clone git://github.com/ontohub/bioportal_importer.git
cd bioportal_importer
bundle install

Configuration

Copy the config.yml.sample to config.yml and fill in your credentials.

cp config.yml.sample config.yml

If you want to specify a mapping of categories from bioportal to categories from bioportal, then create a category-mapping.csv in the project repository with the following columns:

acronym,target1,target2,target3
Chemical,Chemistry,Biochemistry,
Mouse_Anatomy,Space,Biology,Veterinary

A bioportal category can map to multiple ontohub categories. Just add as many target* columns as you want.

Usage

Start the interactive ruby console:

./console

Download metadata of ontologies and submissions:

Bioportal.import_all

Download the file for each sumission:

Bioportal::Downloader.run

Create a repository with all downloaded submissions of ontologies below 1 megabyte:

Bioportal.reset_workspace
Bioportal::Submission.uncommitted.downloaded.order(:created_at).each do |s|
    s.commit if s.ontology.max_filesize < 1024*1024
end

Now you can find the repository in ./workspace/.git

After pushing the repository to Ontohub you can update the ontologies metadata at Ontohub:

Ontohub::API.instance.update_metadata