ontologies_api_client

Models and serializers for ontologies and related artifacts backed by an AllegroGraph or a 4store database. This library can be used for interacting with an AllegroGraph or a 4store instance that stores BioPortal ontology data. Models in the library are based on Graph Oriented Objects for Ruby (Goo). Serializers support RDF serialization as Rack Middleware and automatic generation of hypermedia links.

gem install ontologies_api_client

Configuration is provided by calling the config method

require 'ontologies_api_client'
LinkedData::Client.config do |config|
  config.rest_url   = "http://stagedata.bioontology.org"
  config.apikey     = "your_apikey"
  config.links_attr = "links"
  config.cache      = false
end

Once configured, you can utilize the existing resources that are defined (see lib/ontologies_api_client/models) to access a resource, its information, and related resources.

There are multiple ways to retrieve individual or groups of resources.

Find

To retrieve a single record by ID:

Category.find("http://data.bioontology.org/categories/all_organisms")

Where

To retrieve all records that match a particular in-code filter:

categories = Category.where do |ont|
  ont.name.include?("health")
end

The code is a block that should return a boolean that indicates whether or not the item should be included in the results.

Find By

Use shortcut methods to find by particular attribute/value pairs:

categories = Category.find_by_parentCategory("http://data.bioontology.org/categories/anatomy")

Attributes are named in the method and multiple can be provided by connecting them with 'and'.

Creates are done via HTTP POST, update via HTTP PATCH, and deletes using HTTP DELETE.

ontology_values = {
  acronym: "MY_ONT",
  name: "My Ontology",
  administeredBy: [http://data.bioontology.org/users/my_user]
}
ontology = LinkedData::Client::Models::Ontology.new(values: ontology_values)
response = ontology.save
puts ontology_saved.errors

new_values = {
  administeredBy: [http://data.bioontology.org/users/my_other_user]
}
ontology = LinkedData::Client::Models::Ontology.find_by_acronym("MY_ONT")
ontology.update_from_params(params[:ontology])
response = ontology.update
puts response.errors

ontology = LinkedData::Client::Models::Ontology.find_by_acronym("MY_ONT")
response = ontology.delete

All resources have a collection of hypermedia links, available by calling the 'links' method. These links can be navigated by calling the 'explore' method and chaining the link:

ontology = Category.find("http://data.bioontology.org/categories/all_organisms")
classes = ontology.explore.classes

Links may contain a URI template. In this case, the template can be populated by passing in ordered values for the template tokens:

cls = ontology.explore.single_class("http://my.class.id/class1")

The client is designed to consume resources from the NCBO Ontologies API. Resources are defined in the client using media types that we know about and providing attribute names that we want to retreive for each media type.

For example:

class Category < LinkedData::Client::Base
  include LinkedData::Client::Collection
  @media_type = "http://data.bioontology.org/metadata/Category"
end

Resources that are available via collections should include the Collection mixin (LinkedData::Client::Collection). By 'collection', we mean that the all resources are available at a single endpoint. For example, 'Ontology' is a resource with collections because you can see all ontologgies at the "/ontologies" URL.

Resources that should have save, update, and delete methods will need to include the ReadWrite mixin (LinkedData::Client::ReadWrite).

For questions please email support@bioontology.org

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