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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.

Install

gem install ontologies_api_client

Configuration

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

Usage

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.

Retrieval

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'.

Create / Update / Delete

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

Create

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

Update

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

Delete

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

Hypermedia Navigation

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")

Defining Resources

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

Collections

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.

Read/Write

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

Questions

For questions please email [email protected]

License

Copyright (c) 2024, The Board of Trustees of Leland Stanford Junior University All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE BOARD OF TRUSTEES OF LELAND STANFORD JUNIOR UNIVERSITY ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL The Board of Trustees of Leland Stanford Junior University OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of The Board of Trustees of Leland Stanford Junior University.