The NCBO Resource Index Gem is a Ruby client for NCBO's Rsource Index Web service. The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular concepts. A set of annotations is generated automatically and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations.

gem install ncbo_resource_index

You must always supply an NCBO API Key when using the Resource Index. To get an NCBO API Key, please create an account at NCBO BioPortal.

# Return a set of annotations for a given set of concepts
result = NCBO::ResourceIndex.find_by_concept(["1032/Melanoma"], :apikey => "your API Key")
# Return a set of annotations for a given element/resource pair
result = NCBO::ResourceIndex.find_by_element("E-GEOD-19229", "GEO", :apikey => "your API Key")

ri = NCBO::ResourceIndex.new(:apikey => "your API Key")
result_concept = ri.find_by_concept(["1032/Melanoma"])
result_element = ri.find_by_element("E-GEOD-19229", "GEO")

NCBO::ResourceIndex.resources(:apikey => "your API Key")

The NCBO Resource Index uses a set of ontologies when annotating resources. To see the set currently in use, you can do the following:

NCBO::ResourceIndex.ontologies(:apikey => "your API Key")

The following default options are used with the NCBO Resource Web service via the client.

  @options[:resource_index_location]  = "http://rest.bioontology.org/resource_index/"
  @options[:filterNumber]             = true
  @options[:isStopWordsCaseSensitive] = false
  @options[:isVirtualOntologyId]      = true
  @options[:levelMax]                 = 0
  @options[:longestOnly]              = false
  @options[:ontologiesToExpand]       = []
  @options[:ontologiesToKeepInResult] = []
  @options[:mappingTypes]             = []
  @options[:minTermSize]              = 3
  @options[:scored]                   = true
  @options[:semanticTypes]            = []
  @options[:stopWords]                = []
  @options[:wholeWordOnly]            = true
  @options[:withDefaultStopWords]     = true
  @options[:withSynonyms]             = true
  @options[:conceptids]               = []
  @options[:mode]                     = :union
  @options[:elementid]                = []
  @options[:resourceids]              = []
  @options[:elementDetails]           = false
  @options[:withContext]              = true
  @options[:offset]                   = 0
  @options[:limit]                    = 10
  @options[:format]                   = :xml
  @options[:counts]                   = false
  @options[:request_timeout]          = 300

Default options may be overridden by providing them as follows:

ri = NCBO::ResourceIndex.new(:apikey => "your API Key", :minTermSize => 5, :ontologiesToKeepInResult => [1032, 1084])
ri = NCBO::ResourceIndex.new(:apikey => "your API Key", :wholeWordOnly => false, :levelMax => 2)
ri = NCBO::ResourceIndex.new(:apikey => "your API Key", :semanticTypes => ["T047", "T048", "T191"])

For more information on available option values, please see the NCBO Resource Index Web service documentation.

For questions please email support@bioontology.org.

On Twitter: @palexander, @bioontology

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