Free text search to Concept Wiki URI

Created: 2013-06-24 15:04:27 Last updated: 2013-06-24 15:29:10

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Free text search of concept wiki using the Openphacts "Map free text to a concept url based on semantic tag" ie /search/byTag. Search for either compounds or targets depending on the input uuid for "searchType" and filter by source authority with the "branch" input

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http://myexperiment.org/workflows/3628/download?version=3
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (6)

Name	Description
conceptname	concept name (free text search in ConceptWiki)
limit	Limit on the number of results ConceptWiki will return (the output of the whole workflow depends on that, i.e. this number or less).
app_key	OPS Developer API Application Key. Get on from https://dev.openphacts.org
app_id	OPS Developer API Application ID. Generate one at https://dev.openphacts.org
searchType	UUID of the tag concept; required. Specifies the 'semantic type' required for the search results. E.g. 07a84994-e464-4bbf-812a-a4b96fa3d197 for compounds and eeaec894-d856-4106-9fa1-662b1dc6c6f1 for targets
branch	The search results will be filtered by this source authority; optional. Possible values: 1 = Community, 2 = UMLS, 3 = SwissProt, 4 = ChemSpider, 5 = ConceptWiki

Processors (3)

Name	Type	Description
concept_wiki_free_text_to_concept	rest	This OpenPHACTS REST call retrieves the concept URIs from ConceptWiki that match the input query. It is a 'greedy' free text search, i.e. adding more terms will typically produce more precise results.
response_format_as_xml	stringconstant	Value xml
concept_wiki_URI_from_free_text_response	xpath	extract the target URI from the ConceptWiki output Xpath Expression /result/primaryTopic/result/item/@href

Beanshells (0)

Outputs (4)

Name	Description
concept_wiki_xml_response
concept_wiki_concept_uris
concept_wiki_concept_hrefs
request_url

Datalinks (12)

Source	Sink
response_format_as_xml:value	concept_wiki_free_text_to_concept:responseformat
conceptname	concept_wiki_free_text_to_concept:conceptname
limit	concept_wiki_free_text_to_concept:limit
app_id	concept_wiki_free_text_to_concept:app_id
app_key	concept_wiki_free_text_to_concept:app_key
branch	concept_wiki_free_text_to_concept:branch
searchType	concept_wiki_free_text_to_concept:searchType
concept_wiki_free_text_to_concept:responseBody	concept_wiki_URI_from_free_text_response:xml_text
concept_wiki_free_text_to_concept:responseBody	concept_wiki_xml_response
concept_wiki_URI_from_free_text_response:nodelist	concept_wiki_concept_uris
concept_wiki_URI_from_free_text_response:nodelistAsXML	concept_wiki_concept_hrefs
concept_wiki_free_text_to_concept:actualURL	request_url