Free text search to Concept Wiki URI
Created: 2013-06-24 15:04:27
Last updated: 2013-06-24 15:29:10
Workflow to retrieve target information for the concepts as refered to by humans (the input).
PLEASE DO NOT DISTRIBUTE
Known issues:
It produces error values for the concepts returned by ConceptWiki that are apparently not present in OPS (e.g. for "ezh2" and limit=10, it gives 7/10 error values vs "ezh2 (homo sapiens)" giving 2 valid values).
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Authors (1)
| Marco Roos
Paul Groth
Katy Wolstencroft |
Titles (1)
Descriptions (1)
| Workflow to retrieve target information for the concepts as refered to by humans (the input).
PLEASE DO NOT DISTRIBUTE
Known issues:
It produces error values for the concepts returned by ConceptWiki that are apparently not present in OPS (e.g. for "ezh2" and limit=10, it gives 7/10 error values vs "ezh2 (homo sapiens)" giving 2 valid values). |
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 |
Valuexml |
| concept_wiki_URI_from_free_text_response |
xpath |
extract the target URI from the ConceptWiki output Xpath Expression/result/primaryTopic/result/item/@href |
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 |
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