OPS_FreetextToTargetInfo

Created: 2013-06-18 18:40:28

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Workflow to retrieve target information for the concepts as refered to by humans (the input).

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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http://www.myexperiment.org/workflows/3625/download?version=1
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (4)

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	Application key from OpenPHACTS. A 32 character alphanumeric string. See http://dev.openphacts.org/
app_id	Key identifier from OpenPHACTS, a 8 character alphanumeric string. See dev.openphacts.com.

Processors (8)

Name	Type	Description
OPS_URI_from_Text	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.
responseformat_value	stringconstant	Value xml
metadata_value	stringconstant	Value all
geturls	xpath	extract the target URI from the ConceptWiki output Xpath Expression /result/primaryTopic/result/item/@href
URLencode	beanshell	Script uri = new URI(url); String enc = uri.toASCIIString();
OPS_getTargetInfo	rest
get_prefLabel	xpath	Xpath Expression /result/primaryTopic/prefLabel
get_function	xpath	Xpath Expression /result/primaryTopic/exactMatch/item/Function_Annotation

Beanshells (1)

Name	Description	Inputs	Outputs
URLencode		url	enc

Outputs (5)

Name	Description
conceptwiki_xml
conceptwiki_urls
targetInfo_xml
prefLabel
function

Datalinks (19)

Source	Sink
responseformat_value:value	OPS_URI_from_Text:responseformat
metadata_value:value	OPS_URI_from_Text:metadata
conceptname	OPS_URI_from_Text:conceptname
limit	OPS_URI_from_Text:limit
app_key	OPS_URI_from_Text:app_key
app_id	OPS_URI_from_Text:app_id
OPS_URI_from_Text:responseBody	geturls:xml_text
geturls:nodelist	URLencode:url
responseformat_value:value	OPS_getTargetInfo:responseformat
URLencode:enc	OPS_getTargetInfo:url
app_key	OPS_getTargetInfo:app_key
app_id	OPS_getTargetInfo:app_id
OPS_getTargetInfo:responseBody	get_prefLabel:xml_text
OPS_getTargetInfo:responseBody	get_function:xml_text
OPS_URI_from_Text:responseBody	conceptwiki_xml
geturls:nodelist	conceptwiki_urls
OPS_getTargetInfo:responseBody	targetInfo_xml
get_prefLabel:nodelist	prefLabel
get_function:nodelist	function