Concept profile calculation CPGP

Created: 2014-05-27 11:40:24 Last updated: 2014-06-30 09:21:05

Download Workflow

Part of the CPGP workflow that makes concept pairs, uses these to calculate a contingency table and the uncertainty coefficient. The values generated are inserted into a premade mysql table.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/4298/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
db_properties	Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.

Processors (3)

Name	Type	Description
Calculate Uncertainty Coefficient	workflow	A nested workflow to calculate the Uncertainty coefficient with the contingency values of the concept pairs. The calculated values are afterwards inserted into a SQL table.
Calculate Contincengy table	workflow	A nested workflow that retrieves the values of a 2x2 contingency table and puts the co-occurence of made concept pairs into the SQL table TableName_co_occurence. This is done by creating concept pairs which is retrieved from the Sql table TableName_occurence. This contincengy table consits out of a matrix where two concepts co-occur, concept A only occurs and not concept B, concept B occurs and not concept A and neither concepts occur in literature. B Not B A AB A not A B not A not B This is calculated for every possible concept pair.
table_name	stringconstant	Value alpha

Beanshells (6)

Name	Description	Inputs	Outputs
Beanshell_SQL_INSERT_UC_values_INTO_table	A Beanshell script that generates a SQL statement to insert the calculated values of uncertainty coefficient per concept pair into the table.	timestamp concept_pairs UC_value	output_SQL
Beanshell_calculate_Uncertainty_Coefficient	A Beanshell script that calculates the Uncertainty coefficient based on the script of Herman van Haagen.	corrected_contingency_values	UC_value
Beanshell_SQL_generate_contingency_table	A Beanshell script that generates a SQL statement to retrieve the amount two concepts co-occur, concept A only occurs and not concept B, concept B occurs and not concept A and neither concepts occur in literature. The output of only concept A and only concept B needs to be corrected. This is done in the Beanshell script called: "Beanshell_correct_contincengy_table". Because the output of those two values were with the co-occurence. This needed to be subtracted.	concept_pairs table_name	out1
Beanshell_correct_contincengy_table	A Beanshell script that corrects the output SQL retrieved contincengy table by subtracting the co-occurence values of the concept only a and of concept only b value.	contingency_values	corrected_contingency_values
Beanshell_generate_SQL_statement_Get_destinct_concept	A Beanshell script that retrieves every concept from the Sql table TableName_occurence.	table_name	out1
Beanshell_make_concept_pairs	A Beanshell script that gets as input a list of concepts to create concept pairs.	concept_B concept_A	concept_pair

Outputs (1)

Name	Description
end

Datalinks (7)

Source	Sink
Calculate Contincengy table:outputlist	Calculate Uncertainty Coefficient:concept_pairs
Calculate Contincengy table:corrected_contingency_values	Calculate Uncertainty Coefficient:corrected_contingency_values
db_properties	Calculate Uncertainty Coefficient:propertyString
table_name:value	Calculate Uncertainty Coefficient:timestamp
db_properties	Calculate Contincengy table:propertyString
table_name:value	Calculate Contincengy table:table_name
Calculate Uncertainty Coefficient:output	end