Concept profile calculation CPGP

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

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Requirements:

Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader.

Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI

Change lvg.properties LVG_DIR=/home/path/to/lvg2013lite/ This file can be found in:

/home/path/to/lvg2013lite/data/config/lvg.properties

Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI

Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI

Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer.

If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale. Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c. Please make sure this is also set into the indexer tool part.

Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows.

The nested workflow Get_abstract uses a sql command to retrieve abstracts which assumes are located in the database mydb. If this is not the case, please change the database in the SQL value.

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Descriptions (1)

Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change lvg.properties LVG_DIR=/home/path/to/lvg2013lite/ This file can be found in: /home/path/to/lvg2013lite/data/config/lvg.properties Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer. If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale. Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c. Please make sure this is also set into the indexer tool part. Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows. The nested workflow Get_abstract uses a sql command to retrieve abstracts which assumes are located in the database mydb. If this is not the case, please change the database in the SQL value.

Dependencies (1)

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 (4)

Name	Type	Description
Calculate_Uncertainty_Coefficient	workflow	A nested workflow to calculate the Uncertainty coefficient with the contingency table values of the concept pairs. The calculated values are afterwards inserted into the uncertainty coefficient SQL table. The row with the same concepts in column name concept_uri_1 is the concept profile. The values in the columns name concept_uri_2 are the concepts that are used for calculating the uncertainty coefficient (similarity measure). Example of the constructed SQL table: 1 A A UC value of concept pair AA 2 A B UC value of concept pair AB 3 A C UC value of concept pair AC Example of a concept profile made of concept A: A \| \|__UC value__A \|__UC value__B \|__UC value__C
Calculate_Contingency_Table	workflow	A nested workflow that retrieves the values of a 2x2 contingency table and puts the co-occurrence of made concept pairs into the SQL table TableName_co_occurrence. This is done by creating concept pairs which is retrieved from the Sql table TableName_occurrence. This contingency 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. Example of a 2x2 contingency table of concept pair A B: B Not B A AB A not A B not A not B This is calculated for every possible concept pair.
table_name_value	stringconstant	Value alpha
timestamp_value	stringconstant	Value alpha

Beanshells (7)

Name	Description	Inputs	Outputs
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. When a concept pair is the same. As in concept pair A A or B B etc. It will use the first SQL statement. Else it will use the second SQL statement. The output of only concept A and only concept B needs to be corrected and the value to get when neither concepts occur in literature is done in the Beanshell script called: "Beanshell_correct_contincengy_table".	concept_pairs table_name	out1
Beanshell_correct_contingency_table	A Beanshell script that corrects the output SQL retrieved contingency table by subtracting the co-occurence values of the concept only A and of concept only B value. It also uses the value of the total amount of abstracts there are in the dataset for calculating the value of when neither concepts occure.	contingency_values total_nr_abtracts	corrected_contingency_values
Beanshell_generate_SQL_statement_Get_distinct_concept	A Beanshell script that retrieves every concept from the Sql table TableName_occurrence.	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
Beanshell_SQL_count_abstracts			out1
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 a script of Herman van Haagen.	corrected_contingency_values	UC_value

Outputs (1)

Name	Description
end

Datalinks (7)

Source	Sink
Calculate_Contingency_Table:outputlist	Calculate_Uncertainty_Coefficient:concept_pairs
Calculate_Contingency_Table:corrected_contingency_values	Calculate_Uncertainty_Coefficient:corrected_contingency_values
db_properties	Calculate_Uncertainty_Coefficient:propertyString
timestamp_value:value	Calculate_Uncertainty_Coefficient:timestamp
db_properties	Calculate_Contingency_Table:propertyString
table_name_value:value	Calculate_Contingency_Table:table_name
Calculate_Uncertainty_Coefficient:output	end