CPGP 2x2 Contingency table
Created: 2014-05-27 11:34:06
Last updated: 2014-06-30 09:18:32
Part of the CPGP contingency table workflow
which creates concepts pairs, contingency tables of these pairs and insert co-occurrence into a table premade with the workflow CPGP Create Table get abstract get peregrine
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Authors (1)
Titles (1)
| Concept Profile Generation Pipeline |
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.
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 presumes that it uses the mydb database. Please change this when using a other sql database. |
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 (2)
| Name |
Type |
Description |
| 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. |
| Text_constant |
stringconstant |
Valuealpha |
Beanshells (5)
| 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 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_SQL_insert_into_co_occurence_table |
A Beanshell script that generates SQL statement to insert into the co-occurence table the amount two given concepts co-occur together in literature. |
contingency_values
timestamp
concept_pairs
|
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 (3)
| Name |
Description |
| concept_pairs |
|
| corrected_contingency_values |
|
| Co_occurrence_inserted_into_table |
|
Datalinks (5)
| Source |
Sink |
| db_properties |
Calculate Contincengy table:propertyString |
| Text_constant:value |
Calculate Contincengy table:table_name |
| Calculate Contincengy table:outputlist |
concept_pairs |
| Calculate Contincengy table:corrected_contingency_values |
corrected_contingency_values |
| Calculate Contincengy table:Co_occurrence_inserted_into_table |
Co_occurrence_inserted_into_table |
Uploader
License
All versions of this Workflow are
licensed under:
Version 1 (earliest)
(of 3)
Credits (1)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (0)
None
Featured In Packs (1)
Log in to add to one of your Packs
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Statistics
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
Download Workflow
]
Reviews
(0)
No comments yet
Log in to make a comment