CPGP Peregrine Get Abstracts Create tables

Created: 2014-05-27 11:29:40 Last updated: 2014-06-30 09:15:55

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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.

Optional:

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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Workflow Components

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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. Optional: 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 (3)

Name	Description
Ontology_input	A Skos formated dictionary/thesaurus of predefined concepts.
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.
Path_Peregrine_Indexer	Give the full path where the production.properties and peregrine-skos-cli.jar files are located of the Peregrine Indexer Tool. Which are supposed to be in the same path/Directory. path/to/ production.properties path/to/ peregrine-skos-cli.jar

Processors (3)

Name	Type	Description
Peregrine_Indexer	workflow	The nested workflow Peregrine Indexer uses a java peregrine skos cli.jar file to index the occurrence of concepts in documents. The Peregrine indexer program can be downloaded from trac.nbic.nl/biosemantics/downloads. Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Copy properties file from production.properties which can be downloaded from: 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 Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. normalizer.lvg.properties =/home/path/to/lvg2013lite/data/config/config/lvg.properties normalizer.lvg.binaryCahce=/home/path/to/lvg2013lite/standartNormCache2013.bin Have MySQL installed with a database called mydb or please create one. Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files.
Create_Tables	workflow	This nested workflows creates the necessary tables for inserting the generated values. The following tables are created: - Co-occurrence table - Occurrence table - Uncertainty coefficient table - Inner product table - Summary table
Get_abstracts	workflow	A nested workflow to retrieve abstracts from a sql table. This table is assumed to have atleast two columns consisting out of pmid and abstract text.

Beanshells (5)

Name	Description	Inputs	Outputs
Beanshell_get_timestamp	A Beanshell script which retreives the time the program started. As in year, month, day, hour, minutes and seconds in military time.		timeStamp
Beanshell_SQL_Create_Tables	A Beanshell script for creating the tables.	timeStamp	Table_sql
Beanshell_SQL_query_generator_Concept_Doc_occurrence	A Beanshell script that generates a Sql statement to INSERT the concept URI and document URI in the table named after the timestamp/tablename the workflow started. It uses a database called mydb. If there is not a database/schema named mydb, please create one.	table_name concept_occurence_document	out1
Beanshell_extract_uri_doc_and_abstract	A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs.	Input	doc_uri abstracts
Beanshell_remove_dot_and_correct_doc_uri_in_con_doc	A Beanshell script that replaces the temp created Taverna file with the correct Document URI.	concept_occurence_document doc_uri	out1

Outputs (1)

Name	Description
end

Datalinks (8)

Source	Sink
Create_Tables:timeStamp	Peregrine_Indexer:table_name
Ontology_input	Peregrine_Indexer:ontology
Get_abstracts:db_results	Peregrine_Indexer:Input
db_properties	Peregrine_Indexer:propertyString
Path_Peregrine_Indexer	Peregrine_Indexer:Path
db_properties	Create_Tables:db_properties
db_properties	Get_abstracts:propertyString
Peregrine_Indexer:output	end