Component: KorvasieniAnnotator

KorvasieniAnnotator

Converts gene, transcription, and translation identifiers using Korvasieni. This component can be used to annotate findings and to integrate information between various sources.

An example list of supported (source and target) databases includes a snapshot of known Ensembl links. You may prefix these databases with an underscore (_) for real database identifiers.

Version	1.9
Bundle	microarray
Categories	Annotation GO
Authors	Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker	View/Report issues
Requires	mysql-connector-java-5.1.6-bin.jar (jar)
Source files	component.xml
Usage	Example with default values KorvasieniAnnotator( sourceKeys = CSV, //connection = Properties, echoColumns = "", goFilter = "", indicator = true, inputDB = "", inputType = "Any", isListKey = false, keyColumn = "", maxHits = 100000, primary = false, rename = "", skipLevel = "never", targetDB = <string>, unique = false )

Version

1.9

Bundle

microarray

Categories

Annotation GO

Authors

Marko Laakso (Marko.Laakso@Helsinki.FI)

Issue tracker

View/Report issues

Requires

mysql-connector-java-5.1.6-bin.jar (jar)

Source files

component.xml

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
sourceKeys	CSV	Mandatory	A list of source database keys.
connection	Properties	Optional	Database connection can be defined using this file. The definition of parameters: database.url, database.user, database.password, database.timeout, database.recycle, and database.driver can be found from the documentation of Korvasieni.

Name

Type

Mandatory

Description

sourceKeys

CSV

Mandatory

A list of source database keys.

connection

Properties

Optional

Database connection can be defined using this file. The definition of parameters: database.url, database.user, database.password, database.timeout, database.recycle, and database.driver can be found from the documentation of Korvasieni.

Name	Type	Description
bioAnnotation	AnnotationTable	Table that contains columns for all types of annotation given in the parameter "types". Indicator column is 1 if the input key is found from the database.

Name

Type

Description

bioAnnotation

AnnotationTable

Table that contains columns for all types of annotation given in the parameter "types". Indicator column is 1 if the input key is found from the database.

Parameters

Name	Type	Default	Description
echoColumns	string	""	A comma separated list of column names for the columns that will be copied to the output. An asterisk (*) can be used to denote all columns except the keyColumn.
goFilter	string	""	A comma separated list of the Gene Ontology evidence codes that shall be excluded. This parameter is only used for the 'GO' annotations.
indicator	boolean	true	Enables an indicator column that tells (=1) if the source key was matching the database or not (=0).
inputDB	string	""	Type of input keys. This must be a database supported by Korvasieni. If the parameter is omitted, the component tries to derive the database from the type of geneID. If this is not possible, an error is returned. You may define three columns in form of chromosome:start-end in case the inputDB is .DNARegion. This format provides a comfortable compatibility with DNARegion datatype. The end positions can be left out if they would be the same as the start positions (=single nucleotides).
inputType	string	"Any"	Ensembl object type for the input keys (Any, Gene, Transcript, Translation)
isListKey	boolean	false	Enables the automatic value splits for the comma separated key column
keyColumn	string	""	Name of the key column withing sourceKeys file or an empty string for the first column. See inputDB for further information about the DNA regions.
maxHits	int	100000	Maximum number of target identifiers for a single source identifier
primary	boolean	false	Skip secondary identifiers such as LGR identifiers.
rename	string	""	Comma separated list of column renaming rules (oldname=newname)
skipLevel	string	"never"	Skip result rows if the source identifier is unknown or target identifiers are not available. Possible values are: never (no filtering), source (skip if the source ID is unknown), target (skip if no target IDs are found), any (skip if any of the target IDs is missing).
targetDB	string	(no default)	Comma-separated list of annotation types. Possible values are all databases supported by Korvasieni.
unique	boolean	false	This flag can be turned on in order to eliminate duplicate annotations.

Name

Type

Default

Description

echoColumns

string

A comma separated list of column names for the columns that will be copied to the output. An asterisk (*) can be used to denote all columns except the keyColumn.

goFilter

string

A comma separated list of the Gene Ontology evidence codes that shall be excluded. This parameter is only used for the 'GO' annotations.

indicator

boolean

true

Enables an indicator column that tells (=1) if the source key was matching the database or not (=0).

inputDB

string

Type of input keys. This must be a database supported by Korvasieni. If the parameter is omitted, the component tries to derive the database from the type of geneID. If this is not possible, an error is returned. You may define three columns in form of chromosome:start-end in case the inputDB is .DNARegion. This format provides a comfortable compatibility with DNARegion datatype. The end positions can be left out if they would be the same as the start positions (=single nucleotides).

inputType

string

"Any"

Ensembl object type for the input keys (Any, Gene, Transcript, Translation)

isListKey

boolean

false

Enables the automatic value splits for the comma separated key column

keyColumn

string

Name of the key column withing sourceKeys file or an empty string for the first column. See inputDB for further information about the DNA regions.

maxHits

int

100000

Maximum number of target identifiers for a single source identifier

primary

boolean

false

Skip secondary identifiers such as LGR identifiers.

rename

string

Comma separated list of column renaming rules (oldname=newname)

skipLevel

string

"never"

Skip result rows if the source identifier is unknown or target identifiers are not available. Possible values are: never (no filtering), source (skip if the source ID is unknown), target (skip if no target IDs are found), any (skip if any of the target IDs is missing).

targetDB

string

(no default)

Comma-separated list of annotation types. Possible values are all databases supported by Korvasieni.

unique

boolean

false

This flag can be turned on in order to eliminate duplicate annotations.

Test cases

Test case	Parameters▼	IN sourceKeys	IN connection	OUT bioAnnotation
case1	properties	sourceKeys	connection	bioAnnotation
	inputType=Gene, inputDB =.GeneName, targetDB =.GeneId,UniGene
case2	properties	sourceKeys	connection	bioAnnotation
	inputType=Gene, inputDB=.GeneName, targetDB=.GeneId,UniGene,.DNARegion,.DNABand, keyColumn=gene name, isListKey=true, echoColumns=gene name, primary=true
case3_DNARegion	properties	sourceKeys	connection	bioAnnotation
	inputType =Gene, inputDB =.DNARegion, targetDB =.GeneName,.DNARegion, keyColumn =chromosome:start-end, echoColumns=*
case4_colconflict	properties	sourceKeys	connection	bioAnnotation
	inputType=Gene, inputDB =.GeneName, targetDB =EntrezGene,_EntrezGene,_WikiGene,WikiGene,EntrezGene,_WikiGene, rename =WikiGene3=TheLastWikiGene, indicator=false
case5	properties	sourceKeys	connection	bioAnnotation
	inputType = Gene, inputDB = .DNARegion, targetDB = .GeneName,.DNARegion, keyColumn = chr:pos
case6_DNARegion	properties	sourceKeys	(missing)	bioAnnotation
	inputType =Gene, inputDB =.DNARegion, targetDB =.GeneName,.DNARegion, keyColumn =chromosome:start, echoColumns=*

Test case

Parameters▼

IN
sourceKeys

IN
connection

OUT
bioAnnotation

case1

inputType=Gene,
inputDB =.GeneName,
targetDB =.GeneId,UniGene

case2

inputType=Gene,
inputDB=.GeneName,
targetDB=.GeneId,UniGene,.DNARegion,.DNABand,
keyColumn=gene name,
isListKey=true,
echoColumns=gene name,
primary=true

case3_DNARegion

inputType =Gene,
inputDB =.DNARegion,
targetDB =.GeneName,.DNARegion,
keyColumn =chromosome:start-end,
echoColumns=*

case4_colconflict

inputType=Gene,
inputDB =.GeneName,
targetDB =EntrezGene,_EntrezGene,_WikiGene,WikiGene,EntrezGene,_WikiGene,
rename =WikiGene3=TheLastWikiGene,
indicator=false

case5

inputType = Gene,
inputDB = .DNARegion,
targetDB = .GeneName,.DNARegion,
keyColumn = chr:pos

case6_DNARegion

properties

sourceKeys

(missing)

bioAnnotation

inputType =Gene,
inputDB =.DNARegion,
targetDB =.GeneName,.DNARegion,
keyColumn =chromosome:start,
echoColumns=*