Difference between revisions of "Dictionary Import Element From CSV File"

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[[Category:HOWTOs]]
 
[[Category:HOWTOs]]
  
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This operation allows the user to import information from a CSV file organized (see examples below) to a dictionary.  
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== Operation ==
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To add elements to the dictionary the user must press the right mouse button and select the '''Update From CSV File''' option in Dictionaries sub-menu.
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You can import information from a CSV file (see examples below) to add terms to a dictionary.  
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For that purpose, right click over the dictionary data-type and select the '''Update From CSV File''' option in the Dictionaries sub-menu: '''Resources - Dictionary -> Update From CSV File'''.
  
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''Resources - Dictionary -> Update From CSV File''
 
  
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[[File:Dictionary_Update_CSV_1.png|800px|boarder|center]]
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[[File:Dictionary_Update_CSV_1.png|1500px|boarder|center]]
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== Configuration ==
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A GUI is shown that allows to select the CSV file to load and select the options.
  
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Appears a graphical interface that allows the user to select the CSV file and option.
 
  
 
[[File:Dictionary_Update_CSV_2.png|800px|center]]
 
[[File:Dictionary_Update_CSV_2.png|800px|center]]
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Basic Options:
 
Basic Options:
  
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* File: pressing the File button the user can browse and select csv file on your computer.
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* File: pressing the File button, you can browse and select the csv file from the file system (in black)
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*  
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* General Delimiter: The overall file delimiter that separates the contents of the columns in the file (in Blue)
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* Text Delimiter: The delimiter used to encapsulate individual text strings (if any) (in Green)
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* Synonyms Delimiter: The delimiter for separating synonyms within the list in the specified column (in Red)
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* ExternalID Delimiter: The delimiter for separating External Id instances within the list in the specified column (in maroon)
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* ExternalID Source Delimiter: The delimiter for separating ExternalIDs and Sources within the list in the specified column (in yellow).  
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* Default Value: Default value used to represent empty records (in orange)
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* Column Options: Allows to select the columns of the file (automatically detected if using the headers check box) used as sources for the different fields: Term and Class are mandatory; Synonyms and ExternalIds are optional (in violet)
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[[File:Dictionary_Update_CSV_3.png|800px|center]]
 
[[File:Dictionary_Update_CSV_3.png|800px|center]]
  
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The .csv file examples :
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== Examples ==
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Next, we provide examples of csv files currently handled by @Note:
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'''Example 1'''
 
'''Example 1'''
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''General delimiter:'' TAB ( \t )
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''text Delimiter:'' NONE
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''Synonym Delimiter:'' Vertical Bar (|)
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''ExternalID Delimiter:'' Vertical Bar (|)
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''ExternalID Source Delimiter: Semi-colon (;)
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<pre>
 
<pre>
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GRF1        Protein  -                                          zma:542291;KEGG|P49106;IntAct
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GRF2        Protein  14-3-3-like protein GF14-12|GRF2a          Q01526;SMR
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ATPA        Protein  ATP synthase subunit alpha, mitochondrial  -
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CYPLXXVIII  Protein  Cytochrome P450 78A1|CYP78A1|CYP78          -
  
 
</pre>
 
</pre>
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'''Example 2'''
 
'''Example 2'''
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''General delimiter:'' Semi-colon ( ; )
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''text Delimiter:'' QUOTATIONS MARK (")
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''Synonym Delimiter:'' Vertical Bar (|)
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''ExternalID Delimiter:'' Vertical Bar (|)
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''ExternalID Source Delimiter: WHITE SPACE ( )
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''Column number''
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* Term: 2
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* Class: 1
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* Synonyms: 4
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* ExternalID: 3
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''Default Delimiter:'' HYPHEN (-)
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<pre>
 
<pre>
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"Protein";"GRF1";"KEGG" "zma:542291"|"P49106" "IntAct";-
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"Protein";"GRF2;"SMR" "Q01526" ;"14-3-3-like protein GF14-12"|"GRF2a"
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"Protein";"ATPA";-;"ATP synthase subunit alpha, mitochondrial"
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"Protein";"CYPLXXVIII";-;"Cytochrome P450 78A1"|"CYP78A1"|"CYP78"
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</pre>
  
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</pre>
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== Results ==
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In the end of this operation you can check the [[Resources_Update_Report|Resources update report]]

Latest revision as of 11:43, 23 January 2014

Operation

You can import information from a CSV file (see examples below) to add terms to a dictionary. For that purpose, right click over the dictionary data-type and select the Update From CSV File option in the Dictionaries sub-menu: Resources - Dictionary -> Update From CSV File.


boarder


Configuration

A GUI is shown that allows to select the CSV file to load and select the options.


Dictionary Update CSV 2.png


Basic Options:

  • File: pressing the File button, you can browse and select the csv file from the file system (in black)
  • General Delimiter: The overall file delimiter that separates the contents of the columns in the file (in Blue)
  • Text Delimiter: The delimiter used to encapsulate individual text strings (if any) (in Green)
  • Synonyms Delimiter: The delimiter for separating synonyms within the list in the specified column (in Red)
  • ExternalID Delimiter: The delimiter for separating External Id instances within the list in the specified column (in maroon)
  • ExternalID Source Delimiter: The delimiter for separating ExternalIDs and Sources within the list in the specified column (in yellow).
  • Default Value: Default value used to represent empty records (in orange)
  • Column Options: Allows to select the columns of the file (automatically detected if using the headers check box) used as sources for the different fields: Term and Class are mandatory; Synonyms and ExternalIds are optional (in violet)


Dictionary Update CSV 3.png


Examples

Next, we provide examples of csv files currently handled by @Note:


Example 1


General delimiter: TAB ( \t )

text Delimiter: NONE

Synonym Delimiter: Vertical Bar (|)

ExternalID Delimiter: Vertical Bar (|)

ExternalID Source Delimiter: Semi-colon (;) 


GRF1         Protein   -                                           zma:542291;KEGG|P49106;IntAct
GRF2         Protein   14-3-3-like protein GF14-12|GRF2a           Q01526;SMR
ATPA         Protein   ATP synthase subunit alpha, mitochondrial   -
CYPLXXVIII   Protein   Cytochrome P450 78A1|CYP78A1|CYP78          -


Example 2

General delimiter: Semi-colon ( ; )

text Delimiter: QUOTATIONS MARK (")

Synonym Delimiter: Vertical Bar (|)

ExternalID Delimiter: Vertical Bar (|)

ExternalID Source Delimiter: WHITE SPACE ( )

Column number

  • Term: 2
  • Class: 1
  • Synonyms: 4
  • ExternalID: 3

Default Delimiter: HYPHEN (-) 

"Protein";"GRF1";"KEGG" "zma:542291"|"P49106" "IntAct";-
"Protein";"GRF2;"SMR" "Q01526" ;"14-3-3-like protein GF14-12"|"GRF2a"
"Protein";"ATPA";-;"ATP synthase subunit alpha, mitochondrial"
"Protein";"CYPLXXVIII";-;"Cytochrome P450 78A1"|"CYP78A1"|"CYP78"

Results

In the end of this operation you can check the Resources update report

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