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

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[[Category:HOWTOs]]
 
[[Category:HOWTOs]]
  
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The user can import information from a CSV file (see examples below) to adding term to dictionary. For that user must press the right mouse button in dictionary data-type and select '''Update From CSV File''' option in Dictionaries sub-menu. '''Resources - Dictionary -> Update From CSV File'''
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== Operation ==
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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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[[File:Dictionary_Update_CSV_1.png|800px|boarder|center]]
 
  
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Appears a graphical interface that allows the user to select the CSV file and option.
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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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[[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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* General Delimiter: The overall file delimiter to separate the contents of columns  
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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 to encapsulate information
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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 separate synonyms present in a column.
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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 separate ExternalId present in a column.
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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 separate ExternalID and Source.
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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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Beyond these parameters there are other advanced options. To access advance option the user must press ''Advance Options'' and will appear in graphical interface a new panel with advanced options.
 
  
 
[[File:Dictionary_Update_CSV_3.png|800px|center]]
 
[[File:Dictionary_Update_CSV_3.png|800px|center]]
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Advanced Options:
 
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* Default Value: Default value for empty value;
 
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* Column Options: Select the column indices in which appears interest terms (term, class, synonyms and external IDs)
 
  
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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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'''Example 2'''
 
  
 
''General delimiter:'' TAB ( \t )
 
''General delimiter:'' TAB ( \t )
Line 41: Line 47:
 
''ExternalID Delimiter:'' Vertical Bar (|)
 
''ExternalID Delimiter:'' Vertical Bar (|)
  
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''ExternalID Source Delimiter: WHITE SPACE (;)
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''ExternalID Source Delimiter: Semi-colon (;)
  
 
<pre>
 
<pre>
  
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GRF1        Protein  -                                          KEGG;zma:542291|P49106;IntAct
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GRF1        Protein  -                                          zma:542291;KEGG|P49106;IntAct
 
GRF2        Protein  14-3-3-like protein GF14-12|GRF2a          Q01526;SMR
 
GRF2        Protein  14-3-3-like protein GF14-12|GRF2a          Q01526;SMR
 
ATPA        Protein  ATP synthase subunit alpha, mitochondrial  -
 
ATPA        Protein  ATP synthase subunit alpha, mitochondrial  -
Line 80: Line 86:
 
"Protein";"CYPLXXVIII";-;"Cytochrome P450 78A1"|"CYP78A1"|"CYP78"
 
"Protein";"CYPLXXVIII";-;"Cytochrome P450 78A1"|"CYP78A1"|"CYP78"
 
</pre>
 
</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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