enteropathway_api_tutorial

• Enteropathway is a manually curated human gut specific database for metabolic pathways.

• Registration of a user account is needed to access Enteropathway by REST API.

• This tutorial is based on the Enteropathway REST API.

Requirements

• jq

How to use

Authorization token

• The username and password can be obtained by registration of a user account on the registration page.

• user_name and pass_word should be changed to their own username and password respectively.

• Obtained TOKEN can be confirmed by echo $TOKEN.

• TOKEN will be expired in one day.

  • If TOKEN will be expired, Try to get TOKEN again.

TOKEN=`curl -X POST -H "Accept: application/json" \
 --header "Content-Type: application/json" \
 --data '{"username":"user_name","password":"pass_word"}' \
 https://enteropathway.org/api/authenticate | \
 jq '.access_token' -r`

Customization via uploading JSON format data

• Customization setting which is defined as the JSON format can be uploaded by REST API to customize metabolic pathways.

• The customization parameters are shown in this link.

curl -X POST -H "Authorization: Bearer $TOKEN" \
 -H "Content-Type: application/json" \
 --data \
 '{
  "mapping": {
    "customizations": [
      "EPR0001 #FF0000 W20 0.5",
      "EPR0002",
      "C07316 #FF0000 W15",
      "EPC0003 #FF0000 W15 0.5"
    ],
    "highlight_whole_module": false,
    "clear_original_colors": false,
    "module_box_highlight": "none"
  }
 }' \
 https://enteropathway.org/api/customization/mapping \
 --output mapping.pdf

Customization via uploading file

• Customization setting file can be uploaded by REST API to customize metabolic pathways.

• The customization parameters are shown in this link.

curl -X POST -H "Authorization: Bearer $TOKEN" \
 -F 'customization_file=@customization.txt' \
 -F 'highlight_whole_module=false' \
 -F 'clear_original_colors=true' \
 -F 'module_box_highlight=box-only' \
 https://enteropathway.org/api/customization/mapping/file \
 --output mapping.pdf

Enrichment analysis via uploading JSON format data

• List of KO or reaction can be uploaded by REST API to perform enrichment analysis.

• The enrichment analysis parameters are shown in this link.

curl -X POST -H "Authorization: Bearer $TOKEN" \
 -H "Content-Type: application/json" \
 --data \
 '{
  "mapping": {
    "elements": [
      "EPR0001",
      "EPR0002"
    ],
    "color": "#FF0000",
    "input_type": "reactions",
    "p_value": 0.05,
    "clear_original_colors": false,
    "module_box_highlight": "none"
  }
 }' \
 https://enteropathway.org/api/customization/mapping/enrichment \
 --output enrichment.pdf

Enrichment analysis via uploading file

• KO list file or Reaction list file can be uploaded by REST API to perform enrichment analysis.

• The enrichment analysis parameters are shown in this link.

curl -X POST -H "Authorization: Bearer $TOKEN" \
 -F 'elements_file=@ko_list.txt' \
 -F 'color=#ff0000' \
 -F 'input_type=ko' \
 -F 'p_value=0.05' \
 -F 'clear_original_colors=true' \
 -F 'module_box_highlight=none' \
 https://enteropathway.org/api/customization/mapping/enrichment/file \
 --output enrichment.pdf

Common parameters for customization

• customization_file : The input file name [string].
• --output : The output file name [string].
• highlight_whole_module : Highlifht all the module if at least one reaction is matched [boolean: true/false].
• clear_original_colors : Sets the default elements color to grey [boolean: true/false].
• module_box_highlight : How to highlight the module box of mateched modules [string: box/box-only/none].
  • box : highlights the module title box in addition to module reactions.
  • box-only : highlights the module title box only, and ignores module reactions.
  • none : do not highlight the box.

Common parameters for enrichment analysis

• elements_file : The input file name [string].
• --output : The output file name [string].
• input_type : The type of the list [string: ko/reactions].
• color : Color of enriched modules [string].
• p_value : The cutoff value for p-value filtering [float number].
• clear_original_colors : Sets the default elements color to grey [boolean: true/false].
• module_box_highlight : How to highlight the module box of mateched modules [string: box/box-only/none].
  • box : highlights the module title box in addition to module reactions.
  • box-only : highlights the module title box only, and ignores module reactions.
  • none : do not highlight the box.