Glycan API usage

GlyTouCan

For registering new glycans

• URL: https://api.glytoucan.org/glycan/register
• Method: POST
• Authentication: Authorization: Basic <userId>:<apiKey> see application.yml file for these variables
• Payload: { "sequence": <wurcs_sequence> }
• Response:

{
   "timestamp" : <timestamp>,
   "status" : <status>,
   "error" : <error>,
   "message" : <glytoucan_id or hash>,
   "path" : <path>
}

• Documentation for the registration is here.
• We are using glygenarray.api@gmail.com account for registration and send WURCS sequence for the glycan.

GlyCosmos

Retrieve accession number (GlyTouCan ID) for a glycan (with WURCS sequence)

• URL: https://api.glycosmos.org/sparqlist/wurcs2gtcids?wurcs=
• Method: GET
• Response:

[{ 
   "id" : <accession_number>,
   "wurcs" : <wurcs_sequence>,
   "message: <error_message>
}]

• Documentation is here.

Retrieve glycan with the given accession number (GlyTouCan ID)

• URL: https://sparqlist.glycosmos.org/sparqlist/api/gtc_wurcs_by_accession?accNum=
• Method: GET
• Response:

[ 
   {
     "AccessionNumber" : <accession_number>,
     "HashKey" : <hash_key>,
     "NormalizedWurcs" : <wurcs_sequence>
]

• Could not locate the current documentation.
• This might be the documentation but it is not the same URL (beta)
• We use this service when we cannot get GlycanObject for a glycan with GlycoCT but the glycan has a GlyTouCan ID. In this case we try the get the WURCS sequence using the API and use WURCS parser to get GlycanObject. There is also a web service getGlycanFromGlytoucan that uses this API.

Validation

• URL: https://api.glycosmos.org/wurcsframework/wurcsvalidator/1.0.1/
• WURCS sequence as a URL parameter (encoded)
• Method: GET
• Response:

{
  "m_sInputString" : <input_sequence>,
  "m_sStandardString" : <standard_sequence>,
  "m_mapTypeToReports" : { 
      "WARNING": [],
      "ERROR" : [
        {
          "strMessage: <message>,
          "exception" : {
              "m_strInput" : <input>,
              "m_strMessage" : <message>
           }
        }
      ]
   }
}

• Documentation of the latest version is here
• We are using the initial release version.
• Need to update to the latest!

Get Image

• URL: https://api.glycosmos.org/wurcs2image/latest/png/binary/
• By appending the GlyTouCan ID to the URL
• Method: GET
• Documentation is here

Check Status for a registered glycan

• URL: https://sparqlist.glycosmos.org/sparqlist/api/check_batch_processing_by_hashkey?hashKey=
• hashKey is the hash returned for a glycan after submitting for registration
• Method: GET
• Response:

[
   { 
      "batch_p" : "AccessionNumber",
      "batch_value" : <url_with_accession_number> 
   }
]

GlycoNAVI

Retrieve accession number (GlyTouCan ID) for a glycan (with WURCS sequence)

• This is a fall back API if GlyCosmos API fails
• URL: https://sparqlist.glyconavi.org/api/WURCS2GlyTouCan?WURCS=
• Method: GET
• Documentation is here.
• Response:

[{ 
   "GlyTouCan" : <accession_number>,
   "WURCS" : <wurcs_sequence>,
   "message: <error_message>
}]

Web Service(s) that use one/more of these APIs

• GlyTableMaker
  • api/data/addglycan. (see)
  • api/data/addglycanfromlist (see)
  • api/data/addglycanfromfile (see)
  • api/util/getcartoon (uses retrieveGlycan as necessary)

Projects(Classes) that use one/more of these APIs

• GlytoucanUtil.java in GlyTableMaker

• Scheduled task in GlyTableMaker to see if the glycans submitted to GlyTouCan has been registered and assigned a GlyTouCan accession number

• GlytoucanUtil.java in glygen-array-backend

  • validateURL needs to be updated to use the latest version (1.0.1 -> 1.2.13)
  • glycanURL needs to be updated to a valid URL (https://sparqlist.beta.glytoucan.org/sparqlist/gtc_wurcs_by_accession) after confirming if this is the latest API

• GlytoucanUtil.java in gws2xlsx

  • validateURL needs to be updated to use the latest version (1.0.1 -> 1.2.13)
  • glycanURL needs to be updated to a valid URL (https://sparqlist.beta.glytoucan.org/sparqlist/gtc_wurcs_by_accession) after confirming if this is the latest API

• GlyTouCanApiClient.java in glytoucan.registry.client

  • GLYCAN_URL needs to be updated to a valid URL (https://sparqlist.beta.glytoucan.org/sparqlist/gtc_wurcs_by_accession) after confirming if this is the latest API
  • GET_ACCESSION_FOR_WURCS_URL is using glycosmos.org instead of glyconavi API, needs to be updated