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We want to offer a group insert of multiple building blocks at once. To do this we transport the information in the form of a process.json file. Which is specified here.

Changed Specifications

To keep these files simple we only use certain fields, which in return are required. The required field are still subject to change (v0.3.0).

{
    "@id": "#process/standard_trypsin_digestion",
    "name": "standard_trypsin_digestion",
    "executesProtocol": {
        "@id": "#protocols/peptide_digestion",
        "name": "peptide_digestion",
    
        "protocolType": {
            "@id": "protein_digestion",
            "annotationValue": "Protein Digestion",
            "termSource": "NCIT",
            "termAccession": "http://purl.obolibrary.org/obo/NCIT_C70845",
            "comments": []
        },
        "description": "The isolated proteins get solubilized. Given protease is added and the solution is heated to a given temperature. After a given amount of time, the digestion is stopped by adding a denaturation agent.",
        "uri": "http://madeUpProtocolWebsize.org/protein_digestion",
        "version": "1.0.0",
        "parameters": [
            {
                "parameterName": {
                  "@id": "protease",
                  "annotationValue": "Peptidase",
                  "termSource": "MS",
                  "termAccession": "http://purl.obolibrary.org/obo/NCIT_C16965",
                  "comments": []
                }
            },
            {
                "parameterName": {
                  "@id": "temperature",
                  "annotationValue": "temperature",
                  "termSource": "Ontobee",
                  "termAccession": "http://purl.obolibrary.org/obo/NCRO_0000029",
                  "comments": []

                }
            },
            {
                "parameterName": {
                    "@id": "time",
                    "annotationValue": "time",
                    "termSource": "EFO",
                    "termAccession": "http://www.ebi.ac.uk/efo/EFO_0000721",
                    "comments": []
                }
            }
        ]
    },
    "parameterValues": [
        {
            "category": {
                "@id": "protease",
                "parameterName": {
                    "@id": "protease",
                    "annotationValue": "Peptidase",
                    "termSource": "MS",
                    "termAccession": "http://purl.obolibrary.org/obo/NCIT_C16965",
                    "comments": []
                }
            },
            "value": {
                "@id": "trypsin",
                "annotationValue": "Trypsin/P",
                "termSource": "NCI",
                "termAccession": "http://purl.obolibrary.org/obo/MS_1001313",
                "comments": []
                
            }
        },
        {
            "category": {
                "@id": "temperature",
                "parameterName": {
                    "@id": "temperature",
                    "annotationValue": "temperature",
                    "termSource": "Ontobee",
                    "termAccession": "http://purl.obolibrary.org/obo/NCRO_0000029",
                    "comments": []

                }
            },
            "value": 37,
            "unit": {
              "@id": "degree_celcius",
              "annotationValue": "degree Celsius",
              "termSource": "UO",
              "termAccession": "http://purl.obolibrary.org/obo/UO_0000027",
              "comments": []
            }
        },
        {
            "category": {
                "@id": "time",
                "parameterName": {
                    "@id": "time",
                    "annotationValue": "time",
                    "termSource": "EFO",
                    "termAccession": "http://www.ebi.ac.uk/efo/EFO_0000721",
                    "comments": []
                }
            },
            "value": 1,
            "unit": {
                "@id": "h",
                "annotationValue": "hour",
                "termSource": "UO",
                "termAccession": "http://purl.obolibrary.org/obo/UO_0000032",
                "comments": []
            }
        }
    ]
}