FHIR Standards

Profiles Used

Resource	Profile URL
Patient	https://fhir.kemkes.go.id/r4/StructureDefinition/Patient
Specimen	https://fhir.kemkes.go.id/r4/StructureDefinition/Specimen
Organization	https://fhir.kemkes.go.id/r4/StructureDefinition/Organization
Practitioner	https://fhir.kemkes.go.id/r4/StructureDefinition/Practitioner
PractitionerRole	https://fhir.kemkes.go.id/r4/StructureDefinition/PractitionerRole
Observation	http://hl7.org/fhir/StructureDefinition/Observation
Bundle	https://fhir.kemkes.go.id/r4/StructureDefinition/Bundle

Observation (PhIP-Seq Epitope Binding)

Each enriched peptide generates an Observation resource:

Field	Value
Status	final
Category	laboratory (HL7 observation-category)
Code	LOINC 94531-1 — Epitope binding signal intensity
Value	Z-score as valueQuantity (unit: z-score)
Method	SNOMED CT 708049000 — Phage immunoprecipitation sequencing
Tag	phipseq (system: http://terminology.kemkes.go.id/sp)

Observation Interpretation

Z-score	Interpretation Code	Display
> 3.5	POS	Positive — Strong viral epitope binding signal detected
≤ 3.5	NEG	Negative — No significant viral epitope binding

The interpretation threshold of 3.5 matches the default zscore_threshold parameter.

Standard Terminologies

LOINC Codes

Code	Display Name	Usage
94531-1	Epitope binding signal intensity	Observation code

SNOMED CT Codes

Code	Display Name	Usage
708049000	Phage immunoprecipitation sequencing	Observation method
119364003	Serum specimen	Specimen type
33747003	Blood specimen collection	Specimen collection method

Example: Observation Resource

   {
      "fullUrl": "...",
      "resource": {
        "resourceType": "Observation",
        "id": "1-obs-392",
        "meta": {
          "profile": [
            "http://hl7.org/fhir/StructureDefinition/Observation"
          ],
          "tag": [
            {
              "system": "http://terminology.kemkes.go.id/sp",
              "code": "phipseq",
              "display": "PhIP-Seq"
            }
          ]
        },
        "status": "final",
        "category": [
          {
            "coding": [
              {
                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
                "code": "laboratory",
                "display": "Laboratory"
              }
            ]
          }
        ],
        "code": {
          "coding": [
            {
              "system": "http://loinc.org",
              "code": "94531-1",
              "display": "Epitope binding signal intensity"
            }
          ],
          "text": "PhIP-Seq Viral Epitope Binding Signal"
        },
        "subject": {
          "reference": "Patient/1-patient",
          "display": "Patient_1"
        },
        "specimen": {
          "reference": "Specimen/1-specimen",
          "display": "Serum specimen from Patient_1"
        },
        "effectiveDateTime": "2026-05-18T04:31:50.518299+00:00",
        "issued": "2026-05-18T04:31:50.518299+00:00",
        "performer": [
          {
            "reference": "Organization/aa",
            "display": "aa"
          },
          {
            "reference": "Practitioner/aa",
            "display": "aa"
          }
        ],
        "valueQuantity": {
          "value": 15.798,
          "unit": "z-score",
          "system": "http://unitsofmeasure.org",
          "code": "{score}"
        },
        "interpretation": [
          {
            "coding": [
              {
                "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation",
                "code": "POS",
                "display": "Positive"
              }
            ]
          }
        ],
        "note": [
          {
            "text": "Strong viral epitope binding signal detected"
          },
          {
            "text": "Peptide ID: 391, Z-score: 15.798"
          }
        ],
        "method": {
          "coding": [
            {
              "system": "http://snomed.info/sct",
              "code": "708049000",
              "display": "Phage immunoprecipitation sequencing"
            }
          ],
          "text": "PhIP-Seq using Vir3 Library"
        },
        "component": [
          {
            "code": {
              "coding": [
                {
                  "system": "http://sys-ids.kemkes.go.id/phipseq",
                  "code": "epitope-organism",
                  "display": "Epitope Source Organism"
                }
              ]
            },
            "valueString": "HKU1_SI17244_replicase_polyprotein_1ab"
          },
          {
            "code": {
              "coding": [
                {
                  "system": "http://sys-ids.kemkes.go.id/phipseq",
                  "code": "epitope-protein",
                  "display": "Epitope Source Protein"
                }
              ]
            },
            "valueString": "replicase_polyprotein_1ab"
          },
          {
            "code": {
              "coding": [
                {
                  "system": "http://sys-ids.kemkes.go.id/phipseq",
                  "code": "epitope-position",
                  "display": "Epitope Start Position in Protein"
                }
              ]
            },
            "valueInteger": 6481
          }
        ]
      },
      "request": {
        "method": "PUT",
        "url": "Observation/1-obs-392"
      }
    }