# 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

```json
   {
      "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"
      }
    }
```