SGHI FHIR Profile Implementation Guide
0.1.0 - ci-build
SGHI FHIR Profile Implementation Guide, published by Kathurima Kimathi. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/savannahghi/sil_fhir_profile_ig/ and changes regularly. See the Directory of published versions
| Active as of 2026-09-15 |
{
"resourceType" : "CodeSystem",
"id" : "specimen-collection-codesystem",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem specimen-collection-codesystem</b></p><a name=\"specimen-collection-codesystem\"> </a><a name=\"hcspecimen-collection-codesystem\"> </a><p>This case-sensitive code system <code>https://fhir.slade360.co.ke/fhir/CodeSystem/specimen-collection-codesystem</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">swab<a name=\"specimen-collection-codesystem-swab\"> </a></td><td>Swab</td><td>Material collected on a swab, whatever the site. The site is recorded on the specimen, not in this code.</td></tr><tr><td style=\"white-space:nowrap\">edta-tube<a name=\"specimen-collection-codesystem-edta-tube\"> </a></td><td>EDTA tube (purple top)</td><td>Tube carrying potassium EDTA anticoagulant, used for haematology.</td></tr><tr><td style=\"white-space:nowrap\">sst-gel-tube<a name=\"specimen-collection-codesystem-sst-gel-tube\"> </a></td><td>SST gel tube (gold top)</td><td>Serum separator tube with a polymer gel barrier, used for most chemistry and serology.</td></tr><tr><td style=\"white-space:nowrap\">plain-tube<a name=\"specimen-collection-codesystem-plain-tube\"> </a></td><td>Plain tube (red top)</td><td>Tube with no additive, letting the sample clot for serum.</td></tr><tr><td style=\"white-space:nowrap\">citrate-tube<a name=\"specimen-collection-codesystem-citrate-tube\"> </a></td><td>Sodium citrate tube (blue top)</td><td>Tube carrying buffered sodium citrate at a fixed blood-to-additive ratio, used for coagulation. Sensitive to a short draw.</td></tr><tr><td style=\"white-space:nowrap\">fluoride-oxalate-tube<a name=\"specimen-collection-codesystem-fluoride-oxalate-tube\"> </a></td><td>Fluoride oxalate tube (grey top)</td><td>Tube carrying sodium fluoride and potassium oxalate, which halts glycolysis for glucose and lactate.</td></tr><tr><td style=\"white-space:nowrap\">lithium-heparin-tube<a name=\"specimen-collection-codesystem-lithium-heparin-tube\"> </a></td><td>Lithium heparin tube (green top)</td><td>Tube carrying lithium heparin anticoagulant, used for plasma chemistry.</td></tr><tr><td style=\"white-space:nowrap\">blood-culture-aerobic<a name=\"specimen-collection-codesystem-blood-culture-aerobic\"> </a></td><td>Blood culture bottle (aerobic)</td><td>Culture bottle for organisms that grow in the presence of oxygen.</td></tr><tr><td style=\"white-space:nowrap\">blood-culture-anaerobic<a name=\"specimen-collection-codesystem-blood-culture-anaerobic\"> </a></td><td>Blood culture bottle (anaerobic)</td><td>Culture bottle for organisms that grow in the absence of oxygen.</td></tr><tr><td style=\"white-space:nowrap\">sterile-universal-container<a name=\"specimen-collection-codesystem-sterile-universal-container\"> </a></td><td>Sterile universal container</td><td>A sterile screw-top pot for urine, stool, sputum and other unpreserved samples.</td></tr><tr><td style=\"white-space:nowrap\">formalin-pot<a name=\"specimen-collection-codesystem-formalin-pot\"> </a></td><td>Formalin pot (10% neutral buffered)</td><td>Pot pre-filled with 10% neutral buffered formalin, for tissue going to histopathology.</td></tr><tr><td style=\"white-space:nowrap\">cytology-fixative-pot<a name=\"specimen-collection-codesystem-cytology-fixative-pot\"> </a></td><td>Cytology fixative pot</td><td>Pot pre-filled with cytology fixative, for samples going to cytology.</td></tr><tr><td style=\"white-space:nowrap\">amies-swab<a name=\"specimen-collection-codesystem-amies-swab\"> </a></td><td>Transport swab (Amies medium)</td><td>A swab in Amies transport medium, keeping organisms viable on the way to microbiology.</td></tr><tr><td style=\"white-space:nowrap\">clean-draw<a name=\"specimen-collection-codesystem-clean-draw\"> </a></td><td>Clean draw</td><td>The draw went cleanly and the sample is fit for testing.</td></tr><tr><td style=\"white-space:nowrap\">difficult-draw<a name=\"specimen-collection-codesystem-difficult-draw\"> </a></td><td>Difficult draw</td><td>The draw needed more than one attempt or prolonged venous access. The sample stands, but results sensitive to a traumatic draw are read with it in mind.</td></tr><tr><td style=\"white-space:nowrap\">short-draw<a name=\"specimen-collection-codesystem-short-draw\"> </a></td><td>Short draw, under volume</td><td>The container was filled below its target volume. It matters most where the blood-to-additive ratio is fixed, as in a citrate tube.</td></tr></table></div>"
},
"url" : "https://fhir.slade360.co.ke/fhir/CodeSystem/specimen-collection-codesystem",
"version" : "0.1.0",
"name" : "SGHISpecimenCollectionCodeSystem",
"title" : "SGHI Specimen Collection Code System",
"status" : "active",
"experimental" : false,
"date" : "2026-09-15T11:40:24+00:00",
"publisher" : "Kathurima Kimathi",
"contact" : [
{
"name" : "Kathurima Kimathi",
"telecom" : [
{
"system" : "url",
"value" : "https://www.linkedin.com/in/kathurima-kimathi/"
},
{
"system" : "email",
"value" : "kathurimakimathi415@gmail.com"
}
]
},
{
"name" : "Oscar John",
"telecom" : [
{
"system" : "email",
"value" : "oscarjohnotieno@gmail.com",
"use" : "work"
}
]
},
{
"name" : "Kennedy Omondi",
"telecom" : [
{
"system" : "email",
"value" : "kennankole@gmail.com",
"use" : "work"
}
]
}
],
"description" : "A code system enumerating the specimen collection concepts with no home in HL7 terminology: the containers a sample is collected into, and how the draw itself went.",
"caseSensitive" : true,
"content" : "complete",
"count" : 16,
"concept" : [
{
"code" : "swab",
"display" : "Swab",
"definition" : "Material collected on a swab, whatever the site. The site is recorded on the specimen, not in this code."
},
{
"code" : "edta-tube",
"display" : "EDTA tube (purple top)",
"definition" : "Tube carrying potassium EDTA anticoagulant, used for haematology."
},
{
"code" : "sst-gel-tube",
"display" : "SST gel tube (gold top)",
"definition" : "Serum separator tube with a polymer gel barrier, used for most chemistry and serology."
},
{
"code" : "plain-tube",
"display" : "Plain tube (red top)",
"definition" : "Tube with no additive, letting the sample clot for serum."
},
{
"code" : "citrate-tube",
"display" : "Sodium citrate tube (blue top)",
"definition" : "Tube carrying buffered sodium citrate at a fixed blood-to-additive ratio, used for coagulation. Sensitive to a short draw."
},
{
"code" : "fluoride-oxalate-tube",
"display" : "Fluoride oxalate tube (grey top)",
"definition" : "Tube carrying sodium fluoride and potassium oxalate, which halts glycolysis for glucose and lactate."
},
{
"code" : "lithium-heparin-tube",
"display" : "Lithium heparin tube (green top)",
"definition" : "Tube carrying lithium heparin anticoagulant, used for plasma chemistry."
},
{
"code" : "blood-culture-aerobic",
"display" : "Blood culture bottle (aerobic)",
"definition" : "Culture bottle for organisms that grow in the presence of oxygen."
},
{
"code" : "blood-culture-anaerobic",
"display" : "Blood culture bottle (anaerobic)",
"definition" : "Culture bottle for organisms that grow in the absence of oxygen."
},
{
"code" : "sterile-universal-container",
"display" : "Sterile universal container",
"definition" : "A sterile screw-top pot for urine, stool, sputum and other unpreserved samples."
},
{
"code" : "formalin-pot",
"display" : "Formalin pot (10% neutral buffered)",
"definition" : "Pot pre-filled with 10% neutral buffered formalin, for tissue going to histopathology."
},
{
"code" : "cytology-fixative-pot",
"display" : "Cytology fixative pot",
"definition" : "Pot pre-filled with cytology fixative, for samples going to cytology."
},
{
"code" : "amies-swab",
"display" : "Transport swab (Amies medium)",
"definition" : "A swab in Amies transport medium, keeping organisms viable on the way to microbiology."
},
{
"code" : "clean-draw",
"display" : "Clean draw",
"definition" : "The draw went cleanly and the sample is fit for testing."
},
{
"code" : "difficult-draw",
"display" : "Difficult draw",
"definition" : "The draw needed more than one attempt or prolonged venous access. The sample stands, but results sensitive to a traumatic draw are read with it in mind."
},
{
"code" : "short-draw",
"display" : "Short draw, under volume",
"definition" : "The container was filled below its target volume. It matters most where the blood-to-additive ratio is fixed, as in a citrate tube."
}
]
}