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 |
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="specimen-collection-codesystem"/>
<text>
<status value="generated"/>
<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>
</text>
<url
value="https://fhir.slade360.co.ke/fhir/CodeSystem/specimen-collection-codesystem"/>
<version value="0.1.0"/>
<name value="SGHISpecimenCollectionCodeSystem"/>
<title value="SGHI Specimen Collection Code System"/>
<status value="active"/>
<experimental value="false"/>
<date value="2026-09-15T11:40:24+00:00"/>
<publisher value="Kathurima Kimathi"/>
<contact>
<name value="Kathurima Kimathi"/>
<telecom>
<system value="url"/>
<value value="https://www.linkedin.com/in/kathurima-kimathi/"/>
</telecom>
<telecom>
<system value="email"/>
<value value="kathurimakimathi415@gmail.com"/>
</telecom>
</contact>
<contact>
<name value="Oscar John"/>
<telecom>
<system value="email"/>
<value value="oscarjohnotieno@gmail.com"/>
<use value="work"/>
</telecom>
</contact>
<contact>
<name value="Kennedy Omondi"/>
<telecom>
<system value="email"/>
<value value="kennankole@gmail.com"/>
<use value="work"/>
</telecom>
</contact>
<description
value="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 value="true"/>
<content value="complete"/>
<count value="16"/>
<concept>
<code value="swab"/>
<display value="Swab"/>
<definition
value="Material collected on a swab, whatever the site. The site is recorded on the specimen, not in this code."/>
</concept>
<concept>
<code value="edta-tube"/>
<display value="EDTA tube (purple top)"/>
<definition
value="Tube carrying potassium EDTA anticoagulant, used for haematology."/>
</concept>
<concept>
<code value="sst-gel-tube"/>
<display value="SST gel tube (gold top)"/>
<definition
value="Serum separator tube with a polymer gel barrier, used for most chemistry and serology."/>
</concept>
<concept>
<code value="plain-tube"/>
<display value="Plain tube (red top)"/>
<definition
value="Tube with no additive, letting the sample clot for serum."/>
</concept>
<concept>
<code value="citrate-tube"/>
<display value="Sodium citrate tube (blue top)"/>
<definition
value="Tube carrying buffered sodium citrate at a fixed blood-to-additive ratio, used for coagulation. Sensitive to a short draw."/>
</concept>
<concept>
<code value="fluoride-oxalate-tube"/>
<display value="Fluoride oxalate tube (grey top)"/>
<definition
value="Tube carrying sodium fluoride and potassium oxalate, which halts glycolysis for glucose and lactate."/>
</concept>
<concept>
<code value="lithium-heparin-tube"/>
<display value="Lithium heparin tube (green top)"/>
<definition
value="Tube carrying lithium heparin anticoagulant, used for plasma chemistry."/>
</concept>
<concept>
<code value="blood-culture-aerobic"/>
<display value="Blood culture bottle (aerobic)"/>
<definition
value="Culture bottle for organisms that grow in the presence of oxygen."/>
</concept>
<concept>
<code value="blood-culture-anaerobic"/>
<display value="Blood culture bottle (anaerobic)"/>
<definition
value="Culture bottle for organisms that grow in the absence of oxygen."/>
</concept>
<concept>
<code value="sterile-universal-container"/>
<display value="Sterile universal container"/>
<definition
value="A sterile screw-top pot for urine, stool, sputum and other unpreserved samples."/>
</concept>
<concept>
<code value="formalin-pot"/>
<display value="Formalin pot (10% neutral buffered)"/>
<definition
value="Pot pre-filled with 10% neutral buffered formalin, for tissue going to histopathology."/>
</concept>
<concept>
<code value="cytology-fixative-pot"/>
<display value="Cytology fixative pot"/>
<definition
value="Pot pre-filled with cytology fixative, for samples going to cytology."/>
</concept>
<concept>
<code value="amies-swab"/>
<display value="Transport swab (Amies medium)"/>
<definition
value="A swab in Amies transport medium, keeping organisms viable on the way to microbiology."/>
</concept>
<concept>
<code value="clean-draw"/>
<display value="Clean draw"/>
<definition
value="The draw went cleanly and the sample is fit for testing."/>
</concept>
<concept>
<code value="difficult-draw"/>
<display value="Difficult draw"/>
<definition
value="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."/>
</concept>
<concept>
<code value="short-draw"/>
<display value="Short draw, under volume"/>
<definition
value="The container was filled below its target volume. It matters most where the blood-to-additive ratio is fixed, as in a citrate tube."/>
</concept>
</CodeSystem>