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Difference between revisions of "Specimen FHIR Resource Proposal"

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This page documents a [[:category:Pending FHIR Resource Proposal|Pending]] [[:category:FHIR Resource Proposal|FHIR Resource Proposal]]
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This page documents an [[:category:Approved FHIR Resource Proposal|Approved]] [[:category:FHIR Resource Proposal|FHIR Resource Proposal]]
 
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[[Category:FHIR Resource Proposal]]
 
[[Category:FHIR Resource Proposal]]
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[[Category:Pending FHIR Resource Proposal]]
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[[Category:Approved FHIR Resource Proposal]]
  
  
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=specimen=
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=Specimen=
  
  
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DEFINITION (SPECIMEN):
 
DEFINITION (SPECIMEN):
−
Any material sample taken from a biological entity, including a sample obtained from a  living organism or taken from the biological object after halting of all its  life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and  body excretory products (source: NCIt, modified).
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Any material sample:
 +
# taken from a biological entity, living or dead
 +
# taken from a physical object or the environment
  
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The specimen resource covers substances used for diagnostic and environmental testing. This includes all types of living and non-living subjects where a subject is defined as the host from which the specimen was obtained.
+
Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products (source: NCIt, modified).
 +
 
 +
The specimen resource covers substances used for diagnostic and environmental testing.
 +
 
 +
The focus of the specimen resource is the process for gathering, maintaining and processing the specimen as well as where the specimen originated.  This is distinct from the use of Substance which is only used when these other aspects are not relevant.
  
 
==RIM scope==
 
==RIM scope==
  
 
<!-- Identify the formal RIM mapping for the root concept of the resource.  The expectation is that the RIM mapping will be sufficiently precise so as to not overlap with any other resource definition. -->
 
<!-- Identify the formal RIM mapping for the root concept of the resource.  The expectation is that the RIM mapping will be sufficiently precise so as to not overlap with any other resource definition. -->
 +
*Role: Specimen (RoleClass=SPM)
 +
**Entity (player): Material (EntityClass="MAT")
 +
**Entity (scoper): Choice - Person, Non-Human Living Subject, Material)
 +
*Entity: Place (EntityClass="PLC")
  
 
==Resource appropriateness==
 
==Resource appropriateness==
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* Have the characteristics of high cohesion & low coupling – need to explore whether coupling is good some places, not elsewhere – layers from Bo’s document  
 
* Have the characteristics of high cohesion & low coupling – need to explore whether coupling is good some places, not elsewhere – layers from Bo’s document  
 
  -->
 
  -->
 +
Specimens are primarily of importance in healthcare for diagnostic testing and in public health for environmental testing.  Because of the frequent biologic nature of specimens, they are uniquely identified.  Additionally, specimens are tracked, transported, and stored, sometimes for years.
  
 
==Expected implementations==
 
==Expected implementations==
  
 
<!-- For resources not deemed "key", what interest is there by implementers in using this particular resource.  (Should ideally have multiple independent implementations) -->
 
<!-- For resources not deemed "key", what interest is there by implementers in using this particular resource.  (Should ideally have multiple independent implementations) -->
 +
 +
The Specimen resource is used by other resources such as the Diagnostic Report to record the entity that is being reported against. The Procedure resource may also reference a specimen removed during a procedure.
 +
Essential to support Lab
  
 
==Content sources==
 
==Content sources==
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Are there any source specifications that you wish to consult but are concerned about access to or expertise to consider? -->
 
Are there any source specifications that you wish to consult but are concerned about access to or expertise to consider? -->
 +
 +
*HL7 v3 Laboratory Standard - Normative
 +
*HL7 v2.x
 +
*HL7 OO Specimen DAM Project
 +
*OpenEHR?
 +
 +
 +
==Example Scenarios==
 +
* A tumour excised from a patient during a procedure is sent for histological examination. It is referenced in the Procedure, DiagnosticOrder and the Diagnostic report.
 +
* A blood sample
 +
* A laboratory counter swab
  
 
==Resource Relationships==
 
==Resource Relationships==
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Reference to resources is really only relevant at the "same or higher level" (Bo – fix this wording)
 
Reference to resources is really only relevant at the "same or higher level" (Bo – fix this wording)
 
  -->
 
  -->
 +
*Order
 +
*DiagnosticOrder
 +
*DiagnosticReport
 +
*ImagingStudy
 +
*Procedure
  
 
==Timelines==
 
==Timelines==
  
 
<!-- Indicate the target date for having the resource complete from a committee perspective and ready for vetting and voting -->
 
<!-- Indicate the target date for having the resource complete from a committee perspective and ready for vetting and voting -->
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 +
*Proposal Approved by WG at May 2013 WGM
 +
*Planned Ballot: September 2013
  
 
==gForge Users==
 
==gForge Users==
  
 
<!-- Identify the userids who will require commit access to gForge to maintain the resource.  (Ensure all users have registered for gForge.) -->
 
<!-- Identify the userids who will require commit access to gForge to maintain the resource.  (Ensure all users have registered for gForge.) -->
 +
*Lorraine Constable
 +
*Patrick Loyd
 +
 +
==Issues==
 +
* Added to scope to differentiate between Specimen and Material.
 +
* Is Specimen used for things like donated blood, other materials that might be re-implanted in someone else?
 +
* Is Specimen used when there's a need to refer to a specific "part" of a patient even though that hasn't necessarily been removed?
 +
* Don't understand the RIM mapping of Entity: Place (EntityClass="PLC")
 +
* Need explanation of relationships to other resources

Latest revision as of 05:50, 22 May 2014

OpenHotTopic.GIF

This page documents an Approved FHIR Resource Proposal



Specimen

Owning committee name

Orders & Observations WG

Interested Work Groups

  • Anatomic Pathology
  • Clinical Genomics
  • Imaging Integration
  • Public Health and Emergency Response

FHIR Resource Development Project Insight ID

952

Scope of coverage

DEFINITION (SPECIMEN): Any material sample:

  1. taken from a biological entity, living or dead
  2. taken from a physical object or the environment

Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products (source: NCIt, modified).

The specimen resource covers substances used for diagnostic and environmental testing.

The focus of the specimen resource is the process for gathering, maintaining and processing the specimen as well as where the specimen originated. This is distinct from the use of Substance which is only used when these other aspects are not relevant.

RIM scope

  • Role: Specimen (RoleClass=SPM)
    • Entity (player): Material (EntityClass="MAT")
    • Entity (scoper): Choice - Person, Non-Human Living Subject, Material)
  • Entity: Place (EntityClass="PLC")

Resource appropriateness

Specimens are primarily of importance in healthcare for diagnostic testing and in public health for environmental testing. Because of the frequent biologic nature of specimens, they are uniquely identified. Additionally, specimens are tracked, transported, and stored, sometimes for years.

Expected implementations

The Specimen resource is used by other resources such as the Diagnostic Report to record the entity that is being reported against. The Procedure resource may also reference a specimen removed during a procedure. Essential to support Lab

Content sources

  • HL7 v3 Laboratory Standard - Normative
  • HL7 v2.x
  • HL7 OO Specimen DAM Project
  • OpenEHR?


Example Scenarios

  • A tumour excised from a patient during a procedure is sent for histological examination. It is referenced in the Procedure, DiagnosticOrder and the Diagnostic report.
  • A blood sample
  • A laboratory counter swab

Resource Relationships

  • Order
  • DiagnosticOrder
  • DiagnosticReport
  • ImagingStudy
  • Procedure

Timelines

  • Proposal Approved by WG at May 2013 WGM
  • Planned Ballot: September 2013

gForge Users

  • Lorraine Constable
  • Patrick Loyd

Issues

  • Added to scope to differentiate between Specimen and Material.
  • Is Specimen used for things like donated blood, other materials that might be re-implanted in someone else?
  • Is Specimen used when there's a need to refer to a specific "part" of a patient even though that hasn't necessarily been removed?
  • Don't understand the RIM mapping of Entity: Place (EntityClass="PLC")
  • Need explanation of relationships to other resources
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