ARCHETYPE Specimen (openEHR-EHR-CLUSTER.specimen.v0)

Type: openEHR ARCHETYPE
Purpose: To record details about a physical sample for investigation, examination or analysis, collected from or related to an individual.
Use:

Use to record details about a physical sample for investigation, examination or analysis, collected from or related to an individual.

The level of detail in this archetype runs ahead of current practices in many labs. It's intended to be usable in both cases where there isn't a lot of detail required, and in cases where minute detail about the preparation and subdivision of specimens is required.

This CLUSTER archetype is designed to be used in several different contexts:

Within an INSTRUCTION archetype to describe a specimen that is to be collected, or to describe a specimen that accompanies a laboratory service request.
Within an ACTION archetype to describe specimen collection, or for testing within a laboratory setting.
Within an OBSERVATION archetype to describe a specimen being reported on.

The exact semantics of several elements of this archetype may change based on the context provided by the container archetype. For example the 'Collection method' element in the context of an INSTRUCTION archetype is the requested collection method, while the same element in the context of an ACTION archetype in the 'completed' state is the actual collection method.

This archetype is intended to be complemented by other CLUSTER archetypes for concepts such as Specimen container, Specimen preparation, and specimen transportation and storage.

This archetype can be used together with the Specimen container archetype in two main ways: 'Specimen container' nested within 'Specimen' (for example when a venous blood specimen is divided between two vials, or a whole large intestine is divided into three buckets), or 'Specimen' nested within 'Specimen container' (for example when a bucket of formalin contains a section of large intestine and a rectum, or a jar contains five individually marked moles).

The word 'collection' used in this archetype always refers to the action of obtaining the specimen directly from the individual, not the transport of the specimen after it's been removed from the individual.

Misuse: Not to be used to record information about specimens that are not related to a specific individual, such as some environmental samples.

Available formats: ADL XML

ARCHETYPE ID	openEHR-EHR-CLUSTER.specimen.v0
Concept	Specimen
Description	A physical sample for investigation, examination or analysis, collected from or related to an individual.
Use	Use to record details about a physical sample for investigation, examination or analysis, collected from or related to an individual. The level of detail in this archetype runs ahead of current practices in many labs. It's intended to be usable in both cases where there isn't a lot of detail required, and in cases where minute detail about the preparation and subdivision of specimens is required. This CLUSTER archetype is designed to be used in several different contexts: Within an INSTRUCTION archetype to describe a specimen that is to be collected, or to describe a specimen that accompanies a laboratory service request. Within an ACTION archetype to describe specimen collection, or for testing within a laboratory setting. Within an OBSERVATION archetype to describe a specimen being reported on. The exact semantics of several elements of this archetype may change based on the context provided by the container archetype. For example the 'Collection method' element in the context of an INSTRUCTION archetype is the requested collection method, while the same element in the context of an ACTION archetype in the 'completed' state is the actual collection method. This archetype is intended to be complemented by other CLUSTER archetypes for concepts such as Specimen container, Specimen preparation, and specimen transportation and storage. This archetype can be used together with the Specimen container archetype in two main ways: 'Specimen container' nested within 'Specimen' (for example when a venous blood specimen is divided between two vials, or a whole large intestine is divided into three buckets), or 'Specimen' nested within 'Specimen container' (for example when a bucket of formalin contains a section of large intestine and a rectum, or a jar contains five individually marked moles). The word 'collection' used in this archetype always refers to the action of obtaining the specimen directly from the individual, not the transport of the specimen after it's been removed from the individual.
Misuse	Not to be used to record information about specimens that are not related to a specific individual, such as some environmental samples.
Purpose	To record details about a physical sample for investigation, examination or analysis, collected from or related to an individual.
References	Hl7 FHIR Specimen resource: HL7 FHIR; Available from http://www.hl7.org/implement/standards/fhir/specimen.html Laboratory Technical Framework, Volume 3: Content, Revision 3.0 [Internet]. USA: IHE International; 2011 May 19; [cited 2011 Jul 11]. Available from: http://www.ihe.net/Technical_Framework/index.cfm#laboratory
Copyright	© openEHR Foundation
Authors	Author name: Dr Ian McNicoll Organisation: freshEHR Clinical Informatics Email: ian.mcnicoll@oceaninformatics.com Date originally authored: 2009-01-27
Other Details Language	Author name: Dr Ian McNicoll Organisation: freshEHR Clinical Informatics Email: ian.mcnicoll@oceaninformatics.com Date originally authored: 2009-01-27
Other Details (Language Independent)	Licence: This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/. Custodian Organisation: openEHR Foundation References: Hl7 FHIR Specimen resource: HL7 FHIR; Available from http://www.hl7.org/implement/standards/fhir/specimen.html Laboratory Technical Framework, Volume 3: Content, Revision 3.0 [Internet]. USA: IHE International; 2011 May 19; [cited 2011 Jul 11]. Available from: http://www.ihe.net/Technical_Framework/index.cfm#laboratory Original Namespace: org.openehr Original Publisher: openEHR Foundation Custodian Namespace: org.openehr MD5-CAM-1.0.1: E744F0D00DCD4A49F4E1929EC0EF0D31 Build Uid: 8d7d6a8a-384a-41ae-a564-426aa862e48f Revision: 0.0.1-alpha
Keywords	specimen, laboratory, sample, collection, sampling, biopsy, tissue, cytology
Lifecycle	in_development
UID	192457f6-6bdd-4e67-bf11-e15c590af499
Language used	en
Citeable Identifier	1013.1.331
Revision Number	0.0.1-alpha
Archetype Concept Comment	For example: Tissue, body fluid or food.
items
Specimen type	Specimen type: The type of specimen. For example: Venous blood, prostatic biopsy. Coding of the specimen type with a terminology is preferred, where possible. Optional[{fhir_mapping=Specimen.type}]
Laboratory specimen identifier	Laboratory specimen identifier: A unique identifier of the specimen, normally assigned by the laboratory. Sometimes called the Accession Identifier. Optional[{fhir_mapping=Specimen.accessionIdentifier}]
External identifier	External identifier: A unique identifier of the specimen, assigned by a party external to the laboratory such as the requester. Optional[{fhir_mapping=Specimen.identifier}]
Datetime received	Datetime received: The date and time that the sample was received at the laboratory. Optional[{fhir_mapping=Specimen.receivedTime}]
Sampling condition	Sampling condition: A condition that should be or was present when the sample is to be or was taken. For example: 'Fasting', 'full bladder', 'sterile field' or any special instructions on the handling or immediate processing of the sample, for example 'centrifuge on receipt'. Can also be used to document any known deviations from collection or handling instructions, for example that the patient was not fasted. Coding of the sampling condition with a terminology is preferred, where possible. Whether this element contains conditions that 'should be' or 'was' present during the sampling is based on the context of the containing archetype, usually an INSTRUCTION or an ACTION. The content of this element in the context of a ACTION archetype in a completed state may be used to decide whether there were significant confounding factors related to the collection, which may be used to populate the 'Confounding factors' element of an OBSERVATION.laboratory_test_result archetype.
Physical properties	Physical properties: Physical dimensions, mass or non-measurable properties of the specimen. For example: Volume, mass, circumference, colour, smell, turbidity. This element can be used to specify the properties of the specimen to be collected, in the context of an INSTRUCTION archetype, or the properties of the specimen which was collected, in the context of an ACTION or OBSERVATION archetype. For example, an INSTRUCTION may request the collection of 20 ml of blood, while the corresponding ACTION records that only 15 ml was collected. Optional[{fhir_mapping=Specimen.collection.quantity}] Include: openEHR-EHR-CLUSTER.physical_properties.v1 and specialisations or openEHR-EHR-CLUSTER.exam-body_fluid.v0 and specialisations or openEHR-EHR-CLUSTER.exam-body_fluid.v1 and specialisations or openEHR-EHR-CLUSTER.physical_properties.v0 and specialisations
Collection method	Collection method: The method of collection that is to be or was used. For example: venepuncture, biopsy, resection. Coding of the collection method with a terminology is preferred, where possible. If the collection method is included in the 'Specimen type' via precoordinated codes, this data element becomes redundant. Optional[{fhir_mapping=Specimen.collection.method}]
Collector comment	Collector comment: Additional narrative description about the collection of the specimen.
Source site	Source site: Identification of a simple source site from where the specimen was taken. Coding of the name of the source site with a terminology is preferred, where possible. Use this data element to record precoordinated source sites. If the requirements for recording the source site are determined at run-time by the application or require more complex modelling such as relative locations then use the 'Structured source site' SLOT in this archetype. If the source site is included in the 'Specimen type' via precoordinated codes, this data element becomes redundant.
Structured source site	Structured source site: A structured anatomical site from where the specimen was taken. Use this SLOT to insert the CLUSTER.anatomical_location, CLUSTER.relative_location or CLUSTER.anatomical_location_clock archetypes if the requirements for recording the source site are determined at run-time by the application or require more complex modelling such as relative locations. If the source site is included in the 'Specimen type' via precoordinated codes, the use of this SLOT becomes redundant. Optional[{fhir_mapping=Specimen.collection.sourceSite}] Include: openEHR-EHR-CLUSTER.anatomical_location.v1 and specialisations or openEHR-EHR-CLUSTER.anatomical_location_relative.v1 and specialisations or openEHR-EHR-CLUSTER.anatomical_location_circle.v1 and specialisations
Collection datetime	Collection datetime: The date and time that collection has been ordered to take place or has taken place. This datetime will be captured primarily in the INSTRUCTION timing, ACTION time or OBSERVATION times. However, as this is a critical piece of information, it can be useful to also associate it directly with the specimen itself. Choice of: Date/Time Interval of Date/Time
Potential risk	Potential risk: Any risk or biohazard associated with collecting or handling the specimen. For example: 'blood borne virus', 'polonium poisoning', "nerve agent poisoning'.
Collection setting	Collection setting: Identification of the physical setting in which the specimen was collected. For example: laboratory outpatient clinic, at home, or hospital ward. This specifies the specimen collection location within the healthcare environment. It enables the laboratory to ask questions about the collection of the specimen, if required. The specimen collection setting may provide additional information relevant to the analysis of the result.
Specimen collector identifier	Specimen collector identifier: Identifier of the person or agency responsible for collecting the specimen. This element is intended to be used where the specimen has already been collected and the actual collector is known. Optional[{fhir_mapping=Specimen.collection.collector}]
Specimen collector details	Specimen collector details: The person or organisation responsible for collecting the specimen. Optional[{fhir_mapping=Specimen.collection.collector}]
Additional collection details	Additional collection details: Addtional details related to specific collection methods. For example details about needle biopsies in prostate cancer, where both the request and reporting about the specimen are detailed and specific.
Number of containers	Number of containers: The total number of physical units holding this specimen. For example: Number of buckets, jars, vials, tubes, blocks, slides or grids. min: >=0
Container details	Container details: Details about container(s) used. Include: openEHR-EHR-CLUSTER.specimen_container.v0 and specialisations or openEHR-EHR-CLUSTER.specimen_container.v1 and specialisations
Processing details	Processing details: Details about a preparation or processing step normally performed in the laboratory. For example: Staining or fixation. Include: openEHR-EHR-CLUSTER.specimen_preparation.v1 and specialisations or openEHR-EHR-CLUSTER.specimen_preparation.v0 and specialisations
Transport details	Transport details: Details about transport of the specimen. Include: openEHR-EHR-CLUSTER.specimen_transport.v0 and specialisations or openEHR-EHR-CLUSTER.specimen_transport.v1 and specialisations
Parent specimen identifier	Parent specimen identifier: Unique identifier of the parent specimen, where the specimen is split into sub-samples. For example: A specific histology slide specimen would have a specific paraffin wax block as its parent specimen.
Specimen quality issue	Specimen quality issue: A specific quality issue with a specimen. Coding of the specimen quality issues with a terminology is preferred, where possible. Choice of: Coded Text at0052::Haemolysed [The specimen was haemolysed.] at0053::Lipaemic [The specimen was lipaemic.] at0089::Icteric [The specimen was icteric.] at0094::Clotted [The specimen was clotted.] at0054::Incorrect transport medium [An incorrect transport medium or preservative was added to the specimen.] at0055::Insufficient amount [The available amount of specimen was insufficient to undertake the examination.] at0090::Handling error [An error arose when handling the specimen. For example: The specimen was spilled, or stored outside the recommended temperature range.] at0091::Age [The specimen was too old to analyse accurately.] at0092::Technical failure [The specimen could not be analysed for technical reasons.] Text
Adequacy for testing	Adequacy for testing: Information about whether the specimen was adequate for testing. This element is intended to be used to record a judgement about whether or not the specimen quality was good enough for testing, and whether or not testing has been carried out. Coding of the specimen quality issues with a terminology is preferred, where possible. Choice of: Coded Text at0062::Satisfactory [The specimen is of sufficient quality to allow reporting.] at0063::Unsatisfactory - processed [The specimen is unsatisfactory but has been processed.] at0064::Unsatisfactory - not processed [The specimen is unsatisfactory and has not been processed.] Text
Comment	Comment: An narrative comment about the specimen.
Other contributors	Marit Alice Venheim, Helse Vest IKT, Norway Erling Are Hole, Helse Bergen, Norway Vebjørn Arntzen, Oslo University Hospital, Norway (openEHR Editor) Koray Atalag, University of Auckland, New Zealand Heidi Aursand, Oslo universitetssykehus, Norway Silje Ljosland Bakke, Nasjonal IKT HF, Norway (openEHR Editor) SB Bhattacharyya, Sudisa Consultancy Services, India Greg Burch, Tiny Medical Apps, United Kingdom Ady Angelica Castro Acosta, CIBERES-Hospital 12 de Octubre, Spain Shahla Foozonkhah, Iran ministry of health and education, Iran Heather Grain, Llewelyn Grain Informatics, Australia Åshild Halvorsen, Helse Nord RHF, Norway Sam Heard, Ocean Informatics, Australia Evelyn Hovenga, EJSH Consulting, Australia Ronald Krawec, Alberta Health Services, Canada Tomi Laptoš, Marand, Slovenia Liv Laugen, Oslo universitetssykehus, Norway Sabine Leh, Helse Bergen, Norway Heather Leslie, Atomica Informatics, Australia (openEHR Editor) Jens Lien, Bouvet Norge AS, Norway Neranga Liyanaarachchi, Ministry of Health, Postgraduate Institute of Medicine, Sri Lanka Gunn Marit Barstad, Stavanger Universitetssykehus HF, Norway Ole Martin Sand, DIPS ASA, Norway Shane McKee, Belfast Health & Social Care Trust, United Kingdom Ian McNicoll, freshEHR Clinical Informatics, United Kingdom (openEHR Editor) Arunakiry Natarajan, Management 4 health, Germany Andrej Orel, Marand d.o.o., Slovenia Jayashree Panickar, Karolinska Institute, Sweden Ana Pereira, CINTESIS, CUF-Porto, Portugal Ingrid Skard, Edproof, Norway Lídia Sousa, CINTESIS; Faculty of Medicine of Oporto University, Portugal Natalia Strauch, Medizinische Hochschule Hannover, Germany Norwegian Review Summary, Nasjonal IKT HF, Norway Rowan Thomas, St. Vincent's Hospital Melbourne, Australia John Tore Valand, Helse Bergen, Norway (openEHR Editor) Ørjan Vermeer, Haukeland Universitetssjukehus, Kvinneklinikken, Norway Lin Zhang, Taikang Insurance Group, China
Translators	Norwegian Bokmal: Kristian Berg, Gro-Hilde Ulriksen, Line Silsand, Universitetssykehuset Nord-Norge, kristian.berg@unn.no, gro-hilde.ulriksen@unn.no, line.silsand@unn.no, * Portuguese (Brazil): Adriana Kitajima, Débora Farage, Fernanda Maia, Laíse Figueiredo, Marivan Abrahão, Core Consulting, contato@coreconsulting.com.br, Hospital Alemão Oswaldo Cruz (HAOC) Arabic (Syria): Mona Saleh