Healthcare Interoperability: Exploring the Potential of the FHIR Specimen Resource

The FHIR (Fast Healthcare Interoperability Resources) Specimen resource is an integral component of the FHIR standard, designed to facilitate the exchange of laboratory and diagnostic testing information within the healthcare ecosystem. As part of the broader FHIR framework, which aims to enhance interoperability and data exchange in the health domain, the Specimen resource plays a crucial role in representing and managing information related to biological specimens used in clinical testing and research.


In the context of healthcare, specimens refer to biological materials, such as blood, urine, tissue samples, or any other bodily substances, collected from patients for diagnostic, research, or monitoring purposes. These specimens are central to the process of disease diagnosis, treatment planning, and monitoring treatment effectiveness. The FHIR Specimen resource provides a standardized and structured way to capture essential details about these specimens, ensuring consistency and compatibility across different healthcare systems and applications.

The primary goal of the FHIR Specimen resource is to enable seamless sharing of specimen-related information among healthcare providers, laboratories, researchers, and other stakeholders. By adopting a common data model, FHIR ensures that crucial details, including the type of specimen, collection method, storage conditions, and associated metadata, are consistently represented and easily accessible. This not only streamlines clinical workflows and enhances data accuracy but also supports more efficient research and clinical decision-making.

FHIR Specimen resource defines a set of standardized data elements and their associated semantics, allowing for clear and unambiguous communication of specimen-related information. This ensures that all parties involved in the healthcare process can interpret and utilize the data accurately, reducing the risk of misinterpretation and errors that may occur when using disparate or proprietary data formats.

FHIR Specimen Resource
FHIR Specimen Resource

Moreover, the FHIR Specimen resource is highly adaptable and extensible, accommodating a wide range of specimen types and attributes. This flexibility enables healthcare organizations to incorporate new types of specimens or additional details without disrupting existing systems, promoting future-proof solutions and adaptability to evolving medical practices and research requirements.

The FHIR Specimen resource is a critical component of the FHIR standard, designed to standardize the representation and exchange of vital information about biological specimens in the healthcare domain. By fostering interoperability and data consistency, it plays a pivotal role in supporting better clinical decision-making, more efficient laboratory processes, and advancements in medical research, ultimately leading to improved patient care and outcomes.

Structure of FHIR Specimen Resource

Here is the structure of the FHIR Specimen resource in JSON format along with an explanation of each element. Other format like XML and Turtle is also present, but for simplicity here we will take the example of JSON format. The complete structure details can be found here.

  "resourceType": "Specimen",
  "id": "example-specimen",
  "identifier": [
      "system": "",
      "value": "SPM-00123"
  "status": "available",
  "type": {
    "coding": [
        "system": "",
        "code": "25836-8",
        "display": "Venous blood specimen"
    "text": "Venous Blood"
  "subject": {
    "reference": "Patient/example-patient"
  "receivedTime": "2023-08-03T10:30:00Z",
  "collection": {
    "collectedDateTime": "2023-08-03T10:00:00Z",
    "collector": {
      "reference": "Practitioner/example-nurse"
    "method": {
      "coding": [
          "system": "",
          "code": "LNV",
          "display": "Venipuncture"
      "text": "Venipuncture"
  "processing": [
      "description": "Centrifuged",
      "procedure": {
        "coding": [
            "system": "",
            "code": "279157007",
            "display": "Centrifugation"
        "text": "Centrifugation"
      "timeDateTime": "2023-08-03T10:15:00Z"
  "container": [
      "id": "1",
      "type": {
        "coding": [
            "system": "",
            "code": "SER",
            "display": "Serum"
        "text": "Serum"
      "capacity": {
        "value": 10,
        "unit": "mL",
        "system": "",
        "code": "mL"
      "specimenQuantity": {
        "value": 8,
        "unit": "mL",
        "system": "",
        "code": "mL"
  "note": [
      "text": "Specimen taken from the left arm."
  "extension": [
      "url": "",
      "valueQuantity": {
        "value": 120,
        "unit": "bpm",
        "system": "",
        "code": "/min"

Explanation of the JSON elements:

  • resourceType: Indicates the type of resource, which is “Specimen” in this case.
  • id: An identifier for the specimen resource.
  • identifier: A list of identifiers associated with the specimen, in this case, an example identifier using a custom system.
  • status: The status of the specimen, indicating whether it is available, in transit, etc.
  • type: The type of specimen, represented as a coding system with a code and display value, along with a text representation.
  • subject: Reference to the patient from whom the specimen was collected.
  • receivedTime: The date and time when the specimen was received in the laboratory.
  • collection: Details about the specimen collection process, including the collection date and time, the collector, and the collection method (coded and text representation).
  • processing: Information about any processing steps the specimen underwent, such as centrifugation, represented by a description, procedure (coded and text representation), and time of processing.
  • container: Details about the container used to store the specimen, including an identifier, type (coded and text representation), capacity, and the quantity of specimen inside the container (with value and unit).
  • note: Additional notes or comments related to the specimen.
  • extension: An extension element to include additional information, in this case, a device metric value representing the heart rate (120 beats per minute) associated with the specimen.

Commonly used fields in FHIR Specimen Resource

The FHIR Specimen resource contains a variety of fields that can be used to represent different aspects of a biological specimen. The most commonly used fields in the FHIR Specimen resource include:

  • identifier: An identifier assigned to the specimen to uniquely identify it. This could be a local identifier from the source system or a standardized identifier.
  • status: Indicates the current status of the specimen, such as available, unavailable, in transit, etc.
  • type: Represents the type of specimen, typically coded using standard terminologies like LOINC.
  • subject: Reference to the patient or entity from whom the specimen was collected.
  • receivedTime: The date and time when the specimen was received in the laboratory or testing facility.
  • collection: Contains details about the collection process, including the collection date and time, the collector, and the collection method.
  • container: Information about the container used to store the specimen, including the type of container, capacity, and the quantity of specimen within the container.
  • processing: Represents any processing steps the specimen may have undergone, such as centrifugation or aliquoting, including the time of processing and the procedure description.
  • note: Additional notes or comments related to the specimen, providing contextual information or clarifications.

These fields are commonly used across various healthcare scenarios, such as clinical care, laboratory testing, research, and public health reporting. Additionally, specific use cases may utilize additional fields or extensions based on their requirements and the level of detail needed to represent the specimen adequately. As the FHIR specification evolves and new implementations emerge, the usage of fields may vary to accommodate diverse healthcare workflows and data exchange scenarios.

A use case where FHIR Specimen Resource can be utilized

Use Case: Specimen Tracking in a Clinical Laboratory

Description: In a busy clinical laboratory, efficient specimen tracking is crucial to ensure accurate and timely test results, prevent errors, and provide optimal patient care. Specimens, such as blood, urine, and tissues, arrive at the laboratory from various sources, including clinics, hospitals, and research centers. Managing and monitoring these specimens throughout their journey from collection to testing and result reporting is a complex process. Manual tracking systems may lead to delays, misidentification, or loss of specimens, compromising patient safety and overall laboratory efficiency.

Solution: Implementing the FHIR Specimen Resource can significantly improve specimen tracking in the clinical laboratory. Here’s how the solution can be implemented:

  1. Specimen Registration: When a specimen arrives at the laboratory, a unique identifier is assigned to it, and the details of the specimen, including its type, collection time, collector information, and any notes, are recorded using the FHIR Specimen Resource. This information is entered into the laboratory’s information system.
  2. Status Tracking: The status of the specimen is continuously updated in the FHIR Specimen Resource as it progresses through various stages, such as reception, processing, testing, and storage. The laboratory staff can easily update the status using appropriate FHIR codes, ensuring real-time visibility of each specimen’s location and progress.
  3. Container and Processing Information: The FHIR Specimen Resource captures container details, including the container type and quantity of specimen, ensuring that the laboratory can properly manage and store the specimens. Additionally, any processing steps, such as centrifugation or aliquoting, are documented within the resource.
  4. Electronic Data Exchange: With FHIR’s standardized data format, the laboratory can easily exchange specimen information with other healthcare systems, such as Electronic Health Record (EHR) systems, research databases, and public health agencies. This facilitates seamless integration and data sharing, reducing the need for manual data entry and minimizing the risk of transcription errors.
  5. Interoperability with Instruments: Modern laboratory instruments can be integrated with the FHIR Specimen Resource, allowing the automatic capture of instrument-generated data, such as test results and device metrics, associated with the specimen. This further streamlines the laboratory workflow and ensures result accuracy.
  6. Audit Trail and Security: FHIR’s built-in capabilities for auditing and security ensure that the access and modification of specimen information are tracked, and appropriate permissions are enforced, enhancing data integrity and compliance with privacy regulations.

By utilizing the FHIR Specimen Resource in this manner, the clinical laboratory can streamline specimen management, reduce errors, and improve overall efficiency. The real-time visibility and electronic data exchange capabilities enable faster decision-making, ensuring that patients receive timely and accurate test results, thereby enhancing the quality of healthcare services provided by the laboratory.

Here are a few general or interview questions related to the Specimen resource, which aims to gauge your knowledge about the resource, its practical application, and your understanding of healthcare interoperability principles.

1. What is the purpose of the FHIR Specimen Resource, and how does it contribute to healthcare data exchange?

The FHIR Specimen Resource serves as a standardized way to represent and exchange information about biological specimens used in clinical testing and research. It includes essential details such as specimen type, collection method, processing steps, and container information. By adopting the FHIR Specimen Resource, healthcare organizations can ensure consistency in data representation, making it easier to share specimen-related information across different systems and applications. This facilitates improved laboratory workflows, more accurate clinical decision-making, and better data integration across the healthcare ecosystem.

2. What are the key elements of the FHIR Specimen Resource? Can you give examples of how each element might be used?

The key elements of the FHIR Specimen Resource include “identifier,” “status,” “type,” “subject,” “receivedTime,” “collection,” “container,” “processing,” and “note.”

  • For example, “identifier” represents a unique identifier for the specimen in the laboratory system, ensuring proper tracking and identification.
  • “Status” indicates the current state of the specimen, such as available or in transit, providing real-time visibility of its status.
  • “Type” defines the category or kind of specimen, such as blood, urine, or tissue, ensuring standardization of specimen classification.
  • “Subject” references the patient or entity from whom the specimen was collected, linking the specimen to the appropriate individual’s health record.
  • “ReceivedTime” represents the date and time when the laboratory received the specimen, helping with timely processing and result reporting.

3. How does FHIR ensure the standardization and consistency of data representation in the Specimen Resource?

FHIR achieves standardization and consistency by defining a structured data model for the Specimen Resource, specifying the required and optional data elements, their data types, and their semantics. FHIR relies on established healthcare terminologies and coding systems, such as LOINC and SNOMED CT, to ensure consistent representation of specimen types, collection methods, and other relevant information. This standardized approach makes it easier for different systems to interpret and exchange data accurately, regardless of the source or destination.

4. Can you describe a real-world use case where the FHIR Specimen Resource would be beneficial in a healthcare setting?

One real-world use case for the FHIR Specimen Resource is in a large healthcare network with multiple clinics and laboratories. When a patient visits a clinic for a blood test, the clinician collects a blood specimen and records the details using the FHIR Specimen Resource. The information, including specimen type, collection time, and patient details, is then electronically transmitted to the central laboratory.

At the central laboratory, the FHIR Specimen Resource is used to track the specimen throughout its journey. The laboratory staff updates the specimen status as it goes through processing, testing, and storage. Test results generated by laboratory instruments are associated with the specimen using FHIR references, ensuring data linkage.

The laboratory can then share the test results with the patient’s electronic health record (EHR) system using FHIR data exchange. The EHR system can easily interpret the standardized specimen data and incorporate the test results into the patient’s record, allowing clinicians to make informed decisions based on the latest information. This use case demonstrates how the FHIR Specimen Resource facilitates seamless data exchange, enhances coordination between clinics and laboratories, and improves patient care outcomes.

5. How does FHIR handle the exchange of specimen-related data between different healthcare systems and applications?

FHIR facilitates the exchange of specimen-related data between different healthcare systems and applications through its well-defined API (Application Programming Interface) using standard web-based protocols like HTTP and RESTful principles. FHIR resources, including the Specimen Resource, are represented in a standardized format such as JSON or XML, ensuring consistency in data representation. Healthcare systems can communicate using FHIR messages, bundles, or queries, making it easier to retrieve, store, and update specimen data across various interoperable systems.

6. What are some of the challenges or limitations associated with implementing the FHIR Specimen Resource in a healthcare environment?

While FHIR offers numerous benefits, there are challenges and limitations to consider when implementing the FHIR Specimen Resource. Some common challenges include ensuring consistent adoption of FHIR across different healthcare organizations, addressing data privacy and security concerns during data exchange, and achieving data standardization when integrating with legacy systems. Additionally, mapping local or proprietary terminologies to FHIR standard terminologies can be complex. It’s essential to have a robust data governance strategy and clear data-sharing agreements to overcome these challenges.

7. How does FHIR support the capture and exchange of device metrics related to specimens in the Specimen Resource?

FHIR supports the capture and exchange of device metrics related to specimens through the use of extensions. Extensions in FHIR allow for the inclusion of additional data elements that are not part of the core specification. For example, to include device metrics such as temperature, weight, or heart rate related to the specimen, an extension can be defined using FHIR’s extensibility mechanisms. This enables seamless integration with devices, laboratory instruments, or monitoring equipment, ensuring that relevant device metrics are associated with the respective specimens.

8. In a laboratory setting, how could the FHIR Specimen Resource be used to track and manage specimens throughout their lifecycle?

In a laboratory setting, the FHIR Specimen Resource can be utilized to track and manage specimens throughout their lifecycle by maintaining a comprehensive record of each specimen’s journey. From the point of collection, the Specimen Resource can record information such as collection time, collector details, and collection method. As the specimen progresses through processing, testing, and storage, its status can be updated in real time within the resource. The Specimen Resource also captures container details and processing steps, providing a complete audit trail of specimen management activities.

9. What are some of the common data exchange standards and terminologies used in conjunction with the FHIR Specimen Resource?

In conjunction with the FHIR Specimen Resource, common data exchange standards, and terminologies include:

  • LOINC (Logical Observation Identifiers Names and Codes): Used for specifying laboratory observations and test results, including specimen types and observations related to specimen processing.
  • SNOMED CT (Systematized Nomenclature of Medicine – Clinical Terms): Used for describing clinical concepts and relationships, including standardized representations of specimen types and collection methods.
  • HL7 v2 Messaging: A widely used messaging standard for exchanging clinical and administrative data, which can include FHIR resources like the Specimen Resource as part of a message payload.

These standards and terminologies promote data interoperability and help ensure that specimen-related information is consistently represented and understood across different healthcare systems and organizations.

10. How would you approach extending the FHIR Specimen Resource to accommodate additional information or specific requirements for a particular use case?

Extending the FHIR Specimen Resource can be achieved through the use of FHIR extensions. For specific use cases or additional information not covered by the standard Specimen Resource, a custom extension can be defined. This extension should follow FHIR’s extension framework and reference a well-defined URL, specifying the new data elements and their semantics. Implementers can then use these extensions in conjunction with the core Specimen Resource to represent the specific information required for their use case, ensuring compatibility with the FHIR standard.

11. Can you describe the security and privacy considerations when exchanging sensitive specimen-related data using FHIR?

When exchanging sensitive specimen-related data using FHIR, security and privacy are critical considerations. FHIR supports several security features, such as OAuth 2.0 for authorization and HTTPS for secure communication. Implementers must ensure that access to specimen data is appropriately controlled through authentication mechanisms and access control lists. Additionally, data encryption during transmission and storage helps protect against unauthorized access. Compliance with healthcare data privacy regulations, such as HIPAA (Health Insurance Portability and Accountability Act), is crucial to safeguard patient information during data exchange.

12. How does FHIR ensure backward compatibility and versioning of the Specimen Resource?

FHIR maintains backward compatibility and versioning through the use of a standardized versioning approach. Each release of FHIR introduces a new version that may include updates, improvements, or new features. Changes to resources like the Specimen Resource are managed through version-specific URLs, ensuring that implementations using a specific version will continue to function correctly even as new versions are introduced. FHIR also provides tools and guidelines to help developers migrate from one version to another while preserving data integrity and compatibility.

13. How would you handle a scenario where data from multiple sources needs to be aggregated and harmonized within the FHIR Specimen Resource?

Aggregating and harmonizing data from multiple sources within the FHIR Specimen Resource can be accomplished through data integration and mapping processes. Each source’s data format and terminology may vary, so a data transformation and mapping strategy is essential. Data integration tools or ETL (Extract, Transform, Load) processes can be utilized to gather and transform data from disparate sources into the FHIR Specimen Resource’s standardized format. This ensures that all specimen-related information is consistent and compatible, facilitating effective data aggregation and interpretation.


In conclusion, the FHIR Specimen Resource plays a vital role in revolutionizing healthcare data exchange and management within the clinical laboratory and broader healthcare ecosystem. By providing a standardized and structured representation of specimen-related information, FHIR ensures seamless interoperability and consistency, enabling healthcare organizations to efficiently share and utilize critical data for improved patient care, research, and decision-making.

With the FHIR Specimen Resource, laboratories can accurately track specimens throughout their lifecycle, from collection to testing and storage, reducing errors and delays in the laboratory workflow. The resource’s flexibility and extensibility allow for easy adaptation to diverse use cases and evolving medical practices, ensuring that healthcare providers and researchers can capture and exchange all relevant specimen details with ease. Furthermore, FHIR’s adherence to robust security and privacy measures ensures that sensitive specimen-related data remains protected during transmission and storage, bolstering patient trust and regulatory compliance.

In essence, the FHIR Specimen Resource empowers the healthcare industry with a standardized and efficient means of handling biological specimens, fostering enhanced data exchange, and promoting collaborative efforts towards improved patient outcomes and medical advancements. As healthcare continues to evolve, the FHIR Specimen Resource stands as a pivotal component in achieving the overarching goal of seamless and patient-centric healthcare data exchange.

I hope you find this post helpful. Cheers!!!

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