PathLex, a single lexicon in the Anatomic Pathology domain

The PathLex project is launched by IHE and HL7 Anatomic Pathology, with the collaboration of other Anatomic Pathology organizations, including the College of American Pathologists, the French Society of Pathologists and the SEAP (Spanish Society of Pathology). The purpose and scope of the PathLex project is very similar to those of the RadLex project in the radiology domain. The Pathlex project has been “designed to satisfy the needs of Anatomic Pathology information system vendors and users by adopting the best features of existing terminology systems, while producing new terms to fill critical gaps. Rather than “re-inventing the wheel”, PathLex unifies and supplements other terminology systems”, such as SNOMED-CT, CIM-O or various vocablary tables defined by DICOM and HL7. With the recent advances achieved by IHE and HL7 Anatomic Pathology (APW, ARPH and APSR integration and content profiles1) and DICOM WG 26 (supplement 122 & 145) standard-based informatics transactions has been defined to support the basic diagnostic workflow in anatomic pathology departments including managing whole-slide images and semantically rich structured reports in the diagnostic workflow. As part of these standardization efforts, a key issue is to guaranty that standard messages and document structures are semantically consistent within and across standards (HL7 v2.5, HL7 v3, DICOM). It is indeed crucial to guaranty that the same structured clinical information carried out through different information systems is attached to the same meaning and uniformly interpreted by both human and machines. Since a variety of terminologies are currently used in the Anatomic pathology domain, there is a need of a single lexicon that could serve all of their needs. PathLex is designed to fill this need.

PathLex, an “interface terminology” mapped to “reference terminology” Standard-based transactions used in IHE integration profiles provide a “model of use”2. Vocabulary tables defined as part of the standards messages (HL7 v2.5, DICOM IOD) or document templates (HL7 CDA templates for AP structured reports) used in the Anatomic Pathology domain contain relatively common clinical terms designed to improve acceptability of information systems to healthcare providers. The aim of PathLex is to unify in a single lexicon this vocabulary. PathLex is a so-called “interface terminology” defined by Rosenbloom et al. as “systematic collections of clinically oriented phrases (i.e., ‘terms’) aggregated to support clinicians’ entry of patient information directly into computer programs, such as clinical documentation (i.e., ‘note capture’) systems”3. Despite their prevalence for electronic data capture, no single standard interface terminology exists for medicine. In contrast, standards have been identified for reference terminologies such as SNOMED CT, the emerging global health terminology standard published by IHTSDO, that provides unified meanings for clinical terms from different languages by

1 Anatomic Pathology Workflow (APW) is an intra hospital integration profiles covering the ordering and performing of anatomic pathology examinations. Anatomic Reporting for Public Health (ARPH) is an integration profile for sending anatomic pathology reports to public health organizations. Anatomic Pathology Structured Report (APSR) is a content profile for sharing or exchanging structured anatomic pathology reports as CDA documents.

2 Benson T. Principles of Health Interoperability HL7 and SNOMED. Springer Verlag, 2009.

3 Rosenbloom ST, Miller RA, Johnson KB. Interface terminologies: facilitating direct entry of clinical data into electronic health record systems. J Am Med In-form Assoc. 2006 May-Jun;13(3):277-88. Rosenbloom ST, Brown SH, Froehling D, Bauer BA, Wahner-Roedler DL, Gregg WM, Elkin PL. Using SNOMED CT to represent two interface terminologies. J Am Med Inform Assoc. 2009 Jan-Feb;16(1):81-8.

PathLex, Draft document – IHE Anatomic Pathology assigning them to language-independent concepts. Furthermore, reference terminologies are typically optimized to support the storage, retrieval, and classification of clinical data. Mapping interface terminologies (as part of a model of use) to standard reference terminologies (as part of the model of meaning) rather than identifying one or more interface terminologies to serve as standards is now a commonly admitted strategy towards semantic interoperability.

PathLex, current status In order to publish, implement and test (during IHE connectathons) IHE APSR content profile) it was decided to use PathLex to encode Anatomic Pathology observations and AP ancillary technique observations and their corresponding value. The current version of PathLex defined by the IHE Anatomic Pathology domain (PathLex - OID : 1.3.6.1.4.1.19376.1.8.2.1) is published as part of the IHE content profile “Anatomic Pathology Structured Report” (APSR)4. This content profile provides 22 HL7 CDA (a generic template for APSR, a generic template for cancer APSR and 20 organ-specific templates for cancer APSR). PathLex derives from the APSR CDA templates; it consists in 1700 terms or expressions corresponding to the display names of the Anatomic Pathology observation (n=99) and AP ancillary techniques (n=16) and of their corresponding value sets (in case of coded observations). Theses value sets are specified in the document “Appendix Value Sets for APSR”. PathLex is available in English and French and is currently being mapped to concept(s) from reference terminologies like SNOMED CT, SNOMED International V3.5, ADICAP, CIM- O.

PathLex a lexicon to support collaborative digital Anatomic Pathology for patient care coordination and research activities An important pre-requisite to the best implementation of Collaborative Digital Anatomic Pathology for both patient care coordination and research activities, is to provide the “model of meaning” corresponding to the data & images that are captured, shared and exchanged. Using a reference terminology such as SNOMED CT offers promising perspectives in terms of scalable semantic queries that could be performed over distributed Anatomic Pathology Information Systems (APIS), EHRs or Clinical Data Warehouses storing these structured reports. Mapping PathLex to SNOMED CT concepts (i.e providing SNOMED CT for Anatomic Pathology observations and AP ancillary technique observations and their value sets) is therefore a key issue. For some observations (e.g histologic type) this process is straightforward, for others (e.g TNM) there is no pre-coordinated SNOMED CT concepts available to represent the meaning of the TNM terms/expressions.

Other issues with regards to the PathLex content could be: To extend PathLex with the coded content available in the other standards (HL7 v2.5 and DICOM IOD) used in the transactions in IHE integration profiles To extend PathLex to other domains (e.g inflammatory domain in nephrology) To extend PathLex with vocabularies used in research activities (clinical research, biorepositories, cytogenetics, etc)

4 Available on the ihe.net web site

PathLex, Draft document – IHE Anatomic Pathology PathLex, as a SNOMED extension There is a need of collaboration between IHTSDO & IHE and especially with IHE Anatomic Pathology (such collaboration exists with DICOM, HL7, OpenEHR). As stated by K.Spackman during the IHE-HL7-IHTSDO Anatomic Pathology joint meeting in Vilnius (July 2010), PathLex could be in the future managed as a SNOMED CT extension. An extension allows authorized organizations to add locally valid content and subsets without compromising the main body of SNOMED CT. Extensions may contain Concepts, Relationships, Subsets, Cross Map Sets. These components have the same structure as core components of SNOMED CT. Concepts in an extension must be subtype descendants from a core concept.

PathLex, a lexicon managed in collaboration (IHE AP, HL7 AP, DICOM WG26, IHTSDO (IPALM), w3c) A working group within IHE Anatomic Pathology and HL7 Anatomic Pathology is in charge of defining the governance of Pathlex and the process and tools required for its management according to this work plan: Defining a planning committee in charge of defining the strategy and the methodology of the process and the priorities in terms of content Establishing formal collaboration with reference terminology centers (IHTSDO (International Pathology and Laboratory Medicine Special Interest Group (IPaLM SIG), NLM, NCI) Defining organ system committees in collaboration with anatomic pathology professional and standards organizations Developing (or selecting an existing) collaborative platform dedicated to the management of PathLex and the mappings with other terminologies

PathLex, Draft document – IHE Anatomic Pathology