Definition of a SNOMED CT pathology subset and microglossary, based on 1.17 million biological samples from the Catalan Pathology Registry

SNOMED CT terminology is not backed by standard norms of encoding among pathologists. The vast number of concepts ordered in hierarchies and axes, together with the lack of rules of use, complicates the functionality of SNOMED CT for coding, extracting, and analyzing the data. Defining subgroups of SNOMED CT by discipline could increase its functionality. The challenge lies in how to choose the concepts to be included in a subset from a total of over 300,000. Besides, SNOMED CT does not cover daily need, as the clinical reality is dynamic and changing. To adapt SNOMED CT to needs in a flexible way, the possibility exists to create extensions. In Catalonia, most pathology departments have been migrating from SNOMED II to SNOMED CT in a bid to advance the development of the Catalan Pathology Registry, which was created in 2014 as a repository for all the pathological diagnoses. This article explains the methodology used to: (a) identify the clinico-pathological entities and the molecular diagnostic procedures not included in SNOMED CT; (b) define the theoretical subset and microglossary of pathology; (c) describe the SNOMED CT concepts used by pathologists of 1.17 million samples of the Catalan Pathology Registry; and d) adapt the theoretical subset and the microglossary according to the actual use of SNOMED CT. Of the 328,365 concepts available for coding the diagnoses (326,732 in SNOMED CT and 1,576 in Catalan extension), only 2% have been used. Combining two axes of SNOMED CT, body structure and clinical findings, has enabled coding most of the morphologies

Differences in the Impact of COVID-19 on Pathology Laboratories and Cancer Diagnosis in Girona

Coronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Càncer; Diagnòstic; PatologiaCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Cancer; Diagnóstico; PatologiaCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Cancer; Diagnosis; PathologyIntroduction: The recent COVID-19 pandemic has compromised socio-health care, with consequences for the diagnosis and follow-up of other pathologies. The aim of this study was to evaluate the impact of COVID-19 on cancer diagnosis in Girona, Spain. Methodology: Observational study of samples received in two pathology laboratories during 2019-2020 (tertiary hospital in Girona and county hospital in Figueres). Date, sample type, and location and morphology were available. Samples were recoded to determine malignancy and grouped by location. Comparisons were made by calendar year and period of exposure to COVID-19. Results: 102,360 samples were included: 80,517 from Girona and 21,843 from Figueres. The reduction in activity in the pathology laboratories in 2020 compared to the previous year was 25.4% in Girona and 27.5% in Figueres. The reduction in cancer diagnoses in 2020 compared to 2019 was 6.8% in Girona and 21% in Figueres. In both laboratories, a decrease was observed in the diagnoses of neoplasms of the lip, oral cavity and pharynx, larynx, colon, rectum and anus, kidney and urinary system, melanoma, and central nervous system. A statistically significant higher probability of a sample received in the pathology laboratory displaying malignancy during COVID-19 was found (Girona: OR = 1.28, 95% CI: 1.23-1.34; Figueres: OR = 1.10, 95% CI: 1.01-1.20) with respect to the COVID-19-free period. Conclusions: The COVID-19 pandemic has resulted in a reduction in cancer diagnoses by pathology departments that varies according to tumor location and type of hospital. Despite this, the optimization of care resources and the recovery effort have partially reduced the impact of the pandemic in certain neoplasms.This work was partially funded by the Josep Carreras Leukaemia Research Institute (grant number: FIJC1100) and the Agency for Management of University and Research Grants, Government of Catalonia (grant number: 2017SGR00733

Definition of a SNOMED CT pathology subset and microglossary, based on 1.17 million biological samples from the Catalan Pathology Registry

SNOMED CT terminology is not backed by standard norms of encoding among pathologists. The vast number of concepts ordered in hierarchies and axes, together with the lack of rules of use, complicates the functionality of SNOMED CT for coding, extracting, and analyzing the data. Defining subgroups of SNOMED CT by discipline could increase its functionality. The challenge lies in how to choose the concepts to be included in a subset from a total of over 300,000. Besides, SNOMED CT does not cover daily need, as the clinical reality is dynamic and changing. To adapt SNOMED CT to needs in a flexible way, the possibility exists to create extensions. In Catalonia, most pathology departments have been migrating from SNOMED II to SNOMED CT in a bid to advance the development of the Catalan Pathology Registry, which was created in 2014 as a repository for all the pathological diagnoses. This article explains the methodology used to: (a) identify the clinico-pathological entities and the molecular diagnostic procedures not included in SNOMED CT; (b) define the theoretical subset and microglossary of pathology; (c) describe the SNOMED CT concepts used by pathologists of 1.17 million samples of the Catalan Pathology Registry; and d) adapt the theoretical subset and the microglossary according to the actual use of SNOMED CT. Of the 328,365 concepts available for coding the diagnoses (326,732 in SNOMED CT and 1,576 in Catalan extension), only 2% have been used. Combining two axes of SNOMED CT, body structure and clinical findings, has enabled coding most of the morphologies

Definition of a SNOMED CT pathology subset and microglossary, based on 1.17 million biological samples from the Catalan Pathology Registry

SNOMED CT terminology is not backed by standard norms of encoding among pathologists. The vast number of concepts ordered in hierarchies and axes, together with the lack of rules of use, complicates the functionality of SNOMED CT for coding, extracting, and analyzing the data. Defining subgroups of SNOMED CT by discipline could increase its functionality. The challenge lies in how to choose the concepts to be included in a subset from a total of over 300,000. Besides, SNOMED CT does not cover daily need, as the clinical reality is dynamic and changing. To adapt SNOMED CT to needs in a flexible way, the possibility exists to create extensions. In Catalonia, most pathology departments have been migrating from SNOMED II to SNOMED CT in a bid to advance the development of the Catalan Pathology Registry, which was created in 2014 as a repository for all the pathological diagnoses. This article explains the methodology used to: (a) identify the clinico-pathological entities and the molecular diagnostic procedures not included in SNOMED CT; (b) define the theoretical subset and microglossary of pathology; (c) describe the SNOMED CT concepts used by pathologists of 1.17 million samples of the Catalan Pathology Registry; and d) adapt the theoretical subset and the microglossary according to the actual use of SNOMED CT. Of the 328,365 concepts available for coding the diagnoses (326,732 in SNOMED CT and 1,576 in Catalan extension), only 2% have been used. Combining two axes of SNOMED CT, body structure and clinical findings, has enabled coding most of the morphologies