Research and applications Permissible values of a data element ‘Lesion Measurable Evaluation Anatomic Site’ from the selected data element samples for human Value meaning Liver Brain Lung Bone Skin Breast Other NCIt code (meaning concept) C12392 C12439 C12468 C12366 C12470 C12971 C17649 Liver Brain Lung Bone Skin Breast Other NCIt concept label Semantic type Type code Semantic group Group code Body Part, Organ, or Organ Component Body Part, Organ, or Organ Component Body Part, Organ, or Organ Component Tissue Anatomical Structure Body Part, Organ, or Organ Component Qualitative Concept T023 T023 T023 T024 T017 T023 T080 Anatomy Anatomy Anatomy Anatomy Anatomy Anatomy Concepts & Ideas ANAT ANAT ANAT ANAT ANAT ANAT CONC Each row represents a permissible value, its asserted NCIt concept code, the linkage to the semantic type and code, and the linkage to its corresponding semantic group name and code. Data element: Lesion Measurable Evaluation Anatomic Site (2003735). Value domain: Lesion Anatomic Site (2017124). NCIt, National Cancer Institute Thesaurus. UMLS semantic group for their asserted NCI concept codes, covering 1350 distinct enumerated value domains, whereas 3093 (26.2%) CDEs had multiple UMLS semantic groups mapped to their asserted NCI concept codes, covering 1848 distinct enumerated value domains. We randomly selected 100 CDEs out of the 3093 CDEs that failed the single semantic group criteria and performed a preliminary evaluation on the permissible values of their enumerated value domains through a manual review. In these 100 CDEs, there were 1415 permissible values from 92 distinct enumerated value domains. The number of permissible values in each enumerated value domain ranged from 2 to 156. For each CDE, we extracted its public ID, long name, the public ID and long name of its value domain, and the data on each permissible value (comprising valid value and value meaning). For each asserted NCIt concept code, we extracted its label name, its semantic type and code, and its corresponding semantic group name and code. Table 1 shows the permissible values of a data element ‘Lesion Measurable Evaluation Anatomic Site’ from the selected data elements. Anchored by the semantic group, the permissible values of all 100 CDEs were reviewed. All three of us have expertise and experience with data collection standards for clinical research, and two (GJ and CGC) have backgrounds in clinical medicine. We identiﬁed 17 CDEs that had inconsistency issues associated with their permissible values and corresponding asserted NCIt concept codes. Table 2 shows the summary of the evaluation results for the 17 CDEs, including the dominant semantic group of permissible values and inconsistent code examples for each CDE. As a case study, we chose two example CDEs to explain how we identiﬁed the inconsistency for their permissible values and corresponding asserted NCIt concept codes. Table 2 Summary of evaluation results for 17 data elements including the dominant semantic group of permissible values and inconsistent code examples for each CDE Data element ID Data element name Number of asserted NCIt codes Dominant semantic group Other semantic group Table 1 review Valid value Liver Brain Lung Bone Skin Breast Other 3179024 2663176 2188290 2672955 2673966 62339 2785775 2783910 3109755 2963645 3197150 2784056 2919627 3162656 2695092 3012793 2755993 PHEN LIVB DISO PHYS, DISO, ACTI DISO DISO ANAT, DEVI, CHEM. OBJC, ACTI CONC, OBJC, ACTI, CHEM, PHYS, PROC, ANAT CONC OCCU, ANAT OCCU, CONC, ANAT, ACTI, OBJC CONC, OBJC CHEM, ACTI DISO, PHEN, PROC, LIVB, ACTI CONC, LIVB OBJC, LIVB, CONC Inconsistent asserted NCIt code examples C17262|X-Ray C25174|Father C35571|Progressive Disease C25379|Course, C28245|Inhalation, C67447|Session C14174|Metastatic C3331|Pleural Effusion, C2885|Ascites Multiple codes Multiple codes C51951|Platelet Count C63921|Radius, C25253|Multifocal C17173|Surgery C17173|Surgery, C25436|Block C25574|Molecular, C25278|Fluid C25158|Capsule, C25397|Application C38757|Negatvie Finding, C38758|Positive Finding C17734|At-Risk Population Multiple codes e133 Malignant Neoplasm Measurable Disease Evaluation Method Clinical Trial Eligibility Criteria Type Template (Object Class) Name Preﬁx Code Disease Response Site Status Preparative Regimen Other Finished Pharmaceutical Product Planned Administered Dose Unit of Measure Name Glioblastoma Pathology Or Primary Neoplasm Metastatic Neoplasm Status Tumor Status Text Name Gynecologic Malignant Neoplasm Progression Anatomic Site Hematopoietic Stem Cell Graft Arrival Facility Shipping Environment Type New Specimen Order Object Specimen Type Specimen Type Collection Text Type National Surgical Adjuvant Breast and Bowel Project Laboratory Procedure Outcome Type Bone Sarcoma Or Soft Tissue Sarcoma Disease or Disorder Primary Occurrence Anatomic Site Type Participant Personal Medical History Cardiac Surgery Type Kidney Biopsy Pathology Surgical Procedure Specimen Procedure Molecular Specimen Class Specimen Class Text Type Study Agent Dosage Unit of Measure Code Laboratory Procedure IgG Or Total Cytomegalovirus Antibody Laboratory Finding Result First Electrocardiogram Right Bundle Branch Block Status Composition Element Type Composing Element Type 6 13 9 49 8 13 10 64 4 47 4 53 4 22 38 5 16 PROC CONC CONC CONC CONC ANAT CONC ANAT CHEM ANAT PROC PROC ANAT CONC CONC DISO CHEM CDE, common data element; NCIt, National Cancer Institute Thesaurus. J Am Med Inform Assoc 2012;19:e129ee136. doi:10.1136/amiajnl-2011-000739