The classification of tumour types and subtypes with somatic mutations in the published literature is extremely variable. Classification systems and terminologies differ between reports and indeed may have changed over time. Rather than simply entering a tumour using the term employed in the published report, COSMIC uses its own internal classification system to provide tissue and histology consistency within the database and reduce redundancy. The tissue and histology information in the curated papers is translated using the COSMIC classification system before entry into the database. It is possible that in some instances we have misunderstood terminology and hence misclassified tumours. Moreover, some users may not favour our classification. In general, however, we have aimed to retain as much useful information as possible, whilst providing a relatively simple classification with generally understood terminology.
The COSMIC classification system is available as a tab delimited text or Excel file in the Download section below. Every sample is defined by both tissue and histology. The example below shows how a paper definition would be translated into a COSMIC definition. Additionally, COSMIC definitions have a unique Phenotype ID and are mapped to NCI Thesaurus (https://ncit.nci.nih.gov/ncitbrowser) and EFO (http://www.ebi.ac.uk/efo) codes.
Type Paper Definition COSMIC Definition Site primary colon large intestine Site subtype 1 descending colon Site subtype 2 NS descending Histology carcinoma carcinoma Histology subtype 1 polypoid type adenocarcinoma Histology subtype 2 with adenoma NS Histology subtype 3 NS NS Phenotype ID COSO28564826 NCI Code C4349 EFO link EFO_1001949
The COSMIC classification system was created in close collaboration with Adrienne Flanagan and Ahmet Dogan from the Royal Free and University College Medical School.