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. 2024 Feb 7;4(1):vbae018.
doi: 10.1093/bioadv/vbae018. eCollection 2024.

CMAT: ClinVar Mapping and Annotation Toolkit

April Shen  1 , Marcos Casado Barbero  1 , Baron Koylass  1 , Kirill Tsukanov  1 , Tim Cezard  1 , Thomas M Keane  1
Affiliations

CMAT: ClinVar Mapping and Annotation Toolkit

April Shen et al. Bioinform Adv. .

Abstract

Summary: Semantic ontology mapping of clinical descriptors with disease outcome is essential. ClinVar is a key resource for human variation with known clinical significance. We present CMAT, a software toolkit and curation protocol for accurately enriching ClinVar releases with disease ontology associations and complex functional consequences.

Availability and implementation: The software and ontology mappings can be obtained from: https://github.com/EBIvariation/CMAT.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Top: CMAT workflow, including automated and manual processes, intermediate files, and indication of where external APIs are leveraged. Bottom: an example of CMAT’s annotation applied to a ClinVar record, showing how the trait “Relapsing remitting multiple sclerosis” is mapped to EFO:0003929 and that the variant 12:54283899: A:G is a missense mutation (SO:0001583) on the gene ENSG00000135486. Portions of the XML are omitted for clarity.
See this image and copyright information in PMC

References

    1. Henrie A, Hemphill SE, Ruiz-Schultz N. et al. ClinVar miner: demonstrating utility of a web-based tool for viewing and filtering ClinVar data. Hum Mutat 2018;39:1051–60. - PMC - PubMed
    1. Kamdar MR, Tudorache T, Musen MA. et al. A systematic analysis of term reuse and term overlap across biomedical ontologies. Semant Web 2017;8:853–71. - PMC - PubMed
    1. Landrum MJ, Chitipiralla S, Brown GR. et al. ClinVar: improvements to accessing data. Nucleic Acids Res 2020;48:D835–44. - PMC - PubMed
    1. Malone J, Holloway E, Adamusiak T. et al. Modeling sample variables with an experimental factor ontology. Bioinformatics 2010;26:1112–8. - PMC - PubMed
    1. McLaren W, Gil L, Hunt SE. et al. The ensembl variant effect predictor. Genome Biol 2016;17:122. - PMC - PubMed