docm

is a Data Source.

DoCM (Database of Curated Mutations) was a highly curated database of known, disease-causing mutations in cancer, specifically focused on mutations with clinical or functional evidence. The project has been retired and succeeded by the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. All DoCM data remains available in archived form.

Domains

precision medicine, genomics, health

License

MIT

Homepage

docm

Repository

GitHub

Infores ID

infores:docm

FAIRsharing ID

Unknown

Product Summary

Contacts

Griffith Lab

Github: griffithlab

Products

From this Resource
ID Name URL Category Format Description
docm.variants.tsv DoCM Variants TSV variants.tsv.gz (35.0 KB) Product tsv Curated cancer mutations in tab-separ...
docm.variants.vcf DoCM Variants VCF variants.vcf.gz (42.9 KB) Product vcf Curated cancer mutations in Variant C...
docm.data.sql DoCM SQL Database data.sql.gz (1.1 MB) ProcessProduct ❔ Complete DoCM database in SQL format ...

Details

Database of Curated Mutations (DoCM)

Project Retirement Notice

⚠️ DEPRECATED: The DoCM project and DoCM.info web service has been retired as of October 2024. The project has been succeeded by CIViC (Clinical Interpretation of Variants in Cancer), which provides a more comprehensive and actively maintained resource for clinical cancer variant curation.

All historical DoCM data remains available in archived form through the GitHub repository.

Overview

DoCM (Database of Curated Mutations) was a curated database of known, disease-causing mutations in cancer. The database was developed and maintained by the Griffith Lab at Washington University and focused specifically on mutations that had clinical or functional evidence in the published literature.

The database cataloged somatic mutations with evidence of driver status in human cancer, providing researchers and clinicians with a high-quality reference of well-characterized cancer mutations.

Data Content

Curated Mutations

DoCM contained manually curated cancer-associated mutations with:

  • Gene information: Gene symbols and identifiers
  • Transcript details: Reference transcripts for each variant
  • Variant nomenclature: Precise mutation descriptions using HGVS notation
  • Disease associations: Specific cancer types linked to each mutation
  • Literature evidence: PubMed references supporting each curation
  • Functional impact: Assessment of mutation effects on protein function

Data Formats

The archived DoCM data is available in three formats:

  1. TSV: Tab-separated values for easy parsing and analysis
  2. VCF: Variant Call Format for genomics pipelines
  3. SQL: Complete database dump for local installation

Key Features

  • High-quality curation: Manual review and annotation by domain experts
  • Evidence-based: All mutations supported by published literature
  • Standardized nomenclature: HGVS variant descriptions
  • Cancer-focused: Specifically targeted somatic mutations in cancer
  • Multiple formats: Data available in TSV, VCF, and SQL formats
  • Open access: Freely available data under MIT license

Successor Project

DoCM has been succeeded by CIViC (Clinical Interpretation of Variants in Cancer), which provides:

  • Broader scope of variant types and clinical significance
  • Community-driven curation model
  • Regular updates and maintenance
  • Enhanced clinical interpretation framework
  • Integration with multiple genomic databases

Users seeking actively maintained cancer variant data should use CIViC instead of DoCM.

Access Methods

  1. Archived Data: Download TSV, VCF, or SQL files from the GitHub repository
  2. GitHub Repository: Access source code and archived data at https://github.com/griffithlab/docm
  3. Historical Web Interface: The original docm.info website is no longer accessible

Use Cases

While DoCM is retired, the archived data remains valuable for:

  1. Historical Analysis: Studying the evolution of cancer mutation knowledge
  2. Benchmark Datasets: Using curated mutations for validation studies
  3. Data Integration: Incorporating legacy DoCM annotations into pipelines
  4. Comparative Studies: Comparing historical curation against current resources
  5. Educational Purposes: Learning about cancer mutation curation practices

Technology Stack

  • Ruby on Rails: Web application framework
  • PostgreSQL: Relational database backend
  • JavaScript: Frontend interactions
  • Haml: Template engine
  • Less/CSS: Styling

Management

Developed and formerly maintained by the Griffith Lab at Washington University School of Medicine in St. Louis. The project was archived in October 2024, with all future curation efforts redirected to CIViC.

  • CIViC: Successor project providing actively maintained clinical cancer variant curation
  • ClinGen: Clinical genome resource for gene-disease validity
  • ClinVar: Public archive of interpretations of clinically relevant variants

Retirement Date

October 15, 2024 - Repository archived; web service discontinued

Is this information incorrect or incomplete? Request an update.

Created: October 30, 2025 | Last modified: January 20, 2025