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How to set up a Mapping Commons

A mapping commons is an open, collaborative space for managing and reconciling mappings. The goal is to collect mappings from a variety of sources into a mapping set registry, standardise them into a common representation, curate some basic metrics such as "confidence" (how much does the community managing the commons trust a specific mapping source?) and provenance (where exactly did this mapping come from before it was integrated).

There is no agreed upon standard for mapping registries yet. SSSOM itself provides a lighweight metadata model for mapping registries which is, as of August 2023, under active development.

Typical setup of a mapping commons

We recommend to base your mapping commons on a combination of GitHub (or GitLab) collaborative workflows (issues and discussions for the community, access management etc) and a git repository based on the Mapping Commons Cookiecutter Template for version control of the mappings.

Using the template system above allows you to:

  1. make use of basic CI and quality control for your mappings,
  2. provides a standard way to document metadata about your mapping sets
  3. provides a basic ETL system based on gnu make (which you dont have to use, its just convenient)
  4. Provides a standardised registry format that can be re-used/imported by others.

Examples of Mapping Commons are:

  1. https://github.com/mapping-commons/mh_mapping_initiative
  2. https://gitlab.c-path.org/c-pathontology/mapping-commons