Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add mapping commons information #139

Open
cthoyt opened this issue Jul 28, 2023 · 3 comments
Open

Add mapping commons information #139

cthoyt opened this issue Jul 28, 2023 · 3 comments

Comments

@cthoyt
Copy link
Member

cthoyt commented Jul 28, 2023

In perma-id/w3id.org#3508, I will get a permalink for the Biomappings SSSOM TSV file: https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv.

I want to do one or both of the following:

  1. Have the appropriate configuration somewhere in this repository such that it can be loaded as a "mapping commons"
  2. Write the appropriate boilerplate information so it can be imported into other mapping commons that would fit in a configuation like https://github.com/mapping-commons/mapping-commons-cookiecutter/blob/main/%7B%7Bcookiecutter.project_name%7D%7D/registry.yml

@matentzn @ehartley any suggestions would be helpful. overall, the goal is to make it as easy as possible to get the content in Biomappings to other places

@matentzn
Copy link

Nice. I mean, you could superimpose a SSSOM mapping registry using the cookie cutter - its quite minimal. Here is an example that was set up with the cookiecutter:

https://gitlab.c-path.org/c-pathontology/mapping-commons

If you want to do it manually I think at the very least you will want:

  1. https://gitlab.c-path.org/c-pathontology/mapping-commons/-/blob/main/registry.yml
  2. SSSOM validation, e.g. https://github.com/mapping-commons/mh_mapping_initiative/blob/master/.github/workflows/qc.yml

From the perspective of interoperability, the registry.yml is the main thing, but its specification is still a bit in flux - suggestions welcome!

@cthoyt
Copy link
Member Author

cthoyt commented Jul 29, 2023

Great, I think by looking at the registry file, there are a few simple renaming suggestions I could give to make it easier to read and use. I'd also say registry.yml isnt very descriptive - maybe calling it mapping-commons.yml would be more explicit and more searchable

@matentzn
Copy link

Cool, for repo level things like filenames and CI, use https://github.com/mapping-commons/mapping-commons-cookiecutter/issues

For improvement suggestions for the mapping registry metadata model use https://github.com/mapping-commons/sssom/issues (current model is barebones: https://mapping-commons.github.io/sssom/MappingRegistry/).

In my presentations, I separate mapping commons, the social collaborative organisational structure that manages the registry, from the registry itself, which is just a list of mapping sets with a bit of metadata.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants