mapping-commons/mapping-commons.github.io

Repo for the user facing documentation of mapping-commons

Welcome to Mapping Commons

Mapping Commons pulls together mappings from various sources with the goal of offering them as simple to read, well provenanced TSV files in the SSSOM format. At first, the effort will focus on biomedical ontologies and controlled vocabularies, see for example the Mouse-Human Ontology Mapping Effort. The initiative was founded early 2021.

Contribute

If you want to contribute mappings or have questions, please use the issue tracker.

mapping-commons.github.io's Issues

Parse all mapping registries as a preprocessing step

Instead of loading the mappings registries client side from the network, lets

1. Create a Makefile with a makegoal

mappings.yml: mapping-server.yml
      python scripts/read_mapping_registry_metadata.py --registry $< --metadata $@

This goal should read the mapping-server.yml, load all the mapping sets and create one big yaml file with mapping set metadata.
2. Use mappings.yml for the VUE component to render.

Add recommended pronunciation to FAQ

I have come across many different pronunciation for SSSOM ("Tripple-Es Oh Em", "Es Es Es Oh Em", "Es Es Som" are more). This can sometimes cause some mild confusion, in particular when there is no written form accompanying the spoken words. During one of the discussions on how to properly pronounce the standard, I took a look at the FAQ, where I would have assumed to find a clarification on the topic but I didn't find any recommended pronunciation there. So I hereby suggest to add one. And for the time being I will stay with "Tripple-Es Oh Em" (analog to IIIF being called "Triple I Ef")until somebody suggest that there is a different and preferred pronunciation.

Create a nicer formatted overview

Right now the table is a bit simple:

Can we create a nicer view here, which probably does not look at all like a table and more like a list?

@souzadevinicius only deal with this for fun, don't prioritise. (Its a cool side project)

Disease mappings content not loaded

Disease mapping content not loaded.. Maybe the problem is with the fact that http URLs are used?

Tragic. Annoying.

make clinical subset of mapping commons

For supporting the clinical communities, we need a mapping commons that is a subset of content that can be deployed in clinical systems. There are multiple strategies for achieving this - individual folders/repos/mappings could be tagged and therefore pulled into the server and systems. Alternatively we could have a secondary mapping commons that is where you put content that is focused on only clinically relevant mappings and terminologies/concept sets as defined by the their sources. @callahantiff @chrisroederucdenver @matentzn @joeflack4