(Apologies for the long delay responding to this. Somehow our system for notifying us for forum posts didn’t recognize this post until just recently.)
What you’re describing sounds like that there are inconsistencies in which models have which identifiers, and that’s not entirely surprising given the separate nature of these different projects. Both Broad and Sanger are physically receiving and screening lines from various sources. As result, there are two distinct registration systems in play, which may have lines unique to each organization.
We do periodically try to reconcile our collections with each other to identify lines which are actually the same between both organizations and resolve disagreements. However, that process is done occasionally, and based on the published data that was available at the time. As a result, the two are unlikely to ever be fully concordant.
One thing I can offer is that I would stick to using depmap_id and sanger_id, but avoid using ccle_id. At this time, the CCLE project lives on as part of DepMap data generation efforts, but the “ccle_id” nomenclature is not being maintained and so I would only use it for historical datasets which were created prior to the existence of depmap_ids.
In other words:
I wouldn’t say that Sanger or Broad can be used as “the standard” because these are two independent efforts which are have activities happening in parallel. Neither collection will be a superset of the other.
However, between CCLE IDs and DepMap IDs, you should use the DepMap IDs as they have replaced the CCLE naming scheme.
Thanks,
Phil
