EFO Cancer Branch Overhaul

[zoependlington]

For a while the cancer branch has not been adequate, however upon investigation the issues are multi-layered and include incorrect synonyms, x-refs and parentage through out the entire neoplasm branch.

After discussions with the Mondo team and those who require cancer annotation for Open Targets, we have decided on the following approach:

• Mondo will ingest important cancer areas of NCIT.
• EFO will add these Mondo terms into the existing import.
• EFO will also begin to replace existing EFO terms with the Mondo terms they are mapped to in order to remove any old and static term information and ensure that the terms will remain updated in the future.

The majority of this work must be done before August 16th release.

[matentzn]

This will be a fun ticket to work on :)

[matentzn]

• Zoe to finish mapping (sorry, automatic matching did not really yield enough to be beneficial here)
• Nico to run pipeline to reclassify neoplasms

[matentzn]

@zoependlington Just so I can schedule it - do we want to do this before this months release? It will take me about 1 day, so it would be good if I knew soon if I should keep it free.

[zoependlington]

Yes, we need this to be in before the August release. I'll finish the mappings this week.