Review biomarker hierarchy

[zoependlington]

Request via Twitter.

We are asked to:

• Add protein IDs
• Look for missing subsumption in the protein biomarkers

[helenp]

twitter ref @Eric_Fauman
I love the potential of the EFO but it needs a ton of work especially in the pQTL and mQTL space. CRP (http://www.ebi.ac.uk/efo/EFO_0004458 ) is ok but it would be nice to link to a gene or protein identifier.

[zoependlington]

Another review of axioms is happening here: #10

[fauman]

Great - glad this is here. Here are a few protein measurements that are not classed as protein measurements in the EFO:
EFO:0003966
EFO:0005080
EFO:0005081

[fauman]

For "protein identifier" I've actually been using HUGO gene symbols, but this isn't entirely proper as the analyte is a protein not a gene. uniprot or ensembl protein identifier might be more appropriate.
I'm happy to help here as I have mapped I believe all published pQTLs (with p <= 5e-8) to gene symbols.

[paolaroncaglia]

At our EFO meeting today, we resolved that we will as a first pass

• Look at, and fix, the 3 cases above
• Add UniProt IDs as annotations (we'll add the details here)
• Classify as many measurement terms under 'protein measurement' where appropriate

[paolaroncaglia]

@fauman
Your first example above is actually not a protein measurement but a disease: https://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0003966
Perhaps that was a typo.
Note for self/EFO editor - the other two examples are true protein measurements and should indeed be classified as such.

[fauman]

Yes - not sure where that one came from.
Here's one not on my list above, PSA:
http://www.ebi.ac.uk/efo/EFO_0004624

Many others fall under a group with "biomarker" in the name, but not the protein biomarker group.
e.g.:
iron biomarker measurement
Ferritin: http://www.ebi.ac.uk/efo/EFO_0004459

With Ferritin you'll have to decide what to do with proteins that are multimers produced by multiple transcripts from multiple genes. Best to include all relevant uniprot IDs.