Review biomarker axioms

EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)

https://www.ebi.ac.uk/efo/

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Review biomarker axioms #10

Closed siiraa closed 2 years ago

siiraa commented 7 years ago

Iron biomarker - done autoimmune disease biomarker - done cancer biomarker - done

@daniwelter please fill in what else are left to review.

simonjupp commented 6 years ago

Are there other biomarkers that need review? @twhetzel please review

daniwelter commented 6 years ago

Virtually all biomarkers need to be reviewed and updated to the correct pattern (is_about some and has role some biomarker). The problem is that the current incorrect pattern wrongly classifies things as biomarkers, so it's not just a case of updating the patterns but also of checking each class currently inferred as a biomarker to make sure it actually is a biomarker. The cardiovascular disease biomarkers are a particularly good (bad?) example of this.

daniwelter commented 5 years ago

Current biomarker measurement equivalent classes:

iron biomarker measurement - OK
cancer biomarker measurement - OK
inflammatory biomarker measurement - needs review!
liver disease biomarker - needs review!
osteoarthritis biomarker measurement - OK
diabetes mellitus biomarker - needs review!
autoimmune disease biomarker - needs review!
infectious disease biomarker - needs review!
Alzheimer's disease biomarker measurement - needs review!
cerebrospinal fluid biomarker measurement - OK
respiratory disease biomarker - needs review!
cardiovascular disease biomarker measurement - needs review!
mental or behavioural disease biomarker - needs review!

Also:

cardiac stress biomarker measurement - not a defined class, should be reviewed to follow the pattern.

zoependlington commented 4 years ago

Tagging this as a potential proposal for Open Targets. @smnorthen I believe you conducted a review of biomarkers, would it be useful to have others aid in this review too?

Also see #287

smnorthen commented 4 years ago

@zoependlington Yes, I had a look at the biomarker groupings in EFO in connection with another project. I am happy to provide input with regards to the structure in the ontology.

@dOchoa Please can you take a look and see if this would be of interest to OT?

d0choa commented 4 years ago

The biomarker problem is within scope, what I'm not sure is what would be the task. The context of the proposal we have discussed would require to define a task that can easily be tackled by a distributed group of people with not much specific training.

paolaroncaglia commented 2 years ago

@zoependlington I suspect that this ticket would be superseded by addressing #1005 , #1087 and #1162 . If so, it can be closed.