Why does OT distinguish between phenotypes and diseases? or sometimes between disease and disease with the same name?

General
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For instance, why two terms, one for ‘Acute pancreatitis/HP_0001735’ and another for ‘Acute pancreatitis/EFO_1000652’? Or for instance ‘amenorrhea/EFO_0010269’ and ‘amenorrhea/MONDO_0001836’?

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Dear Rodrigo,
thank you for reaching out to us and for reporting this issue.

I have now opened a ticket for the the ontology team at EBI to take a look at the duplication of diseases for the amenorrhea example.

The first example you report is more complicated to resolve and we will have to take a closer look. It is due to an ongoing issue in the phenotype/disease ontology space where a condition, such as acute pancreatitis, and a symptom/phenotype, again acute pancreatitis, can be considered both a disease and a phenotype.
EFO (our ontology of reference) imports from both phenotype and disease domains (HP and MONDO). There are also some historical duplications where there may be an EFO phenotype or disease term and an imported disease/phenotype term with the same label. It’s something we’re aware of but currently do not have the perfect solution to fix.

I hope this helps!

Best,

Annalisa

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Yes, it helps. Thank you for your prompt response. Regarding to their impact in biological interpretations, for instance, in the case of obesity/EFO_0001073 and Obesity/HP_0001513, LEP should be well ranked with respect to EuropePMC, but it is not as much (score 0.27 for obesity/EFO_0001073). But it is well ranked in the case of Obesity (score 0.98 for Obesity/HP_0001513).

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