Open matentzn opened 3 years ago
@sbello also asked about close vs narrow/broad. I responded:
This is another hugely important issue: close vs narrow/broad. Intution: narrow should be used if the HP term is “kinda like a subclass”, broad if its “kinda like a superclass” and close if its “kinda not like a sub or super class, perhaps a sibling class”. “relatedMatch” should be used if its none of the above, but the term you map to lives in a completely seperate branch of the ontology (say you map an exposure to a chemical to a chemical).
@matentzn what would you use to relate these types of examples: Neurofibromas (HP:0001067) to increased neurofibroma incidence (MP:0010314) Neuroblastoma (HP:0003006) to increased neuroblastoma incidence (MP:0002039) Basically the difference is that the HP has terms for the tumors and MP has terms for incidence of the tumors. We've been using related for these. Do you think that is correct or would close be better.
Devil is in the details :)
I am assuming that "increased incidence" refers to the likelihood of getting one more.
In this case, I would say, they are related. Questions to ask are: 1) are they exact? -NO 2) Does Neurofibromas imply increased neurofibroma incidence - NO (if YES, then BROAD) 3) Does increased neurofibroma incidence imply Neurofibromas - NO (if YES, then NARROW) 4) What is the common parent between increased neurofibroma incidence and Neurofibromas? Are they sort of similar? Then CLOSE. 5) Else related. Related really is the free for all. You should add a comment why you believe they are related, and if possible, how they are related. The may be another relation here that is more applicable, and we would want to investigate it, like something causal. BUt for your use case, this is enough.
Wouldn't it be better to use a different kind of relationship, like
increased neurofibroma incidence (MP:0010314)
I agree, but this goes beyond the use case that @sbello needs to cover - the question of the relationship needs to be dealt with in uPheno, and generally for all of phenotype modelling. Her task is to produce a reasonable mapping between MP and HP for some set of terms at the moment; I will use her comments though to think about the right modelling ontology level though.
Chiming in, feel free to ignore. I agree it would be ideal to allow for more formally defined and expressive axioms around the mappings, but also worry that it quickly would get too complex for most to do consistently or accurately. Not that most people couldn't do this, but I am guessing they will find it overwhelming. I'd also think if you allow people to do this you'd also want to enforce the use of a reasoner afterward to verify consistency. Just my 12.5 ¢. :D
I think you are absolutely right @callahantiff
Relationships etc should be done on pattern level, i.e. https://github.com/obophenotype/upheno/wiki/Phenotype-Ontologies-Reconciliation-Effort
Mappings should be a level down in terms of semantic precision - especially if we want this whole business to scale.
I have to agree, as you can see by my incessant questions to Nico :) I'm already struggling with fine distinctions between the existing terms. @Nico, I think your description in terms of parent/sibling/child/different branch is very helpful.
This goes to our best practice guide.
@sbello from MGI asked in slack:
I think there are two important assumptions to consider before giving an answer:
My initial intuition is this:
Keeping those in mind, this is my suggestion to @sbello s great question:
Something like that. In the future, I would like to explore that a bit more.. I think its a hugely important thing to get right, if we want to answer questions like: Is there a mapping for term x at all? and others..