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Pathogen-Host Interaction Phenotype Ontology
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Why is the growth medium included in some phenotypes? #286

Closed jseager7 closed 3 years ago

jseager7 commented 3 years ago

While working on mapping uPheno patterns to PHIPO, I noticed the following terms:

These terms are a poor fit for the current phenotype patterns because of the inclusion of the growth medium. Capturing them would necessitate the creation of a pattern like 'abnormally decreased quality of biological process in medium', and uPheno has so far resisted including contextual or causal qualifiers like these, presumably because including them would cause an explosion of patterns.

Furthermore, why is this information included in the terms when Canto can presumably describe growth media in its experimental conditions?

ValWood commented 3 years ago

You are correct that these are representing the media, but it makes sense to model them as phenotypes representing, for example which nutrients an organism can grow on. We have included nutrients because different carbon sources can radically affect growth rate (Note that our classifier for condition vs. phenotype is whether the experimental outcome is affected).

We model these phenotypes in this way at PomBase too. it is such an important aspect of phenotype screens I think it makes sense to include.

@mah11 might be able to explain more clearly, and remember the history, and whether we propose to continue modelling in this way.

mah11 commented 3 years ago

We have been fully aware all along that the pre-composed "cell population growth on $source" FYPO terms incorporate information that normally belongs in conditions, and, indeed, are entirely sematically equivalent to using the "population growth" superclass plus specified conditions. We do avoid a combinatorial explosion by incorporating conditions only into terms in the cell population growth branch (and I can probably find some tickets where I've rejected requests that would break this rule).

We have included nutrients because different carbon sources can radically affect growth rate

Although this is true, I don't think it's the main reason we have instantiated these pre-composed terms instead of asking curators to post-compose using a general growth term plus conditions. Instead, we have the pre-composed terms because we think they are more convenient and intuitive for fission yeast community curators, to a sufficient extent that we bend the rule that conditions belong in conditions. Population growth on plates or in flasks, in other words, is a bit of a special case for biologists who work on lab-friendly microbes.

Every so often, we revisit this question, and so far, we haven't changed what we include (in either direction; we haven't expanded the list of what we're willing to pre-compose with condition information), always because we worry that our users would miss the growth-on-this-or-that terms and not realize they could still capture the same thing by post-composition.

(Note that our classifier for condition vs. phenotype is whether the experimental outcome is affected).

I don't know what this refers to, but it doesn't look accurate.

Anyway, PHI-base is under no obligation to follow the Pombase/FYPO practice in this area, if your curating community does not come in with the same sort of habits and expectations as ours.

jseager7 commented 3 years ago

Thanks for the explanation. I think it's likely that PHI-base will also want to use the precomposed terms for their usability benefits.

The only reason the precomposed terms are a potential problem is because of their lack of compatibility with existing uPheno patterns, but if some workaround is decided for FYPO during the pattern mapping effort we could probably just copy that solution for PHIPO.

Closing now, since my question is answered.

mah11 commented 3 years ago

... if some workaround is decided for FYPO during the pattern mapping effort ...

Yes, we should work something out at some point. I can't offer a timeframe yet, but it's on my and Nico's radar.