Ensure ecocore is complete for mixs value mapping

cmungall commented 3 years ago

We have a number of fields in MIxS that have enums that should be mapped to an OBO, I think many should be in ecocore

https://github.com/microbiomedata/nmdc-metadata/blob/d27b4f6784af5f4508833e6562f316c25fb37a81/schema/mixs.yaml#L400-L412

https://github.com/microbiomedata/nmdc-metadata/blob/d27b4f6784af5f4508833e6562f316c25fb37a81/schema/mixs.yaml#L360-L372

Ideally for each of these terms there would be a clear mapping, and we would not have to make a decision between autotrophic organism vs disposition vs process

Some of these are in the MIXSCV ontology, but this is not up to date with the latest mixs:

https://bioportal.bioontology.org/ontologies/MIXSCV/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMVC_0000010

cc @wdduncan @kaiam @realmarcin @ramonawalls

diatomsRcool commented 3 years ago

on it - do we have term definitions that we want to use or carry over or should I start investigating?

ramonawalls commented 3 years ago

There are no official MIxS definitions -- it is just a CV. Great to have these terms in ecocore.

wdduncan commented 3 years ago

I'm doing some spot checking (on Ontobee), and I'm finding many terms in both BTO (http://purl.obolibrary.org/obo/bto.owl) and ECOCORE, and others (e.g, phototroph) in NCBITaxon.

@diatomsRcool Do you need me to help find ontology terms?

diatomsRcool commented 3 years ago

If you want to start digging around @wdduncan I would appreciate it

diatomsRcool commented 3 years ago

Added oxygen metabolism terms to ecocore-edit

diatomsRcool commented 3 years ago

microanaerobe: is this a synonym of microaerophile? carboxydotroph: an organism capable of tolerating a high concentration of carbon monoxide copiotroph: an organism capable of thriving in environments rich in nutrients, particularly carbon. diazotroph: an organism capable of fixing atmospheric nitrogen gas into a more usable form such as ammonia methanotroph: an organism capable of metabolizing methane as their source of carbon and energy methylotroph: an organism capable of using one-carbon compounds and multi-carbon compounds that contain no carbon-carbon bonds as the carbon source for their growth oligotroph: an organism capable of living in an environment that offers very low levels of nutrients

cmungall commented 3 years ago

@wdduncan - I don't see phototroph in NCBItaxon? I would be surprised if it was as I doubt it's a monophyletic trait

@ramonawalls - should the mixs enum really have values like facultative? Is this intended to be composable? E.g. such that someone could say facultative + methanotroph? Or is this implicitly facultative anaerobe?

@diatomsRcool - definitions look great. For me the key question is whether we want to model these as subclasses of organisms, or as orthogonal characteristics. As you know I am against proliferating shadows (process, disposition, quality, material entity). We should pick one as primary and use synonyms (e.g. follow PATO and model as characteristics with primary labels such as "anaerobic" and have a synonym "anaerobe")

There is a case for simply extending PATO here, e.g

wdduncan commented 3 years ago

@diatomsRcool Are we using metabolic process as a synonym for growth process? I only ask b/c the definition for anaerobe uses growth process.

@cmungall do we want to use has characteristic relation for which ever approach we decide?

FWIIW, I think the process view makes more sense me. But I'm not a biologist, and thus often wrong about such things :)

diatomsRcool commented 3 years ago

@cmungall There is a case for extending PATO. I agree that we don't want to create a bunch of shadows, but I can see a case for having or using organisms, processes, and qualities. Funny, I wonder when those terms were added. I could have swore I looked for them and couldn't find them, but that was years ago. Also, I was assuming that the lone facultative was an error. It doesn't make sense by itself.

@wdduncan I don't think metabolic process should be a synonym of growth process. Does that mean I need to change the definition for anaerobe?

wdduncan commented 3 years ago

@diatomsRcool I didn't think they were synonyms either, but I was wanting make sure.

As for metabolism vs growth, I don't know which is more appropriate. Do the metabolic processes for anaerobes also not require oxygen? For what I read on Wikipedia oxygen is disruptive (or harmful) to metabolic processes. Do we need to capture this too?

Also, how formal do we want the definition for anaerobic organism to be? I discussed this in this issue on kg-microbe.

In brief, taking the process view of growth, we could create an anaerobic growth process class like so:

biological process
  - growth
     - anaerobic growth process

and formally define anaerobic growth process as equivalent to:

growth process and not (has input some oxygen)

I'm a little wary about using the expression not (has input some oxygen).

Also, is this level of formalizm useful?

diatomsRcool commented 3 years ago

new terms are in the 2021-02-17 release

EcologicalSemantics / ecocore

Ensure ecocore is complete for mixs value mapping #131