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PopulationAndCommunityOntology / pco

An ontology about groups of interacting organisms such as populations and communities
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Community #72

Closed Mttbnchtt closed 5 years ago

Mttbnchtt commented 5 years ago

The definition of community in PCO is "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other."

There are three issues:

  1. This makes it wrong to have ecological community as a subclass (as it is the case now), because "ecological community" is defined as a community having populations of different species.
  2. The current definition makes it impossible to talk about a community of priests (no genealogical relations and no mating), although this is a legitimate expression.
  3. In general, the current definition is not suited to talk about things like a community of vulnerable persons.

I wonder whether PCO would be interested in changing the definition to take into account these issues.

@pbuttigieg may also be interested.

yongqunh commented 5 years ago

We also found the same issue in our OHMI (ontology of host-microbiome interactions). The 'microbial community' (http://purl.obolibrary.org/obo/PCO_1000004) definition: An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness.

The 'microbial community' appears to refer to different species. However, as introduced above, the 'community' is for the same species. This is confusing.

In our microbiome research area, a 'microbiota' can be a lot of organisms from the same species, or from different species. We don't want to specify one or more species for 'microbiota'. In this case, it is hard to make 'microbiota' a synonym of 'microbial community'.

@pbuttigieg may also be interested in this.

pbuttigieg commented 5 years ago

Yes, this needs revision.

Ecological community (of which microbial communities are a subclass) necessarily have more than one ecological population in them.

@yongqunh good point. Microbiota can be a broad synonym of microbial community, but should probably be a subclass of collection of organisms with an axiom like 'has part' min 1 'microbial population' where microbial population is under ecological population.

ramonawalls commented 5 years ago

This is clearly a mistake and makes no sense. I will have to go back and look at the history to figure out how it arose so that it can be fixed.

yongqunh commented 5 years ago

Hi Ramona,

Will you attend the ICBO-2019? Happy to chat with you there if you go.

Thanks, Oliver

From: Ramona Walls notifications@github.com Sent: Sunday, July 28, 2019 6:43 PM To: PopulationAndCommunityOntology/pco pco@noreply.github.com Cc: He, Oliver yongqunh@med.umich.edu; Mention mention@noreply.github.com Subject: Re: [PopulationAndCommunityOntology/pco] Community (#72)

This is clearly a mistake and makes no sense. I will have to go back and look at the history to figure out how it arose so that it can be fixed.

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ramonawalls commented 5 years ago

I am around tomorrow and Tuesday. Looking forward to lots of in person conversations!

Enviado de Baja Arizona

On Jul 28, 2019, at 6:45 PM, Yongqun Oliver He notifications@github.com wrote:

Hi Ramona,

Will you attend the ICBO-2019? Happy to chat with you there if you go.

Thanks, Oliver

From: Ramona Walls notifications@github.com Sent: Sunday, July 28, 2019 6:43 PM To: PopulationAndCommunityOntology/pco pco@noreply.github.com Cc: He, Oliver yongqunh@med.umich.edu; Mention mention@noreply.github.com Subject: Re: [PopulationAndCommunityOntology/pco] Community (#72)

This is clearly a mistake and makes no sense. I will have to go back and look at the history to figure out how it arose so that it can be fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/PopulationAndCommunityOntology/pco/issues/72?email_source=notifications&email_token=ABD22QYYDHE5V63PKXJ3AM3QBYOHJA5CNFSM4H2XEKRKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD27ICXQ#issuecomment-515801438, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABD22QYE26O2MISLUHX2KZTQBYOHJANCNFSM4H2XEKRA.

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ramonawalls commented 5 years ago

See #32. I am going to get rid of community, and make ecological community a direct subclass of multi-species collection of organisms.

@Mttbnchtt please advise if you need a term for community that does not fall within ecological community.

ramonawalls commented 5 years ago

I just talked with Pier and he explained the use case for the class community (e.g., for SDGIO and related work). I will add it back in. We might also want to make a class for human community.