i guess we would always be talking about organisms when talking about populations, but there are cases where we use "of the same type" or "of a different type" where we are not talking about populations or organisms. for example, in IDO, we refer to replication where we want to say that the output is of the same type as one of the participants. we want this to apply to things other than organisms. (because you wanted us to include prions!!) i think there are other non-organism examples as well. but using taxonomic rank, if we can figure out a way to tie this to NCBI taxonomy as you mention, might well solve all the organism cases.
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Bjoern makes an important point about the term 'population' being used only in the context of organisms. Does this make the use of 'organism' in 'organism population' unnecessary? Perhaps this clarification should be mentioned in the comments area. Do we really have to worry about 'prions' when trying to define 'population'? As suggested earlier, if '(organism) population=def: an aggregate of organisms' is taken as an operational definition, then prions would be automatically included if they are classified as organisms. The issue would be differed to where it truly belongs.
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Reviving this old thread.
Lindsay Cowell has pointed out that IDO uses the definition
organism population = An aggregate of organisms of the same Species.
and OGMS uses the definition:
organism population = An aggregate of organisms of the same type.
OBI uses the definition:
population = a population is a collection of individuals from the same
taxonomic class living, counted or sampled at a particular site or in a
particular area
(Note: the issue I raised earlier in the thread about a population not
needing to be counted or sampled to exist is no longer a problem because of
the disjuntion 'living, counted OR sampled')
All three definitions suffer from the 'of the same X' problem that Alan
originally pointed out, but perhaps the IDO or OBI definitions are less bad
because they restricts the ontological type X is. As such, I think we need
to change 'of the same type' in OGMS to 'of the same Species' (per IDO),
or 'of the same taxonomic class' (per OBI).
<rdfs:comment xml:lang="en">It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used.</rdfs:comment>
</owl:Class>
On Sep 18, 2012, at 12:43 PM, <o...@googlecode.com<mailto:o...@googlecode.com>> wrote:
Reviving this old thread.
Lindsay Cowell has pointed out that IDO uses the definition
organism population = An aggregate of organisms of the same Species.
and OGMS uses the definition:
organism population = An aggregate of organisms of the same type.
OBI uses the definition:
population = a population is a collection of individuals from the same
taxonomic class living, counted or sampled at a particular site or in a
particular area
(Note: the issue I raised earlier in the thread about a population not
needing to be counted or sampled to exist is no longer a problem because of
the disjuntion 'living, counted OR sampled')
All three definitions suffer from the 'of the same X' problem that Alan
originally pointed out, but perhaps the IDO or OBI definitions are less bad
because they restricts the ontological type X is. As such, I think we need
to change 'of the same type' in OGMS to 'of the same Species' (per IDO),
or 'of the same taxonomic class' (per OBI).
Which of these is preferable?
Dr. Melissa Haendel
Assistant Professor
Ontology Development Group, OHSU Library
http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology
Oregon Health & Science University
haen...@ohsu.edu<mailto:haen...@ohsu.edu>
skype: melissa.haendel
503-407-5970
I think the most pressing issue is which ontology owns this term, and can
we retire all the other, extra URIs for it?
I don't like the "live in the same place" restriction for several reasons:
1. It is ambiguous. You could say "the earth" is the place where any
population lives, modulo astronauts (and all the bacteria , etc. that live
in/on them) who happen to be in outer space, and even then, you can simply
loosen the boundaries of "the place" to get everyone back into the
population.
2. There are probably use cases in the medical domain that want populations
defined by other criteria irrespective of where they live.
3. There are humans who spend 6 months of the year in New York, and the
other 6 months of the year in Florida. Saying where they live irrespective
of time is difficult.
On Tue, Sep 18, 2012 at 3:07 PM, Melissa Haendel <haen...@ohsu.edu> wrote:
> Hi, I think organism population should probably come from the new
> population ontology:
> <owl:Class rdf:about="&obo;pco.owl/pco_0000001">
> <rdfs:label xml:lang="en">biological population</rdfs:label>
> <rdfs:subClassOf rdf:resource="&obo;pco.owl/pco_0000000"/>
> <obo:IAO_0000115 xml:lang="en">A collection of organisms, all of the same
> species, that live in the same place.</obo:IAO_0000115>
> <obo:IAO_0000119>ISBN:0878932739</obo:IAO_0000119>
> <rdfs:comment xml:lang="en">It is sometimes difficult to define the
> physical boundaries of a population. In the case of sexually reproducing
> organisms, the individuals within a population have the potential to
> reproduce with one another during the course of their lifetimes.
> 'Community', as often used to describe a group of humans, is a type
> of population. Classes for population already exist in IDO ('organism
> population', IDO_0000509) and OBI ('population', OBI_0000181).
> The definitions should be standardized across ontologies and only one term
> used.</rdfs:comment>
> </owl:Class>
> On Sep 18, 2012, at 12:43 PM, <o...@googlecode.com> wrote:
> Comment #30 on issue 33 by albertgo...@gmail.com: Proposed term 'Organism
> Reviving this old thread.
> Lindsay Cowell has pointed out that IDO uses the definition
> organism population = An aggregate of organisms of the same Species.
> and OGMS uses the definition:
> organism population = An aggregate of organisms of the same type.
> OBI uses the definition:
> population = a population is a collection of individuals from the same
> taxonomic class living, counted or sampled at a particular site or in a
> particular area
> (Note: the issue I raised earlier in the thread about a population not
> needing to be counted or sampled to exist is no longer a problem because
> of
> the disjuntion 'living, counted OR sampled')
> All three definitions suffer from the 'of the same X' problem that Alan
> originally pointed out, but perhaps the IDO or OBI definitions are less
> bad
> because they restricts the ontological type X is. As such, I think we
> need
> to change 'of the same type' in OGMS to 'of the same Species' (per IDO),
> or 'of the same taxonomic class' (per OBI).
> Which of these is preferable?
> *Dr. Melissa Haendel
> *
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu
> skype: melissa.haendel
> 503-407-5970
On Tue, Sep 18, 2012 at 4:13 PM, Bill Hogan <hoga...@gmail.com> wrote:
> I think the most pressing issue is which ontology owns this term, and can
> we retire all the other, extra URIs for it?
> I don't like the "live in the same place" restriction for several reasons:
> 1. It is ambiguous. You could say "the earth" is the place where any
> population lives, modulo astronauts (and all the bacteria , etc. that live
> in/on them) who happen to be in outer space, and even then, you can simply
> loosen the boundaries of "the place" to get everyone back into the
> population.
> 2. There are probably use cases in the medical domain that want
> populations defined by other criteria irrespective of where they live.
> 3. There are humans who spend 6 months of the year in New York, and the
> other 6 months of the year in Florida. Saying where they live irrespective
> of time is difficult.
> Bill
> On Tue, Sep 18, 2012 at 3:07 PM, Melissa Haendel <haen...@ohsu.edu> wrote:
>> Hi, I think organism population should probably come from the new
>> population ontology:
>> <owl:Class rdf:about="&obo;pco.owl/pco_0000001">
>> <rdfs:label xml:lang="en">biological population</rdfs:label>
>> <rdfs:subClassOf rdf:resource="&obo;pco.owl/pco_0000000"/>
>> <obo:IAO_0000115 xml:lang="en">A collection of organisms, all of the
>> same species, that live in the same place.</obo:IAO_0000115>
>> <obo:IAO_0000119>ISBN:0878932739</obo:IAO_0000119>
>> <rdfs:comment xml:lang="en">It is sometimes difficult to define the
>> physical boundaries of a population. In the case of sexually reproducing
>> organisms, the individuals within a population have the potential to
>> reproduce with one another during the course of their lifetimes.
>> 'Community', as often used to describe a group of humans, is a type
>> of population. Classes for population already exist in IDO ('organism
>> population', IDO_0000509) and OBI ('population', OBI_0000181).
>> The definitions should be standardized across ontologies and only one term
>> used.</rdfs:comment>
>> </owl:Class>
>> On Sep 18, 2012, at 12:43 PM, <o...@googlecode.com> wrote:
>> Reviving this old thread.
>> Lindsay Cowell has pointed out that IDO uses the definition
>> organism population = An aggregate of organisms of the same Species.
>> and OGMS uses the definition:
>> organism population = An aggregate of organisms of the same type.
>> OBI uses the definition:
>> population = a population is a collection of individuals from the same
>> taxonomic class living, counted or sampled at a particular site or in a
>> particular area
>> (Note: the issue I raised earlier in the thread about a population not
>> needing to be counted or sampled to exist is no longer a problem because
>> of
>> the disjuntion 'living, counted OR sampled')
>> All three definitions suffer from the 'of the same X' problem that Alan
>> originally pointed out, but perhaps the IDO or OBI definitions are less
>> bad
>> because they restricts the ontological type X is. As such, I think we
>> need
>> to change 'of the same type' in OGMS to 'of the same Species' (per IDO),
>> or 'of the same taxonomic class' (per OBI).
>> Which of these is preferable?
>> *Dr. Melissa Haendel
>> *
>> Assistant Professor
>> Ontology Development Group, OHSU Library
>> http://www.ohsu.edu/library/ >> Department of Medical Informatics and Epidemiology
>> Oregon Health & Science University
>> haen...@ohsu.edu
>> skype: melissa.haendel
>> 503-407-5970
I would like to see the PCO version of "population" be used in IDO, OBI, and OGMS (etc.).
It is currently defined as:
def: A collection of organisms, all of the same species, that live in the same place.
comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population.
source: ISBN:0878932739 (Hartl's Primer of Population Genetics)
This is a fairly broad definition, but I think it should be inclusive, and people can create more specific subtypes as needed. For example, we could create subclasses like "interbreeding population" or "clonal population" or "experimental population".
I have currently named the term "biological population". I did not want to use "organism population", because that limits its usefulness for for viruses and viroids, and my intention is to define it as a collection of CARO:organism or virus or viroid. I don't know if being defined based on species is a problem for viruses and viroids, though. Perhaps someone with expertise could comment on that. I don't think it is a good idea to say "organisms of the same taxonomic class" as that could include a collection of organism from the same genus or phylum. If species is problematic for viruses, perhaps the definition should say "of the same species or [whatever you call the equivalent of a species in viruses]".
We could just use "population" as a name, but that could be confused with a statistical population. Does anyone object to biological population, or have a better suggestion?
Right now, biological population is a subclass of PCO:collection of organisms, which is a material entity, but perhaps collection of organisms should be moved to the relatively new and more specific BFO term "object aggregate".
I welcome any feedback on the definition or name. If it does not work for you, please let me know.
<rdfs:comment xml:lang="en">It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used.</rdfs:comment>
</owl:Class>
On Sep 18, 2012, at 12:43 PM, <o...@googlecode.com<mailto:o...@googlecode.com>> wrote:
Reviving this old thread.
Lindsay Cowell has pointed out that IDO uses the definition
organism population = An aggregate of organisms of the same Species.
and OGMS uses the definition:
organism population = An aggregate of organisms of the same type.
OBI uses the definition:
population = a population is a collection of individuals from the same
taxonomic class living, counted or sampled at a particular site or in a
particular area
(Note: the issue I raised earlier in the thread about a population not
needing to be counted or sampled to exist is no longer a problem because of
the disjuntion 'living, counted OR sampled')
All three definitions suffer from the 'of the same X' problem that Alan
originally pointed out, but perhaps the IDO or OBI definitions are less bad
because they restricts the ontological type X is. As such, I think we need
to change 'of the same type' in OGMS to 'of the same Species' (per IDO),
or 'of the same taxonomic class' (per OBI).
Which of these is preferable?
Dr. Melissa Haendel
Assistant Professor
Ontology Development Group, OHSU Library
http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology
Oregon Health & Science University
haen...@ohsu.edu<mailto:haen...@ohsu.edu>
skype: melissa.haendel
503-407-5970
On Tue, Sep 18, 2012 at 5:43 PM, Walls, Ramona <rwa...@nybg.org> wrote:
> I would like to see the PCO version of "population" be used in IDO, OBI,
> and OGMS (etc.).
> It is currently defined as:
> def: A collection of organisms, all of the same species, that live in the
> same place.
> comment: It is sometimes difficult to define the physical boundaries of a
> population. In the case of sexually reproducing organisms, the individuals
> within a population have the potential to reproduce with one another during
> the course of their lifetimes. 'Community', as often used to describe a
> group of humans, is a type of population.
> source: ISBN:0878932739 (Hartl's Primer of Population Genetics)
> This is a fairly broad definition, but I think it should be inclusive,
> and people can create more specific subtypes as needed. For example, we
> could create subclasses like "interbreeding population" or "clonal
> population" or "experimental population".
I think the key value of any population term is in how different ontologies
subtype it. In IDO, we have need of several subtypes (e.g., 'infected
population') as well as several terms which explicitly or implicitly refer
to populations (e.g., 'herd immunity').
To Bill's point however, we need to accommodate populations that are
unified by criteria other than geographical proximity, so the "live in the
same place" clause is too strong a restriction in the PCO definition.
> I have currently named the term "biological population". I did not want
> to use "organism population", because that limits its usefulness for for
> viruses and viroids, and my intention is to define it as a collection of
> CARO:organism or virus or viroid. I don't know if being defined based on
> species is a problem for viruses and viroids, though. Perhaps someone with
> expertise could comment on that. I don't think it is a good idea to say
> "organisms of the same taxonomic class" as that could include a collection
> of organism from the same genus or phylum. If species is problematic for
> viruses, perhaps the definition should say "of the same species or
> [whatever you call the equivalent of a species in viruses]".
> We could just use "population" as a name, but that could be confused
> with a statistical population. Does anyone object to biological population,
> or have a better suggestion?
'statistical population' belongs in an ontology of statistics, which talks
about things like sample size...note here though that 'a sample of
registered voters' may be spread out across America and thus not satisfy
the PCO definition (but presumably would satisfy 'statistical
population').
I think 'population' might be the best label because it blocks discussions
of 'what is an organism?' or 'what is biological?'
> Right now, biological population is a subclass of PCO:collection of
> organisms, which is a material entity, but perhaps collection of organisms
> should be moved to the relatively new and more specific BFO term "object
> aggregate".
> I welcome any feedback on the definition or name. If it does not work
> for you, please let me know.
> <owl:Class rdf:about="&obo;pco.owl/pco_0000001">
> <rdfs:label xml:lang="en">biological population</rdfs:label>
> <rdfs:subClassOf rdf:resource="&obo;pco.owl/pco_0000000"/>
> <obo:IAO_0000115 xml:lang="en">A collection of organisms, all of the
> same species, that live in the same place.</obo:IAO_0000115>
> <obo:IAO_0000119>ISBN:0878932739</obo:IAO_0000119>
> <rdfs:comment xml:lang="en">It is sometimes difficult to define the
> physical boundaries of a population. In the case of sexually reproducing
> organisms, the individuals within a population have the potential to
> reproduce with one another during the course of their lifetimes.
> 'Community', as often used to describe a group of humans, is a type
> of population. Classes for population already exist in IDO ('organism
> population', IDO_0000509) and OBI ('population', OBI_0000181).
> The definitions should be standardized across ontologies and only one term
> used.</rdfs:comment>
> </owl:Class>
> On Sep 18, 2012, at 12:43 PM, <o...@googlecode.com> wrote:
> Comment #30 on issue 33 by albertgo...@gmail.com: Proposed term 'Organism
> Reviving this old thread.
> Lindsay Cowell has pointed out that IDO uses the definition
> organism population = An aggregate of organisms of the same Species.
> and OGMS uses the definition:
> organism population = An aggregate of organisms of the same type.
> OBI uses the definition:
> population = a population is a collection of individuals from the same
> taxonomic class living, counted or sampled at a particular site or in a
> particular area
> (Note: the issue I raised earlier in the thread about a population not
> needing to be counted or sampled to exist is no longer a problem because
> of
> the disjuntion 'living, counted OR sampled')
> All three definitions suffer from the 'of the same X' problem that Alan
> originally pointed out, but perhaps the IDO or OBI definitions are less
> bad
> because they restricts the ontological type X is. As such, I think we
> need
> to change 'of the same type' in OGMS to 'of the same Species' (per IDO),
> or 'of the same taxonomic class' (per OBI).
> Which of these is preferable?
> *Dr. Melissa Haendel
> *
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu
> skype: melissa.haendel
> 503-407-5970
Is there non-biological population ? Any example?
If there is no non-biological population, then 'population' as lable is
good.
Otherwise, you may need to say something 'biological population'.
Best,
Asiyah
On Thu, Sep 20, 2012 at 9:13 AM, Albert Goldfain
<albertgoldf...@gmail.com>wrote:
> On Tue, Sep 18, 2012 at 5:43 PM, Walls, Ramona <rwa...@nybg.org> wrote:
>> I would like to see the PCO version of "population" be used in IDO,
>> OBI, and OGMS (etc.).
>> It is currently defined as:
>> def: A collection of organisms, all of the same species, that live in the
>> same place.
>> comment: It is sometimes difficult to define the physical boundaries of a
>> population. In the case of sexually reproducing organisms, the individuals
>> within a population have the potential to reproduce with one another during
>> the course of their lifetimes. 'Community', as often used to describe a
>> group of humans, is a type of population.
>> source: ISBN:0878932739 (Hartl's Primer of Population Genetics)
>> This is a fairly broad definition, but I think it should be inclusive,
>> and people can create more specific subtypes as needed. For example, we
>> could create subclasses like "interbreeding population" or "clonal
>> population" or "experimental population".
> I think the key value of any population term is in how different
> ontologies subtype it. In IDO, we have need of several subtypes (e.g.,
> 'infected population') as well as several terms which explicitly or
> implicitly refer to populations (e.g., 'herd immunity').
> To Bill's point however, we need to accommodate populations that are
> unified by criteria other than geographical proximity, so the "live in the
> same place" clause is too strong a restriction in the PCO definition.
>> I have currently named the term "biological population". I did not want
>> to use "organism population", because that limits its usefulness for for
>> viruses and viroids, and my intention is to define it as a collection of
>> CARO:organism or virus or viroid. I don't know if being defined based on
>> species is a problem for viruses and viroids, though. Perhaps someone with
>> expertise could comment on that. I don't think it is a good idea to say
>> "organisms of the same taxonomic class" as that could include a collection
>> of organism from the same genus or phylum. If species is problematic for
>> viruses, perhaps the definition should say "of the same species or
>> [whatever you call the equivalent of a species in viruses]".
>> We could just use "population" as a name, but that could be confused
>> with a statistical population. Does anyone object to biological population,
>> or have a better suggestion?
> 'statistical population' belongs in an ontology of statistics, which talks
> about things like sample size...note here though that 'a sample of
> registered voters' may be spread out across America and thus not satisfy
> the PCO definition (but presumably would satisfy 'statistical
> population').
> I think 'population' might be the best label because it blocks discussions
> of 'what is an organism?' or 'what is biological?'
>> Right now, biological population is a subclass of PCO:collection of
>> organisms, which is a material entity, but perhaps collection of organisms
>> should be moved to the relatively new and more specific BFO term "object
>> aggregate".
>> I welcome any feedback on the definition or name. If it does not work
>> for you, please let me know.
>> <owl:Class rdf:about="&obo;pco.owl/pco_0000001">
>> <rdfs:label xml:lang="en">biological population</rdfs:label>
>> <rdfs:subClassOf rdf:resource="&obo;pco.owl/pco_0000000"/>
>> <obo:IAO_0000115 xml:lang="en">A collection of organisms, all of the
>> same species, that live in the same place.</obo:IAO_0000115>
>> <obo:IAO_0000119>ISBN:0878932739</obo:IAO_0000119>
>> <rdfs:comment xml:lang="en">It is sometimes difficult to define the
>> physical boundaries of a population. In the case of sexually reproducing
>> organisms, the individuals within a population have the potential to
>> reproduce with one another during the course of their lifetimes.
>> 'Community', as often used to describe a group of humans, is a type
>> of population. Classes for population already exist in IDO ('organism
>> population', IDO_0000509) and OBI ('population', OBI_0000181).
>> The definitions should be standardized across ontologies and only one term
>> used.</rdfs:comment>
>> </owl:Class>
>> On Sep 18, 2012, at 12:43 PM, <o...@googlecode.com> wrote:
>> Reviving this old thread.
>> Lindsay Cowell has pointed out that IDO uses the definition
>> organism population = An aggregate of organisms of the same Species.
>> and OGMS uses the definition:
>> organism population = An aggregate of organisms of the same type.
>> OBI uses the definition:
>> population = a population is a collection of individuals from the same
>> taxonomic class living, counted or sampled at a particular site or in a
>> particular area
>> (Note: the issue I raised earlier in the thread about a population not
>> needing to be counted or sampled to exist is no longer a problem because
>> of
>> the disjuntion 'living, counted OR sampled')
>> All three definitions suffer from the 'of the same X' problem that Alan
>> originally pointed out, but perhaps the IDO or OBI definitions are less
>> bad
>> because they restricts the ontological type X is. As such, I think we
>> need
>> to change 'of the same type' in OGMS to 'of the same Species' (per IDO),
>> or 'of the same taxonomic class' (per OBI).
>> Which of these is preferable?
>> *Dr. Melissa Haendel
>> *
>> Assistant Professor
>> Ontology Development Group, OHSU Library
>> http://www.ohsu.edu/library/ >> Department of Medical Informatics and Epidemiology
>> Oregon Health & Science University
>> haen...@ohsu.edu
>> skype: melissa.haendel
>> 503-407-5970
Sorry to through another wrinkle into the discussion, but a collection of
organisms with symbionts, say obligate, won't fit the definition.
Here as in other cases, I think the attempt to define a general term hurts
and we should be working a little lower down.
Some clear cases, all of which are of importance in the life sciences
A unicellular colony
A microorganism infection (the bacteria in a bacteremia, the viruses[1] in
a viremia.
A herd (bunch of big animals living in close proximity)
The sum of the infectious agents in a herd's infection (all potential
eradictated with the same antibiotic)
A the occupants of a biological niche (most suspeptible to an pan-species
toxin)
My microbiome
Ashkenazi jews (some common genetic elements due to being a herd at some
earlier part of history)
People with malaria
People immune to HIV
OK, it didn't take me long to make that list. Maybe there is something
useful that could be said of the union of those classes. See if there is,
though I expect it will take some effort. If you can figure it out, make it
the defining criterion for your upper class. If you can't give up for now
and define the classes at the level I've laid out.
Why wouldn't these (for the most part, I don't know that I would call them all populations, see below) simply be defined as subclasses with the restrictions largely as you've described them? I agree that the "living in the same place" may not be enough to distinguish population from a collection of organisms, but regardless of logical definition here I think that summarizes the terms' biological use. As per Bill's comments on vagueness, I agree it is vague, but I believe that populations and subpopulations exist via a transitive member or part relation. So there exists the population of humans on the earth, and there exists the population of humans in North America, and the humans in this latter population are by inference members of the former population based on the partonomy of geographical location. If we want to define collections of organisms based not by where they live, then perhaps this can use the super class 'collection of organisms'- this might be more fitting with the actual use of population? At least so far as biodiversity is concerned my understanding is that it is usually (always?) based on geographical location at one level of granularity or another. I defer to the experts on this though.
As for time, well that is the same old BFO problem. A person who lives half the year in Florida is only a member of the Floridian population during that time window.
I agree that the definition should include viruses and virioids, but as Ramona suggested the definition will be updated to include this.
Best
Melissa
On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
Sorry to through another wrinkle into the discussion, but a collection of organisms with symbionts, say obligate, won't fit the definition.
Here as in other cases, I think the attempt to define a general term hurts and we should be working a little lower down.
Some clear cases, all of which are of importance in the life sciences
A unicellular colony
A microorganism infection (the bacteria in a bacteremia, the viruses[1] in a viremia.
A herd (bunch of big animals living in close proximity)
The sum of the infectious agents in a herd's infection (all potential eradictated with the same antibiotic)
A the occupants of a biological niche (most suspeptible to an pan-species toxin)
My microbiome
Ashkenazi jews (some common genetic elements due to being a herd at some earlier part of history)
doesn't meet current definition
People with malaria
nor this
People immune to HIV
nor this
Would most people call these populations? I am not sure that I would- I think I'd think of them as a collection of organisms or viruses, but probably not populations.
OK, it didn't take me long to make that list. Maybe there is something useful that could be said of the union of those classes. See if there is, though I expect it will take some effort. If you can figure it out, make it the defining criterion for your upper class. If you can't give up for now and define the classes at the level I've laid out.
Assistant Professor
Ontology Development Group, OHSU Library
http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology
Oregon Health & Science University
haen...@ohsu.edu<mailto:haen...@ohsu.edu>
skype: melissa.haendel
503-407-5970
On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu> wrote:
> Hi all,
> Why wouldn't these (for the most part, I don't know that I would call
them all populations, see below) simply be defined as subclasses with the
restrictions largely as you've described them? I agree that the "living in
the same place" may not be enough to distinguish population from a
collection of organisms, but regardless of logical definition here I think
that summarizes the terms' biological use.
The definition is: A collection of organisms, all of the same species, that
live in the same place.
You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6 do
either.
4: Not in the same place (at the scale of a bacteria, a cow is a place)
5: Not the same species
6: Not the same species
So I see this definition as only working in only 1/3 of the cases I gave
(and I didn't try that hard to make the list, which could certainly be
extended).
-Alan
> As per Bill's comments on vagueness, I agree it is vague, but I believe
that populations and subpopulations exist via a transitive member or part
relation. So there exists the population of humans on the earth, and there
exists the population of humans in North America, and the humans in this
latter population are by inference members of the former population based
on the partonomy of geographical location. If we want to define collections
of organisms based not by where they live, then perhaps this can use the
super class 'collection of organisms'- this might be more fitting with the
actual use of population?
That's going more general. The test I would make to see if that is worth
that is what of interest could we say about instances of collection of
organisms that would apply to instances of all the suggested subclasses. My
contention is that unless there is some impact of this sort, defining the
general class is of little use.
> At least so far as biodiversity is concerned my understanding is that it
is usually (always?) based on geographical location at one level of
granularity or another. I defer to the experts on this though.
> As for time, well that is the same old BFO problem. A person who lives
half the year in Florida is only a member of the Floridian population
during that time window.
I agree that temporal issues are not primary here.
> I agree that the definition should include viruses and virioids, but as
Ramona suggested the definition will be updated to include this.
> Best
> Melissa
> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
> Sorry to through another wrinkle into the discussion, but a collection of
organisms with symbionts, say obligate, won't fit the definition.
> Here as in other cases, I think the attempt to define a general term
hurts and we should be working a little lower down.
> Some clear cases, all of which are of importance in the life sciences
> 1. A unicellular colony
> 2. A microorganism infection (the bacteria in a bacteremia, the
viruses[1] in a viremia.
> 3. A herd (bunch of big animals living in close proximity)
> 4. The sum of the infectious agents in a herd's infection (all potential
eradictated with the same antibiotic)
> 5. A the occupants of a biological niche (most suspeptible to an
pan-species toxin)
> 6. My microbiome
> 7. Ashkenazi jews (some common genetic elements due to being a herd at
some earlier part of history)
> doesn't meet current definition
> 8. People with malaria
> nor this
> 9. People immune to HIV
> nor this
> Would most people call these populations? I am not sure that I would- I
think I'd think of them as a collection of organisms or viruses, but
probably not populations.
> OK, it didn't take me long to make that list. Maybe there is something
useful that could be said of the union of those classes. See if there is,
though I expect it will take some effort. If you can figure it out, make it
the defining criterion for your upper class. If you can't give up for now
and define the classes at the level I've laid out.
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu
> skype: melissa.haendel
> 503-407-5970
On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu<mailto:haen...@ohsu.edu>> wrote:
> Hi all,
> Why wouldn't these (for the most part, I don't know that I would call them all populations, see below) simply be defined as subclasses with the restrictions largely as you've described them? I agree that the "living in the same place" may not be enough to distinguish population from a collection of organisms, but regardless of logical definition here I think that summarizes the terms' biological use.
The definition is: A collection of organisms, all of the same species, that live in the same place.
You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6 do either.
4: Not in the same place (at the scale of a bacteria, a cow is a place)
yes but the cows live in the same place, by transitivity I'd be ok with this one.
5: Not the same species
agree, this would be a collection of organisms, not a population by current def.
6: Not the same species
same same.
So I see this definition as only working in only 1/3 of the cases I gave (and I didn't try that hard to make the list, which could certainly be extended).
I'm still ok with the use of the superclass "collection of organisms/viruses/viroids" for these, with population being restricted to a geographical location. Lets see what the biodiversity folks say?
-Alan
> As per Bill's comments on vagueness, I agree it is vague, but I believe that populations and subpopulations exist via a transitive member or part relation. So there exists the population of humans on the earth, and there exists the population of humans in North America, and the humans in this latter population are by inference members of the former population based on the partonomy of geographical location. If we want to define collections of organisms based not by where they live, then perhaps this can use the super class 'collection of organisms'- this might be more fitting with the actual use of population?
That's going more general. The test I would make to see if that is worth that is what of interest could we say about instances of collection of organisms that would apply to instances of all the suggested subclasses. My contention is that unless there is some impact of this sort, defining the general class is of little use.
> At least so far as biodiversity is concerned my understanding is that it is usually (always?) based on geographical location at one level of granularity or another. I defer to the experts on this though.
> As for time, well that is the same old BFO problem. A person who lives half the year in Florida is only a member of the Floridian population during that time window.
I agree that temporal issues are not primary here.
> I agree that the definition should include viruses and virioids, but as Ramona suggested the definition will be updated to include this.
> Best
> Melissa
> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
> Sorry to through another wrinkle into the discussion, but a collection of organisms with symbionts, say obligate, won't fit the definition.
> Here as in other cases, I think the attempt to define a general term hurts and we should be working a little lower down.
> Some clear cases, all of which are of importance in the life sciences
> 1. A unicellular colony
> 2. A microorganism infection (the bacteria in a bacteremia, the viruses[1] in a viremia.
> 3. A herd (bunch of big animals living in close proximity)
> 4. The sum of the infectious agents in a herd's infection (all potential eradictated with the same antibiotic)
> 5. A the occupants of a biological niche (most suspeptible to an pan-species toxin)
> 6. My microbiome
> 7. Ashkenazi jews (some common genetic elements due to being a herd at some earlier part of history)
> doesn't meet current definition
> 8. People with malaria
> nor this
> 9. People immune to HIV
> nor this
> Would most people call these populations? I am not sure that I would- I think I'd think of them as a collection of organisms or viruses, but probably not populations.
> OK, it didn't take me long to make that list. Maybe there is something useful that could be said of the union of those classes. See if there is, though I expect it will take some effort. If you can figure it out, make it the defining criterion for your upper class. If you can't give up for now and define the classes at the level I've laid out.
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu<mailto:haen...@ohsu.edu>
> skype: melissa.haendel
> 503-407-5970
Dr. Melissa Haendel
Assistant Professor
Ontology Development Group, OHSU Library
http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology
Oregon Health & Science University
haen...@ohsu.edu<mailto:haen...@ohsu.edu>
skype: melissa.haendel
503-407-5970
On Thursday, September 20, 2012, Melissa Haendel <haen...@ohsu.edu> wrote:
> On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
> On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu>
wrote:
>> Hi all,
>> Why wouldn't these (for the most part, I don't know that I would call
them all populations, see below) simply be defined as subclasses with the
restrictions largely as you've described them? I agree that the "living in
the same place" may not be enough to distinguish population from a
collection of organisms, but regardless of logical definition here I think
that summarizes the terms' biological use.
> The definition is: A collection of organisms, all of the same species,
> You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6 do
either.
> 4: Not in the same place (at the scale of a bacteria, a cow is a place)
> yes but the cows live in the same place, by transitivity I'd be ok with
this one.
> 5: Not the same species
> agree, this would be a collection of organisms, not a population by
current def.
> 6: Not the same species
> same same.
> So I see this definition as only working in only 1/3 of the cases I gave
(and I didn't try that hard to make the list, which could certainly be
extended).
> I'm still ok with the use of the superclass "collection of
organisms/viruses/viroids" for these, with population being restricted to a
geographical location. Lets see what the biodiversity folks say?
Sure, though I think I will maintain my point: looking for the common
superclass will yield little if any use other than as visual grouping -
little will be able to be said about the classes members as a whole.
I would again propose that the project of building ontology resources to
represent these various kinds of population classes focus on, in the next
interval of work, defining a bunch of more specific classes about which we
*can* something interesting about the members, such as the one we want.
The rationale is that we don't really gain much by having people use a term
for annotation which carries no specificity.
-Alan
> -Alan
>> As per Bill's comments on vagueness, I agree it is vague, but I believe
that populations and subpopulations exist via a transitive member or part
relation. So there exists the population of humans on the earth, and there
exists the population of humans in North America, and the humans in this
latter population are by inference members of the former population based
on the partonomy of geographical location. If we want to define collections
of organisms based not by where they live, then perhaps this can use the
super class 'collection of organisms'- this might be more fitting with the
actual use of population?
> That's going more general. The test I would make to see if that is worth
that is what of interest could we say about instances of collection of
organisms that would apply to instances of all the suggested subclasses. My
contention is that unless there is some impact of this sort, defining the
general class is of little use.
>> At least so far as biodiversity is concerned my understanding is that it
is usually (always?) based on geographical location at one level of
granularity or another. I defer to the experts on this though.
>> As for time, well that is the same old BFO problem. A person who lives
half the year in Florida is only a member of the Floridian population
during that time window.
> I agree that temporal issues are not primary here.
>> I agree that the definition should include viruses and virioids, but as
Ramona suggested the definition will be updated to include this.
>> Best
>> Melissa
>> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
>> Sorry to through another wrinkle into the discussion, but a collection
of organisms with symbionts, say obligate, won't fit the definition.
>> Here as in other cases, I think the attempt to define a general term
hurts and we should be working a little lower down.
>> Some clear cases, all of which are of importance in the life sciences
>> 1. A unicellular colony
>> 2. A microorganism infection (the bacteria in a bacteremia, the
viruses[1] in a viremia.
>> 3. A herd (bunch of big animals living in close proximity)
>> 4. The sum of the infectious agents in a herd's infection (all potential
eradictated with the same antibiotic)
>> 5. A the occupants of a biological niche (most suspeptible to an
pan-species toxin)
>> 6. My microbiome
>> 7. Ashkenazi jews (some common genetic elements due to being a herd at
some earlier part of history)
>> doesn't meet current definition
>> 8. People with malaria
>> nor this
>> 9. People immune to HIV
>> nor this
>> Would most people call these populations? I am not sure that I would- I
think I'd think of them as a collection of organisms or viruses, but
probably not populations.
>> OK, it didn't take me long to make that list. Maybe there is something
useful that could be said of the union of those classes. See if there is,
though I expect it will take some effort. If you can figure it out, make it
the defining criterion for your upper class. If you can't give up for now
and define the classes at the level I've laid out.
>> Assistant Professor
>> Ontology Development Group, OHSU Library
>> http://www.ohsu.edu/library/ >> Department of Medical Informatics and Epidemiology
>> Oregon Health & Science University
>> haen...@ohsu.edu
>> skype: melissa.haendel
>> 503-407-5970
> Dr. Melissa Haendel
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu
> skype: melissa.haendel
> 503-407-5970
On Thursday, September 20, 2012, Melissa Haendel <haen...@ohsu.edu<mailto:haen...@ohsu.edu>> wrote:
> On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
> On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu<mailto:haen...@ohsu.edu>> wrote:
>> Hi all,
>> Why wouldn't these (for the most part, I don't know that I would call them all populations, see below) simply be defined as subclasses with the restrictions largely as you've described them? I agree that the "living in the same place" may not be enough to distinguish population from a collection of organisms, but regardless of logical definition here I think that summarizes the terms' biological use.
> The definition is: A collection of organisms, all of the same species, that live in the same place.
> You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6 do either.
> 4: Not in the same place (at the scale of a bacteria, a cow is a place)
> yes but the cows live in the same place, by transitivity I'd be ok with this one.
> 5: Not the same species
> agree, this would be a collection of organisms, not a population by current def.
> 6: Not the same species
> same same.
> So I see this definition as only working in only 1/3 of the cases I gave (and I didn't try that hard to make the list, which could certainly be extended).
> I'm still ok with the use of the superclass "collection of organisms/viruses/viroids" for these, with population being restricted to a geographical location. Lets see what the biodiversity folks say?
Sure, though I think I will maintain my point: looking for the common superclass will yield little if any use other than as visual grouping - little will be able to be said about the classes members as a whole.
I would again propose that the project of building ontology resources to represent these various kinds of population classes focus on, in the next interval of work, defining a bunch of more specific classes about which we *can* something interesting about the members, such as the one we want.
I agree it is helpful to work through real use cases. There may not be a whole lot of interesting things to say about a population, and I don't see the problem with that?
One thing to note though - I do believe that populations can bear phenotypes (whatever relation we decide to use for this, I guess it is no longer inheres_in?) So I suppose this might be interesting :-)
The rationale is that we don't really gain much by having people use a term for annotation which carries no specificity.
I disagree, I think it helps structure peoples' strategies. We don't usually annotate to OGMS disorder, BFO continuant, CARO multi-tissue structure either, we use them as the basis of refinement for specific use cases. I like the idea of working bottom up, but I would urge us to put into place a single, generalized class that we agree largely works for our purposes, and work on use cases with real data from there. Else we will continue to all use different population classes and be back where we started.
>> As per Bill's comments on vagueness, I agree it is vague, but I believe that populations and subpopulations exist via a transitive member or part relation. So there exists the population of humans on the earth, and there exists the population of humans in North America, and the humans in this latter population are by inference members of the former population based on the partonomy of geographical location. If we want to define collections of organisms based not by where they live, then perhaps this can use the super class 'collection of organisms'- this might be more fitting with the actual use of population?
> That's going more general. The test I would make to see if that is worth that is what of interest could we say about instances of collection of organisms that would apply to instances of all the suggested subclasses. My contention is that unless there is some impact of this sort, defining the general class is of little use.
>> At least so far as biodiversity is concerned my understanding is that it is usually (always?) based on geographical location at one level of granularity or another. I defer to the experts on this though.
>> As for time, well that is the same old BFO problem. A person who lives half the year in Florida is only a member of the Floridian population during that time window.
> I agree that temporal issues are not primary here.
>> I agree that the definition should include viruses and virioids, but as Ramona suggested the definition will be updated to include this.
>> Best
>> Melissa
>> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
>> Sorry to through another wrinkle into the discussion, but a collection of organisms with symbionts, say obligate, won't fit the definition.
>> Here as in other cases, I think the attempt to define a general term hurts and we should be working a little lower down.
>> Some clear cases, all of which are of importance in the life sciences
>> 1. A unicellular colony
>> 2. A microorganism infection (the bacteria in a bacteremia, the viruses[1] in a viremia.
>> 3. A herd (bunch of big animals living in close proximity)
>> 4. The sum of the infectious agents in a herd's infection (all potential eradictated with the same antibiotic)
>> 5. A the occupants of a biological niche (most suspeptible to an pan-species toxin)
>> 6. My microbiome
>> 7. Ashkenazi jews (some common genetic elements due to being a herd at some earlier part of history)
>> doesn't meet current definition
>> 8. People with malaria
>> nor this
>> 9. People immune to HIV
>> nor this
>> Would most people call these populations? I am not sure that I would- I think I'd think of them as a collection of organisms or viruses, but probably not populations.
>> OK, it didn't take me long to make that list. Maybe there is something useful that could be said of the union of those classes. See if there is, though I expect it will take some effort. If you can figure it out, make it the defining criterion for your upper class. If you can't give up for now and define the classes at the level I've laid out.
>> Assistant Professor
>> Ontology Development Group, OHSU Library
>> http://www.ohsu.edu/library/ >> Department of Medical Informatics and Epidemiology
>> Oregon Health & Science University
>> haen...@ohsu.edu<mailto:haen...@ohsu.edu>
>> skype: melissa.haendel
>> 503-407-5970
> Dr. Melissa Haendel
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu<mailto:haen...@ohsu.edu>
> skype: melissa.haendel
> 503-407-5970
Dr. Melissa Haendel
Assistant Professor
Ontology Development Group, OHSU Library
http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology
Oregon Health & Science University
haen...@ohsu.edu<mailto:haen...@ohsu.edu>
skype: melissa.haendel
503-407-5970
Sorry I have been offline for a while, but glad to see the discussion.
I agree with pretty much everything that Melissa has already said.
Only Alan's examples 1, 2, and 3 are what I (and most of the ecology and
evolution people I know) would consider populations.
Alan's examples 4,5, and 6 are not populations. Members of population have
to be of the same species (or whatever you call the equivalent in
micro-organisms). This is a very important part of the definitions. I also
feel that living in the same area is an important restriction, even if it
is problematic. The members of a population have to have at least some
possibility of interacting with each other.
The super-class "collection of organisms" is quite useful, not only for
structuring people's thinking, as Melissa suggested, but also for
organizing different types of collections of organism. So far, it only has
two subclasses - population and community. These are classic ecological
terms. Examples 4, 5, and 6 are types of communities.
I think examples like 7, 8, and 9 are quite specific, and are best defined
in more specialized ontologies.. You probably don't really need to model
them as groups of organisms, but rather as a logically defined class (e.g.,
9. People immune to HIV = human X immune to HIV). That type of class is
outside the scope of the PCO.
I think there are a whole lot of interesting things to say about
populations, both in science and in an ontology. There is a whole field of
population ecology that would probably agree. Also, populations are the
unit of evolution, and thus pretty central to biology. Same goes for
community. It is true, that there may not be much we can say about a very
general "collection of organisms", but I still think it is useful for
ontology checking (e.g., does your class have one organism or more than
one?).
On Thu, Sep 20, 2012 at 7:08 PM, Melissa Haendel <haen...@ohsu.edu> wrote:
> On Sep 20, 2012, at 11:00 AM, Alan Ruttenberg wrote:
> V
> On Thursday, September 20, 2012, Melissa Haendel <haen...@ohsu.edu> wrote:
> > On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
> > On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu>
> wrote:
> >> Hi all,
> >> Why wouldn't these (for the most part, I don't know that I would call
> them all populations, see below) simply be defined as subclasses with the
> restrictions largely as you've described them? I agree that the "living in
> the same place" may not be enough to distinguish population from a
> collection of organisms, but regardless of logical definition here I think
> that summarizes the terms' biological use.
> > The definition is: A collection of organisms, all of the same species,
> that live in the same place.
> > You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6
> do either.
> > 4: Not in the same place (at the scale of a bacteria, a cow is a place)
> > yes but the cows live in the same place, by transitivity I'd be ok with
> this one.
> > 5: Not the same species
> > agree, this would be a collection of organisms, not a population by
> current def.
> > 6: Not the same species
> > same same.
> > So I see this definition as only working in only 1/3 of the cases I gave
> (and I didn't try that hard to make the list, which could certainly be
> extended).
> > I'm still ok with the use of the superclass "collection of
> organisms/viruses/viroids" for these, with population being restricted to a
> geographical location. Lets see what the biodiversity folks say?
> Sure, though I think I will maintain my point: looking for the common
> superclass will yield little if any use other than as visual grouping -
> little will be able to be said about the classes members as a whole.
> I would again propose that the project of building ontology resources to
> represent these various kinds of population classes focus on, in the next
> interval of work, defining a bunch of more specific classes about which we
> *can* something interesting about the members, such as the one we want.
> I agree it is helpful to work through real use cases. There may not be a
> whole lot of interesting things to say about a population, and I don't see
> the problem with that?
> One thing to note though - I do believe that populations can bear
> phenotypes (whatever relation we decide to use for this, I guess it is no
> longer inheres_in?) So I suppose this might be interesting :-)
> The rationale is that we don't really gain much by having people use a
> term for annotation which carries no specificity.
> I disagree, I think it helps structure peoples' strategies. We don't
> usually annotate to OGMS disorder, BFO continuant, CARO multi-tissue
> structure either, we use them as the basis of refinement for specific use
> cases. I like the idea of working bottom up, but I would urge us to put
> into place a single, generalized class that we agree largely works for our
> purposes, and work on use cases with real data from there. Else we will
> continue to all use different population classes and be back where we
> started.
> -Alan
> > -Alan
> >> As per Bill's comments on vagueness, I agree it is vague, but I believe
> that populations and subpopulations exist via a transitive member or part
> relation. So there exists the population of humans on the earth, and there
> exists the population of humans in North America, and the humans in this
> latter population are by inference members of the former population based
> on the partonomy of geographical location. If we want to define collections
> of organisms based not by where they live, then perhaps this can use the
> super class 'collection of organisms'- this might be more fitting with the
> actual use of population?
> > That's going more general. The test I would make to see if that is worth
> that is what of interest could we say about instances of collection of
> organisms that would apply to instances of all the suggested subclasses. My
> contention is that unless there is some impact of this sort, defining the
> general class is of little use.
> >> At least so far as biodiversity is concerned my understanding is that
> it is usually (always?) based on geographical location at one level of
> granularity or another. I defer to the experts on this though.
> >> As for time, well that is the same old BFO problem. A person who lives
> half the year in Florida is only a member of the Floridian population
> during that time window.
> > I agree that temporal issues are not primary here.
> >> I agree that the definition should include viruses and virioids, but as
> Ramona suggested the definition will be updated to include this.
> >> Best
> >> Melissa
> >> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
> >> Sorry to through another wrinkle into the discussion, but a collection
> of organisms with symbionts, say obligate, won't fit the definition.
> >> Here as in other cases, I think the attempt to define a general term
> hurts and we should be working a little lower down.
> >> Some clear cases, all of which are of importance in the life sciences
> >> 1. A unicellular colony
> >> 2. A microorganism infection (the bacteria in a bacteremia, the
> viruses[1] in a viremia.
> >> 3. A herd (bunch of big animals living in close proximity)
> >> 4. The sum of the infectious agents in a herd's infection (all
> potential eradictated with the same antibiotic)
> >> 5. A the occupants of a biological niche (most suspeptible to an
> pan-species toxin)
> >> 6. My microbiome
> >> 7. Ashkenazi jews (some common genetic elements due to being a herd at
> some earlier part of history)
> >> doesn't meet current definition
> >> 8. People with malaria
> >> nor this
> >> 9. People immune to HIV
> >> nor this
> >> Would most people call these populations? I am not sure that I would- I
> think I'd think of them as a collection of organisms or viruses, but
> probably not populations.
> >> OK, it didn't take me long to make that list. Maybe there is something
> useful that could be said of the union of those classes. See if there is,
> though I expect it will take some effort. If you can figure it out, make it
> the defining criterion for your upper class. If you can't give up for now
> and define the classes at the level I've laid out.
> >> Assistant Professor
> >> Ontology Development Group, OHSU Library
> >> http://www.ohsu.edu/library/ > >> Department of Medical Informatics and Epidemiology
> >> Oregon Health & Science University
> >> haen...@ohsu.edu
> >> skype: melissa.haendel
> >> 503-407-5970
> > Dr. Melissa Haendel
> > Assistant Professor
> > Ontology Development Group, OHSU Library
> > http://www.ohsu.edu/library/ > > Department of Medical Informatics and Epidemiology
> > Oregon Health & Science University
> > haen...@ohsu.edu
> > skype: melissa.haendel
> > 503-407-5970
> *Dr. Melissa Haendel
> *
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu
> skype: melissa.haendel
> 503-407-5970
Seems like the consensus is for "population" as the name of the class. I
still think this has the potential to be confused with population in the
statistical sense, which has nothing to do with a PCO population and is
also widely used in biology. I do understand that folks don't like a more
specialized name like "biological population". No one ever likes it when we
have specialized names in our ontologies, but they are very helpful in
making an ontology applicable outside its narrow domain.
For the time being, I am going to keep "population" as the primary name,
but add "organismal population" and "biological population" as synonym,
which I hope will help to clarify usage. I am also going to add a comment
that it should not be confused with statistical population.
On Sun, Sep 23, 2012 at 7:39 PM, Ramona Walls <rlwalls2...@gmail.com> wrote:
> Sorry I have been offline for a while, but glad to see the discussion.
> I agree with pretty much everything that Melissa has already said.
> Only Alan's examples 1, 2, and 3 are what I (and most of the ecology and
> evolution people I know) would consider populations.
> Alan's examples 4,5, and 6 are not populations. Members of population have
> to be of the same species (or whatever you call the equivalent in
> micro-organisms). This is a very important part of the definitions. I also
> feel that living in the same area is an important restriction, even if it
> is problematic. The members of a population have to have at least some
> possibility of interacting with each other.
> The super-class "collection of organisms" is quite useful, not only for
> structuring people's thinking, as Melissa suggested, but also for
> organizing different types of collections of organism. So far, it only has
> two subclasses - population and community. These are classic ecological
> terms. Examples 4, 5, and 6 are types of communities.
> I think examples like 7, 8, and 9 are quite specific, and are best defined
> in more specialized ontologies.. You probably don't really need to model
> them as groups of organisms, but rather as a logically defined class (e.g.,
> 9. People immune to HIV = human X immune to HIV). That type of class is
> outside the scope of the PCO.
> I think there are a whole lot of interesting things to say about
> populations, both in science and in an ontology. There is a whole field of
> population ecology that would probably agree. Also, populations are the
> unit of evolution, and thus pretty central to biology. Same goes for
> community. It is true, that there may not be much we can say about a very
> general "collection of organisms", but I still think it is useful for
> ontology checking (e.g., does your class have one organism or more than
> one?).
> Ramona
> On Thu, Sep 20, 2012 at 7:08 PM, Melissa Haendel <haen...@ohsu.edu> wrote:
>> On Sep 20, 2012, at 11:00 AM, Alan Ruttenberg wrote:
>> V
>> On Thursday, September 20, 2012, Melissa Haendel <haen...@ohsu.edu>
>> wrote:
>> > On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
>> > On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu>
>> wrote:
>> >> Hi all,
>> >> Why wouldn't these (for the most part, I don't know that I would call
>> them all populations, see below) simply be defined as subclasses with the
>> restrictions largely as you've described them? I agree that the "living in
>> the same place" may not be enough to distinguish population from a
>> collection of organisms, but regardless of logical definition here I think
>> that summarizes the terms' biological use.
>> > The definition is: A collection of organisms, all of the same species,
>> that live in the same place.
>> > You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6
>> do either.
>> > 4: Not in the same place (at the scale of a bacteria, a cow is a place)
>> > yes but the cows live in the same place, by transitivity I'd be ok with
>> this one.
>> > 5: Not the same species
>> > agree, this would be a collection of organisms, not a population by
>> current def.
>> > 6: Not the same species
>> > same same.
>> > So I see this definition as only working in only 1/3 of the cases I
>> gave (and I didn't try that hard to make the list, which could certainly be
>> extended).
>> > I'm still ok with the use of the superclass "collection of
>> organisms/viruses/viroids" for these, with population being restricted to a
>> geographical location. Lets see what the biodiversity folks say?
>> Sure, though I think I will maintain my point: looking for the common
>> superclass will yield little if any use other than as visual grouping -
>> little will be able to be said about the classes members as a whole.
>> I would again propose that the project of building ontology resources to
>> represent these various kinds of population classes focus on, in the next
>> interval of work, defining a bunch of more specific classes about which we
>> *can* something interesting about the members, such as the one we want.
>> I agree it is helpful to work through real use cases. There may not be a
>> whole lot of interesting things to say about a population, and I don't see
>> the problem with that?
>> One thing to note though - I do believe that populations can bear
>> phenotypes (whatever relation we decide to use for this, I guess it is no
>> longer inheres_in?) So I suppose this might be interesting :-)
>> The rationale is that we don't really gain much by having people use a
>> term for annotation which carries no specificity.
>> I disagree, I think it helps structure peoples' strategies. We don't
>> usually annotate to OGMS disorder, BFO continuant, CARO multi-tissue
>> structure either, we use them as the basis of refinement for specific use
>> cases. I like the idea of working bottom up, but I would urge us to put
>> into place a single, generalized class that we agree largely works for our
>> purposes, and work on use cases with real data from there. Else we will
>> continue to all use different population classes and be back where we
>> started.
>> -Alan
>> > -Alan
>> >> As per Bill's comments on vagueness, I agree it is vague, but I
>> believe that populations and subpopulations exist via a transitive member
>> or part relation. So there exists the population of humans on the earth,
>> and there exists the population of humans in North America, and the humans
>> in this latter population are by inference members of the former population
>> based on the partonomy of geographical location. If we want to define
>> collections of organisms based not by where they live, then perhaps this
>> can use the super class 'collection of organisms'- this might be more
>> fitting with the actual use of population?
>> > That's going more general. The test I would make to see if that is
>> worth that is what of interest could we say about instances of collection
>> of organisms that would apply to instances of all the suggested subclasses.
>> My contention is that unless there is some impact of this sort, defining
>> the general class is of little use.
>> >> At least so far as biodiversity is concerned my understanding is that
>> it is usually (always?) based on geographical location at one level of
>> granularity or another. I defer to the experts on this though.
>> >> As for time, well that is the same old BFO problem. A person who lives
>> half the year in Florida is only a member of the Floridian population
>> during that time window.
>> > I agree that temporal issues are not primary here.
>> >> I agree that the definition should include viruses and virioids, but
>> as Ramona suggested the definition will be updated to include this.
>> >> Best
>> >> Melissa
>> >> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
>> >> Sorry to through another wrinkle into the discussion, but a collection
>> of organisms with symbionts, say obligate, won't fit the definition.
>> >> Here as in other cases, I think the attempt to define a general term
>> hurts and we should be working a little lower down.
>> >> Some clear cases, all of which are of importance in the life sciences
>> >> 1. A unicellular colony
>> >> 2. A microorganism infection (the bacteria in a bacteremia, the
>> viruses[1] in a viremia.
>> >> 3. A herd (bunch of big animals living in close proximity)
>> >> 4. The sum of the infectious agents in a herd's infection (all
>> potential eradictated with the same antibiotic)
>> >> 5. A the occupants of a biological niche (most suspeptible to an
>> pan-species toxin)
>> >> 6. My microbiome
>> >> 7. Ashkenazi jews (some common genetic elements due to being a herd at
>> some earlier part of history)
>> >> doesn't meet current definition
>> >> 8. People with malaria
>> >> nor this
>> >> 9. People immune to HIV
>> >> nor this
>> >> Would most people call these populations? I am not sure that I would-
>> I think I'd think of them as a collection of organisms or viruses, but
>> probably not populations.
>> >> OK, it didn't take me long to make that list. Maybe there is something
>> useful that could be said of the union of those classes. See if there is,
>> though I expect it will take some effort. If you can figure it out, make it
>> the defining criterion for your upper class. If you can't give up for now
>> and define the classes at the level I've laid out.
I will also point out that the PCO has a google group for discussion (
https://groups.google.com/forum/?hl=en&fromgroups#!forum/popcomm-onto...)
and a google code page (http://code.google.com/p/popcomm-ontology/) where
these terms could be discussed. However, I appreciate that the OGMS and IDO
communities are important consumers of terms like population, and it is
important to have the discussion visible to members of those lists, so
leaving this thread here makes sense.
On Sun, Sep 23, 2012 at 7:44 PM, Ramona Walls <rlwalls2...@gmail.com> wrote:
> Seems like the consensus is for "population" as the name of the class. I
> still think this has the potential to be confused with population in the
> statistical sense, which has nothing to do with a PCO population and is
> also widely used in biology. I do understand that folks don't like a more
> specialized name like "biological population". No one ever likes it when we
> have specialized names in our ontologies, but they are very helpful in
> making an ontology applicable outside its narrow domain.
> For the time being, I am going to keep "population" as the primary name,
> but add "organismal population" and "biological population" as synonym,
> which I hope will help to clarify usage. I am also going to add a comment
> that it should not be confused with statistical population.
> Ramona
> On Sun, Sep 23, 2012 at 7:39 PM, Ramona Walls <rlwalls2...@gmail.com>wrote:
>> Sorry I have been offline for a while, but glad to see the discussion.
>> I agree with pretty much everything that Melissa has already said.
>> Only Alan's examples 1, 2, and 3 are what I (and most of the ecology and
>> evolution people I know) would consider populations.
>> Alan's examples 4,5, and 6 are not populations. Members of population
>> have to be of the same species (or whatever you call the equivalent in
>> micro-organisms). This is a very important part of the definitions. I also
>> feel that living in the same area is an important restriction, even if it
>> is problematic. The members of a population have to have at least some
>> possibility of interacting with each other.
>> The super-class "collection of organisms" is quite useful, not only for
>> structuring people's thinking, as Melissa suggested, but also for
>> organizing different types of collections of organism. So far, it only has
>> two subclasses - population and community. These are classic ecological
>> terms. Examples 4, 5, and 6 are types of communities.
>> I think examples like 7, 8, and 9 are quite specific, and are best
>> defined in more specialized ontologies.. You probably don't really need to
>> model them as groups of organisms, but rather as a logically defined class
>> (e.g., 9. People immune to HIV = human X immune to HIV). That type of class
>> is outside the scope of the PCO.
>> I think there are a whole lot of interesting things to say about
>> populations, both in science and in an ontology. There is a whole field of
>> population ecology that would probably agree. Also, populations are the
>> unit of evolution, and thus pretty central to biology. Same goes for
>> community. It is true, that there may not be much we can say about a very
>> general "collection of organisms", but I still think it is useful for
>> ontology checking (e.g., does your class have one organism or more than
>> one?).
>> Ramona
>> On Thu, Sep 20, 2012 at 7:08 PM, Melissa Haendel <haen...@ohsu.edu>wrote:
>>> On Sep 20, 2012, at 11:00 AM, Alan Ruttenberg wrote:
>>> V
>>> On Thursday, September 20, 2012, Melissa Haendel <haen...@ohsu.edu>
>>> wrote:
>>> > On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
>>> > On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu>
>>> wrote:
>>> >> Hi all,
>>> >> Why wouldn't these (for the most part, I don't know that I would call
>>> them all populations, see below) simply be defined as subclasses with the
>>> restrictions largely as you've described them? I agree that the "living in
>>> the same place" may not be enough to distinguish population from a
>>> collection of organisms, but regardless of logical definition here I think
>>> that summarizes the terms' biological use.
>>> > The definition is: A collection of organisms, all of the same species,
>>> that live in the same place.
>>> > You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6
>>> do either.
>>> > 4: Not in the same place (at the scale of a bacteria, a cow is a place)
>>> > yes but the cows live in the same place, by transitivity I'd be ok
>>> with this one.
>>> > 5: Not the same species
>>> > agree, this would be a collection of organisms, not a population by
>>> current def.
>>> > 6: Not the same species
>>> > same same.
>>> > So I see this definition as only working in only 1/3 of the cases I
>>> gave (and I didn't try that hard to make the list, which could certainly be
>>> extended).
>>> > I'm still ok with the use of the superclass "collection of
>>> organisms/viruses/viroids" for these, with population being restricted to a
>>> geographical location. Lets see what the biodiversity folks say?
>>> Sure, though I think I will maintain my point: looking for the common
>>> superclass will yield little if any use other than as visual grouping -
>>> little will be able to be said about the classes members as a whole.
>>> I would again propose that the project of building ontology resources to
>>> represent these various kinds of population classes focus on, in the next
>>> interval of work, defining a bunch of more specific classes about which we
>>> *can* something interesting about the members, such as the one we want.
>>> I agree it is helpful to work through real use cases. There may not be a
>>> whole lot of interesting things to say about a population, and I don't see
>>> the problem with that?
>>> One thing to note though - I do believe that populations can bear
>>> phenotypes (whatever relation we decide to use for this, I guess it is no
>>> longer inheres_in?) So I suppose this might be interesting :-)
>>> The rationale is that we don't really gain much by having people use a
>>> term for annotation which carries no specificity.
>>> I disagree, I think it helps structure peoples' strategies. We don't
>>> usually annotate to OGMS disorder, BFO continuant, CARO multi-tissue
>>> structure either, we use them as the basis of refinement for specific use
>>> cases. I like the idea of working bottom up, but I would urge us to put
>>> into place a single, generalized class that we agree largely works for our
>>> purposes, and work on use cases with real data from there. Else we will
>>> continue to all use different population classes and be back where we
>>> started.
>>> -Alan
>>> > -Alan
>>> >> As per Bill's comments on vagueness, I agree it is vague, but I
>>> believe that populations and subpopulations exist via a transitive member
>>> or part relation. So there exists the population of humans on the earth,
>>> and there exists the population of humans in North America, and the humans
>>> in this latter population are by inference members of the former population
>>> based on the partonomy of geographical location. If we want to define
>>> collections of organisms based not by where they live, then perhaps this
>>> can use the super class 'collection of organisms'- this might be more
>>> fitting with the actual use of population?
>>> > That's going more general. The test I would make to see if that is
>>> worth that is what of interest could we say about instances of collection
>>> of organisms that would apply to instances of all the suggested subclasses.
>>> My contention is that unless there is some impact of this sort, defining
>>> the general class is of little use.
>>> >> At least so far as biodiversity is concerned my understanding is that
>>> it is usually (always?) based on geographical location at one level of
>>> granularity or another. I defer to the experts on this though.
>>> >> As for time, well that is the same old BFO problem. A person who
>>> lives half the year in Florida is only a member of the Floridian population
>>> during that time window.
>>> > I agree that temporal issues are not primary here.
>>> >> I agree that the definition should include viruses and virioids, but
>>> as Ramona suggested the definition will be updated to include this.
>>> >> Best
>>> >> Melissa
>>> >> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
>>> >> Sorry to through another wrinkle into the discussion, but a
>>> collection of organisms with symbionts, say obligate, won't fit the
>>> definition.
>>> >> Here as in other cases, I think the attempt to define a general term
>>> hurts and we should be working a little lower down.
>>> >> Some clear cases, all of which are of importance in the life sciences
>>> >> 1. A unicellular colony
>>> >> 2. A microorganism infection (the bacteria in a bacteremia, the
>>> viruses[1] in a viremia.
>>> >> 3. A herd (bunch of big animals living in close proximity)
>>> >> 4. The sum of the infectious agents in a herd's infection (all
>>> potential eradictated with the same antibiotic)
>>> >> 5. A the occupants of a biological niche (most suspeptible to an
>>> pan-species toxin)
>>> >> 6. My microbiome
>>> >> 7. Ashkenazi jews (some common genetic elements due to being a herd
>>> at some earlier part of history)
On Thu, Sep 20, 2012 at 2:08 PM, Melissa Haendel <haen...@ohsu.edu> wrote:
> On Sep 20, 2012, at 11:00 AM, Alan Ruttenberg wrote:
> V
> On Thursday, September 20, 2012, Melissa Haendel <haen...@ohsu.edu> wrote:
> > On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
> > On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu>
> wrote:
> >> Hi all,
> >> Why wouldn't these (for the most part, I don't know that I would call
> them all populations, see below) simply be defined as subclasses with the
> restrictions largely as you've described them? I agree that the "living in
> the same place" may not be enough to distinguish population from a
> collection of organisms, but regardless of logical definition here I think
> that summarizes the terms' biological use.
> > The definition is: A collection of organisms, all of the same species,
> that live in the same place.
> > You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6
> do either.
> > 4: Not in the same place (at the scale of a bacteria, a cow is a place)
> > yes but the cows live in the same place, by transitivity I'd be ok with
> this one.
> > 5: Not the same species
> > agree, this would be a collection of organisms, not a population by
> current def.
> > 6: Not the same species
> > same same.
> > So I see this definition as only working in only 1/3 of the cases I gave
> (and I didn't try that hard to make the list, which could certainly be
> extended).
> > I'm still ok with the use of the superclass "collection of
> organisms/viruses/viroids" for these, with population being restricted to a
> geographical location. Lets see what the biodiversity folks say?
> Sure, though I think I will maintain my point: looking for the common
> superclass will yield little if any use other than as visual grouping -
> little will be able to be said about the classes members as a whole.
> I would again propose that the project of building ontology resources to
> represent these various kinds of population classes focus on, in the next
> interval of work, defining a bunch of more specific classes about which we
> *can* something interesting about the members, such as the one we want.
> I agree it is helpful to work through real use cases. There may not be a
> whole lot of interesting things to say about a population, and I don't see
> the problem with that?
There are two problems. 1) If you can't say anything about it you can't
rule in or out instances being a member of it. 2) If someone happens to say
something about it then you have no criteria by which to evaluate whether
it is right or wrong.
> One thing to note though - I do believe that populations can bear
> phenotypes (whatever relation we decide to use for this, I guess it is no
> longer inheres_in?) So I suppose this might be interesting :-)
I don't know why it wouldn't be inheres_in? Why do you think so? Saying
that there is some phenotype that inheres in every population is that start
of saying something defining.
> The rationale is that we don't really gain much by having people use a
> term for annotation which carries no specificity.
> I disagree, I think it helps structure peoples' strategies.
I'm not really sure what that means.
> We don't usually annotate to OGMS disorder, BFO continuant, CARO
> multi-tissue structure either, we use them as the basis of refinement for
> specific use cases.
yes, but in each case there are axioms associated. Every continuant is not
an occurrent. Every disorder is a material entity. Disorders are the only
sort of thing that can be the material basis of a disease, etc. We need to
have similar kinds of statements for any term if it is to have a meaning.
> I like the idea of working bottom up, but I would urge us to put into
> place a single, generalized class that we agree largely works for our
> purposes,
How do we evaluate whether it works for our purposes?
> and work on use cases with real data from there. Else we will continue to
> all use different population classes and be back where we started.
Instead, with this strategy, we will all use the same population class that
doesn't mean anything.
> >> As per Bill's comments on vagueness, I agree it is vague, but I believe
> that populations and subpopulations exist via a transitive member or part
> relation. So there exists the population of humans on the earth, and there
> exists the population of humans in North America, and the humans in this
> latter population are by inference members of the former population based
> on the partonomy of geographical location. If we want to define collections
> of organisms based not by where they live, then perhaps this can use the
> super class 'collection of organisms'- this might be more fitting with the
> actual use of population?
> > That's going more general. The test I would make to see if that is worth
> that is what of interest could we say about instances of collection of
> organisms that would apply to instances of all the suggested subclasses. My
> contention is that unless there is some impact of this sort, defining the
> general class is of little use.
> >> At least so far as biodiversity is concerned my understanding is that
> it is usually (always?) based on geographical location at one level of
> granularity or another. I defer to the experts on this though.
> >> As for time, well that is the same old BFO problem. A person who lives
> half the year in Florida is only a member of the Floridian population
> during that time window.
> > I agree that temporal issues are not primary here.
> >> I agree that the definition should include viruses and virioids, but as
> Ramona suggested the definition will be updated to include this.
> >> Best
> >> Melissa
> >> On Sep 20, 2012, at 7:15 AM, Alan Ruttenberg wrote:
> >> Sorry to through another wrinkle into the discussion, but a collection
> of organisms with symbionts, say obligate, won't fit the definition.
> >> Here as in other cases, I think the attempt to define a general term
> hurts and we should be working a little lower down.
> >> Some clear cases, all of which are of importance in the life sciences
> >> 1. A unicellular colony
> >> 2. A microorganism infection (the bacteria in a bacteremia, the
> viruses[1] in a viremia.
> >> 3. A herd (bunch of big animals living in close proximity)
> >> 4. The sum of the infectious agents in a herd's infection (all
> potential eradictated with the same antibiotic)
> >> 5. A the occupants of a biological niche (most suspeptible to an
> pan-species toxin)
> >> 6. My microbiome
> >> 7. Ashkenazi jews (some common genetic elements due to being a herd at
> some earlier part of history)
> >> doesn't meet current definition
> >> 8. People with malaria
> >> nor this
> >> 9. People immune to HIV
> >> nor this
> >> Would most people call these populations? I am not sure that I would- I
> think I'd think of them as a collection of organisms or viruses, but
> probably not populations.
> >> OK, it didn't take me long to make that list. Maybe there is something
> useful that could be said of the union of those classes. See if there is,
> though I expect it will take some effort. If you can figure it out, make it
> the defining criterion for your upper class. If you can't give up for now
> and define the classes at the level I've laid out.
> >> Assistant Professor
> >> Ontology Development Group, OHSU Library
> >> http://www.ohsu.edu/library/ > >> Department of Medical Informatics and Epidemiology
> >> Oregon Health & Science University
> >> haen...@ohsu.edu
> >> skype: melissa.haendel
> >> 503-407-5970
> > Dr. Melissa Haendel
> > Assistant Professor
> > Ontology Development Group, OHSU Library
> > http://www.ohsu.edu/library/ > > Department of Medical Informatics and Epidemiology
> > Oregon Health & Science University
> > haen...@ohsu.edu
> > skype: melissa.haendel
> > 503-407-5970
> *Dr. Melissa Haendel
> *
> Assistant Professor
> Ontology Development Group, OHSU Library
> http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> haen...@ohsu.edu
> skype: melissa.haendel
> 503-407-5970
On Sun, Sep 23, 2012 at 2:44 PM, Ramona Walls <rlwalls2...@gmail.com> wrote:
> Seems like the consensus is for "population" as the name of the class.
Not sure where you see this consensus.
> I still think this has the potential to be confused with population in the
> statistical sense, which has nothing to do with a PCO population and is
> also widely used in biology.
Right, that's my concern, and I think it's a serious argument against using
the label "population" bare.
> I do understand that folks don't like a more specialized name like
> "biological population". No one ever likes it when we have specialized
> names in our ontologies
I've not heard that before. Usually the aim in choosing a primary label is
to make it unambiguous, with community labels allowing globally ambiguous
terms which are unambiguously used within a narrower community.
> , but they are very helpful in making an ontology applicable outside its
> narrow domain.
I don't think the names have anything at all to do with applicability.
Their purpose is to give a first foothold into understandability of what a
term means. The bulk of the understanding is supposed to come from the
definition. Applicability has to do with whether someone has something to
say about entities of the kind denoted by the term.
> For the time being, I am going to keep "population" as the primary name,
> but add "organismal population" and "biological population" as synonym,
> which I hope will help to clarify usage.
I doesn't. For one thing it doesn't capture that the intent is that the
term mean a geographically localized group, which seems to be an important
element of what this term is supposed to mean, nor does it capture that the
organisms are from the same species - if an organism that reproduces
sexually then a group that can interbreed. You have these noted in the
comments but this is not reflected in the definition. It also doesn't make
clear whether the population is intended to be maximal in some sense -
whether, if you give parameters of a subclass as species and location the
term necessarily refers to *all* organisms of the species in the location,
or can refer to some of them.
"Organismal" or "biological" population will easily be confused with
statistical populations whose members are living things.
> I am also going to add a comment that it should not be confused with
> statistical population.
That's a start, but depending on the answer to the issue I raise above re:
whether the population is maximal, some population instances might also be
a statistical population instances, in which case they are legitimately
confused.
Why not make it stronger by defining "statistical population of
organisms", and "population of a species in a habitat" (the latter being a
term which seems to me what you are aiming to define). I think you are also
going to have to modify your stance on the "location" part of your
definition if you intend to include human communities (and assuming you
mean location in the BFO sense), which can aggregate over a distance and
enjoy interaction that are not mediated by proximity. As an example humans
who spend a lot of time playing MMORPGs, a community/population that has
been the subject of sociological and behavioral studies.
> On Sun, Sep 23, 2012 at 7:39 PM, Ramona Walls <rlwalls2...@gmail.com>wrote:
>> Sorry I have been offline for a while, but glad to see the discussion.
>> I agree with pretty much everything that Melissa has already said.
>> Only Alan's examples 1, 2, and 3 are what I (and most of the ecology and
>> evolution people I know) would consider populations.
>> Alan's examples 4,5, and 6 are not populations. Members of population
>> have to be of the same species (or whatever you call the equivalent in
>> micro-organisms). This is a very important part of the definitions. I also
>> feel that living in the same area is an important restriction, even if it
>> is problematic. The members of a population have to have at least some
>> possibility of interacting with each other.
>> The super-class "collection of organisms" is quite useful, not only for
>> structuring people's thinking, as Melissa suggested, but also for
>> organizing different types of collections of organism. So far, it only has
>> two subclasses - population and community. These are classic ecological
>> terms. Examples 4, 5, and 6 are types of communities.
>> I think examples like 7, 8, and 9 are quite specific, and are best
>> defined in more specialized ontologies.. You probably don't really need to
>> model them as groups of organisms, but rather as a logically defined class
>> (e.g., 9. People immune to HIV = human X immune to HIV). That type of class
>> is outside the scope of the PCO.
>> I think there are a whole lot of interesting things to say about
>> populations, both in science and in an ontology. There is a whole field of
>> population ecology that would probably agree. Also, populations are the
>> unit of evolution, and thus pretty central to biology. Same goes for
>> community. It is true, that there may not be much we can say about a very
>> general "collection of organisms", but I still think it is useful for
>> ontology checking (e.g., does your class have one organism or more than
>> one?).
>> Ramona
>> On Thu, Sep 20, 2012 at 7:08 PM, Melissa Haendel <haen...@ohsu.edu>wrote:
>>> On Sep 20, 2012, at 11:00 AM, Alan Ruttenberg wrote:
>>> V
>>> On Thursday, September 20, 2012, Melissa Haendel <haen...@ohsu.edu>
>>> wrote:
>>> > On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:
>>> > On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <haen...@ohsu.edu>
>>> wrote:
>>> >> Hi all,
>>> >> Why wouldn't these (for the most part, I don't know that I would call
>>> them all populations, see below) simply be defined as subclasses with the
>>> restrictions largely as you've described them? I agree that the "living in
>>> the same place" may not be enough to distinguish population from a
>>> collection of organisms, but regardless of logical definition here I think
>>> that summarizes the terms' biological use.
>>> > The definition is: A collection of organisms, all of the same species,
>>> that live in the same place.
>>> > You've noted 7,8,9 don't meet the definition. I don't think 4, 5, or 6
>>> do either.
>>> > 4: Not in the same place (at the scale of a bacteria, a cow is a place)
>>> > yes but the cows live in the same place, by transitivity I'd be ok
>>> with this one.
>>> > 5: Not the same species
>>> > agree, this would be a collection of organisms, not a population by
>>> current def.
>>> > 6: Not the same species
>>> > same same.
>>> > So I see this definition as only working in only 1/3 of the cases I
>>> gave (and I didn't try that hard to make the list, which could certainly be
>>> extended).
>>> > I'm still ok with the use of the superclass "collection of
>>> organisms/viruses/viroids" for these, with population being restricted to a
>>> geographical location. Lets see what the biodiversity folks say?
>>> Sure, though I think I will maintain my point: looking for the common
>>> superclass will yield little if any use other than as visual grouping -
>>> little will be able to be said about the classes members as a whole.
>>> I would again propose that the project of building ontology resources to
>>> represent these various kinds of population classes focus on, in the next
>>> interval of work, defining a bunch of more specific classes about which we
>>> *can* something interesting about the members, such as the one we want.
>>> I agree it is helpful to work through real use cases. There may not be a
>>> whole lot of interesting things to say about a population, and I don't see
>>> the problem with that?
>>> One thing to note though - I do believe that populations can bear
>>> phenotypes (whatever relation we decide to use for this, I guess it is no
>>> longer inheres_in?) So I suppose this might be interesting :-)
>>> The rationale is that we don't really gain much by having people use a
>>> term for annotation which carries no specificity.
>>> I disagree, I think it helps structure peoples' strategies. We don't
>>> usually annotate to OGMS disorder, BFO continuant, CARO multi-tissue
>>> structure either, we use them as the basis of refinement for specific use
>>> cases. I like the idea of working bottom up, but I would urge us to put
>>> into place a single, generalized class that we agree largely works for our
>>> purposes, and work on use cases with real data from there. Else we will
>>> continue to all use different population classes and be back where we
>>> started.
>>> -Alan
>>> > -Alan
>>> >> As per Bill's comments on vagueness, I agree it is vague, but I
>>> believe that populations and subpopulations exist via a transitive member
>>> or part relation. So there exists the population of humans on the earth,
>>> and there exists the population of humans in North America, and the humans
>>> in this latter population are by inference members of the former population
>>> based on the partonomy of geographical location. If we want to define
>>> collections of organisms based not by where they live, then perhaps this
>>> can use the super class 'collection of organisms'- this might be more
>>> fitting with the actual use of population?
>>> > That's going more general. The test I would make to see if that is
>>> worth that is what of interest could we say about instances of collection
>>> of organisms that would apply to
