Re: Issue 33 in ogms: Proposed term 'Organism Population'

[og...@googlecode.com]

Updates:
Status: Started

Comment #2 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

This term will be added in OGMS v0.3

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Comment #3 on issue 33 by mcourtot: Proposed term 'Organism Population'
http://code.google.com/p/ogms/issues/detail?id=33

OBI defines population (OBI_0000181) as "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"

[og...@googlecode.com]

Comment #4 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

We may be able to MIREOT to the OBI definition, but I think there are a few
issues:

(1) organism populations exist even if no one counts or samples them
(although I
understand why you want to say this for OBI)...there is a population of
people with
swine flu distinct from the sampled population.
(2) I am a member of the population of the USA, but I can be living
overseas and
still be considered a member of that population
(3) there may not be well defined taxonomic classes for certain bacteria
(where at
best we can only cluster them into clonal complexes)
(4) [minor issue] 'individuals' may be too broad
(5) [minor issue] how does 'particular site' differ from 'particular area'
(in terms
of spatial regions)

Just FYI, we need 'organism population' in IDO for very different
reasons...to define
infections as organism populations of infectious organisms, and to define
host and
pathogen populations in epidemiological settings.

[og...@googlecode.com]

Comment #5 on issue 33 by hoganwr: Proposed term 'Organism Population'
http://code.google.com/p/ogms/issues/detail?id=33

I agree with Albert, that populations exist even if not counted.

This issue and issue #17 raise the question of where certain terms belong,
so to speak.

I appreciate the pioneering work done on OBI, and that folks working on OBI
had to
create high-level terms because of the absence of something like OGMS. And
to the
extent that folks have been using OBI ids for organism population and
healthcare
provider, we also need to be mindful of that.

Nevertheless, I would suggest that these terms belong in OGMS, and that the
question
then is whether it is worth the effort to move them there.

I certainly don't want to fight turf wars and won't press the issue any
further than
this, but I just to make sure that terms are in the appropriate place. I
don't know
what the OBO Foundry official position is on issues like this, either.

[og...@googlecode.com]

Comment #6 on issue 33 by mcourtot: Proposed term 'Organism Population'
http://code.google.com/p/ogms/issues/detail?id=33

I agree with #1, populations exist even if not counted. I believe this is
an issue
with the OBI definition, I am not sure OBI developers intended to restrict
this. As
you know we had issues with definition of population/aggregate which lead
to the
creation of the MaterialEntity class, so it may very well be that those are
not very
up-to-date. I will email both lists and we'll see.

I am not sure about #2 (population of USA living abroad) that sounds to me
like an
other meaning of the word population, linked to social/legal status, so
maybe more
like a role - it resembles "citizen" for example.

I agree with your other points.

Regarding the need in IDO to define populations of infectious organisms,
again, I am
not sure it is contradictory with the intent of OBI.

Regarding where do terms live, I am happy either way, with the aim of not
creating
duplicate terms.

[og...@googlecode.com]

Updates:
Status: Started

Comment #8 on issue 33 by alanruttenberg: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

Don't close this issue until we have worked out a common definition with OBI

[og...@googlecode.com]

Comment #9 on issue 33 by lgcow...@duke.edu: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

the relevant IDO terms/definitions are:

organism population: an aggregate of organisms
- comment: The aggregate of organisms may be delineated by spatio-temporal
proximity or by demographic
criteria such as age.
simple organism population: An organism population that has as constituents
organisms of the same type.
mixed organism population: An organism population that has as constituents
organisms of different types.

i agree with albert's points above. in addition, i think these terms, as
well as other general terms such as
organism, belong in an ontology that is more general then OGMS, an ontology
that covers general biology
terms that are not specific to medicine. it seems OGMS might have subtypes
that are specific to medicine,
certain types of patient populations perhaps, and OBI might have terms that
are specific to investigations, like
sampled or counted populations/groups. in IDO, we have specific terms like
infectious organism population,
normal resident microbiota, etc.

[og...@googlecode.com]

Comment #10 on issue 33 by alanruttenberg: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

Definitions that make use of the construct "of the same type" don't work,
because all entities are .... entities. So
everything is of the the same type, at least for one type. "different
types" is similarly problematic.

[og...@googlecode.com]

Comment #11 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

I think in this case we could just say "...of the same type of organism".
I always
parse the natural language phrase "...of the same type" to mean of the same
immediate
type in the ontology, without going up (for example) as far as entity, but
I guess we
could always be more precise.

[og...@googlecode.com]

Comment #12 on issue 33 by alanruttenberg: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

same type of organism has the same problem. All subtypes of organism are of
type ... organism. I.e. the same
type.

"Immediate type" isn't something that can be counted on because it isn't
stable in the face of ontology
evolution that makes finer distinctions as science progresses. So I do
think we should figure out some better
way of expressing this.

I volunteer Barry. :)

[og...@googlecode.com]

Comment #13 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

Alan...I don't buy that as an argument for not using "immediate type". I
think it is
well understood that as science progresses that ontologies need to change
(and this
may change what we understand to be immediate types)...but the fact
that 'fungal
organism population' hinges on 'fungus' makes it a fairly stable type (at
least more
stable than types that talk about universals like higgs bosons).

Philosophers like to talk about the case of jade, which was thought to be a
universal, but after some scientific discovery, what we were calling 'jade'
was
actually two minerals 'jadite' and 'nephrite' (see
http://en.wikipedia.org/wiki/Jade )

At that point all ontologies and logical statements about jade had to
change...including implicit references like "immediate type". IMO, we
should never
expect our ontologies aren't going to change in the face of scientific
discovery.

[og...@googlecode.com]

Comment #14 on issue 33 by bjoern.m.peters: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

I agree with Alan. There is no problem in defining 'fungal population' as a
population whose members are fungi. There is a problem in defining 'simple
organism
population' as being homogenous in some way to exclude e.g. a group of
fungi and
zebras being considered one population.

[og...@googlecode.com]

Comment #15 on issue 33 by alanruttenberg: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

When you write "a fungal organism population is an organism population
whose members are organisms of type fungus" and you add a
subtype of the type fungus, the extension of the class does not change.

When you write "a fungal subtype organism population is an organism
population whose members are organisms of the same immediate
type of fungus", the extension does change if you add a subclass.

Suppose you have

Fungus
Fungus type A
Fungus type B

Suppose you have an instance of fungal subtype organism population (call
this instance fsp) all of whose members are fugus type A.

Now suppose you further subdivide into a partition

Fungus type A
Fungus type A1
Fungus type A2

and find that the members of fsp are type A1 and some type A2.

Now the instance fsp is no longer and instance of fungal subtype organism
population.

This kind of change, due solely to adding of detail, isn't acceptable. It
violates monotonicity, for one, and *not for any good reason*.

The definition of fungal organism population doesn't suffer this problem.

In the case of jade, not all statements needed to be changed. That jade is
green and solid remains true. Each statement of the form: "This
little buddha is made of jade" remains true. etc.

-Alan

[og...@googlecode.com]

Comment #16 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

That is *not* how I was proposing to use immediate type...not subtypes like
the
second reading. It was actually more like the first reading

"a fungal organism population is an organism population whose members are
organisms
of type fungus"

where you overwrite 'immediate type' with 'fungus'...this is pretty much
what you are
doing with obi:population...you just use taxonomic class instead of
immediate
type(OBI_0000181). If 'taxonomic class' is the silver bullet that solves
this
problem then I am happy to accept it.

Is there really a confusion that a fungus population is a population of
fungus :-)?

[og...@googlecode.com]

Comment #17 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

Also bjoern, how is it that I understand your use of the word "homogenous"
in your
comment if I don't understand "of the same type"? Do you have a definition
for
homogenous that doesn't mention same type?

[og...@googlecode.com]

Comment #18 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

FYI...sortal logic tries to deal with expressions containing "...the same X
as...",
if we don't have "the same type as" as a (meta)ontology relationship
available, then
we need to do a lot of additional work that likely goes beyond the scope of
OGMS...

http://plato.stanford.edu/entries/sortals/

[og...@googlecode.com]

Comment #19 on issue 33 by alanruttenberg: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

My point is that even if we did have "same type as" as a (meta)ontology
relationship available it would be a bad
idea to use it.

[og...@googlecode.com]

Comment #20 on issue 33 by bjoern.m.peters: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

I think there is a misunderstanding here, and I hope it is not me. I
thought the
problem raised by Alan is that it is not possible to distinguish
simple organism population and mixed organism population as defined in
comment 9, as
something may become 'mixed' as we learn more.

None of us has a problem with 'fungal organism population'.
Alan (and I) would have a problem with 'simple fungal organism population'
defined as
having members of the same type of fungus.

[og...@googlecode.com]

Comment #21 on issue 33 by alanruttenberg: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

I understand it as Bjoern does.

[og...@googlecode.com]

Comment #22 on issue 33 by albertgoldfain: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

Thanks for the elucidation Bjoern,

We don't intend 'simple fungal organism population', but rather 'fungal
organism
population', 'bacterial organism population', etc...to define 'infection',
a central
term in the infectious disease ontology.

[og...@googlecode.com]

Comment #23 on issue 33 by bjoern.m.peters: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

If the 'simple organism population' will not be used, we are fine.

That leaves the definition of 'organism population'=def: an aggregate of
organisms.
As long as everyone is fine with this including the set of me, a zebra and
a fungus,
it will work. It does for me. Anything stronger would have to be subtyped.

[og...@googlecode.com]

Comment #24 on issue 33 by lgcow...@duke.edu: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

I see the problem with "of the same type", but I don't see a way around
it. I am open to alternative suggestions.
The problem comes when distinguishing "regular" and
mixed/complex/polyorganismal infections/diseases. I
can't think of a way to do this without referring to the fact that there
are infectious organisms all of the same
type in one case and of different types in the other. There is a large
community of researchers who study the
ways in which these types of infections are different from simple
co-infections, so we are making a distinction in
IDO between these types of infections and multiple distinct infections that
happen to be in the same host
organism.

[og...@googlecode.com]

Comment #25 on issue 33 by lgcow...@duke.edu: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

maybe you guys can suggest another way to make this distinction.

[og...@googlecode.com]

Comment #26 on issue 33 by lgcow...@duke.edu: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

re the use of "taxonomic class" instead ... to me it seems that "same
taxonomic class" has exactly the same
problem as "same type" (if i correctly understand the complaint). any two
types have some supertype in
common, and any two taxonomic classes have some parent class in common.

in many cases, we could potentially solve the problem by specifying at
which taxonomic rank the organisms have
to be of the same taxonomic class (ie species).

this doesn't help us with the cases where we are not talking about
organisms though.

[og...@googlecode.com]

Comment #27 on issue 33 by bjoern.m.peters: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

I think that would work Lindsey. 'mixed species population' vs. 'single
species
population'. This could work as the taxonomic rank 'species' defines at what
'granularity cutoff' two organisms are considered the same even if we later
learn
about additional differences. Similarly, 'mixed genus population', 'mixed
strain
population' etc. could be defined.

This does require though that we manage to tie taxonomic ranks to the NCBI
taxonomy
which I believe isn't fully worked out.

When would we not talk about organisms for populations?

- Bjoern

[og...@googlecode.com]

Comment #28 on issue 33 by lgcow...@duke.edu: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

good idea. i will try that.

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.

[og...@googlecode.com]

Comment #29 on issue 33 by sivaram.arabandi: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

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.

[og...@googlecode.com]

Comment #30 on issue 33 by albertgo...@gmail.com: Proposed term 'Organism
Population'
http://code.google.com/p/ogms/issues/detail?id=33

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?

[Melissa Haendel]

Hi, I think organism population should probably come from the new population ontology:

http://code.google.com/p/popcomm-ontology/

<!-- http://purl.obolibrary.org/obo/pco.owl/pco_0000001 -->

<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. &#39;Community&#39;, as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO (&#39;organism population&#39;, IDO_0000509) and OBI (&#39;population&#39;, OBI_0000181). The definitions should be standardized across ontologies and only one term used.</rdfs:comment>

</owl:Class>

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
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[Bill Hogan]

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

[Yu Lin]

+ 1 at Bill's comments.

Best,

Asiyah

[Walls, Ramona]

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.

You can provide feedback via at http://code.google.com/p/popcomm-ontology/issues/list.

The PCO can be downloaded from: http://code.google.com/p/popcomm-ontology/source/browse/#svn%2Ftrunk. I can create a stable pre-release version within a week or two, so people can start importing terms they need.

Ramona

[Albert Goldfain]

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?'
 

[Yu Lin]

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

[Alan Ruttenberg]

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.

-Alan

[1] http://www.googlefight.com/index.php?lang=en_GB&word1=viruses&word2=virii

[Melissa Haendel]

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. 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.

-Alan

[1] http://www.googlefight.com/index.php?lang=en_GB&word1=viruses&word2=virii

[Alan Ruttenberg]

On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <hae...@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

[Melissa Haendel]

On Sep 20, 2012, at 8:33 AM, Alan Ruttenberg wrote:

On Thu, Sep 20, 2012 at 10:38 AM, Melissa Haendel <hae...@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 Ruttenberg]

V

On Thursday, September 20, 2012, Melissa Haendel <hae...@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 <hae...@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.

The rationale is that we don't really gain much by having people use a term for annotation which carries no specificity.

-Alan

[Melissa Haendel]

On Sep 20, 2012, at 11:00 AM, Alan Ruttenberg wrote:

V

On Thursday, September 20, 2012, Melissa Haendel <hae...@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 <hae...@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.

[Ramona Walls]

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

[Ramona Walls]

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

[Ramona Walls]

I will also point out that the PCO has a google group for discussion (https://groups.google.com/forum/?hl=en&fromgroups#!forum/popcomm-ontology) 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.

Ramona

[Alan Ruttenberg]

On Thu, Sep 20, 2012 at 2:08 PM, Melissa Haendel <hae...@ohsu.edu> wrote:

On Sep 20, 2012, at 11:00 AM, Alan Ruttenberg wrote:

V

On Thursday, September 20, 2012, Melissa Haendel <hae...@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 <hae...@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.

-Alan

[Alan Ruttenberg]

On Sun, Sep 23, 2012 at 2:44 PM, Ramona Walls <rlwal...@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. 

 

Regards,

Alan