Re: [Obo-taxonomy] Comments and questions on the PCO

[Melissa Haendel]

On Dec 18, 2013, at 9:47 AM, Barry Smith <phis...@buffalo.edu>

 wrote:

Since organisms are independent continuants

It follows logically that a collection of organisms is an independent continuant

this makes sense, just not sure that that is in fact what 'species' is referring to. ccing the obo-taxonomy list, Peter what are your thoughts here?

Should be coordinated in any case, with the taxonomic rank ontology.

BS

On Wed, Dec 18, 2013 at 12:38 PM, Melissa Haendel <hae...@ohsu.edu> wrote:

my gut feeling is that populations are of organisms (or organisms, viruses and/or viroids) and not species. I am not sure that a "species" is an independent continuant. where was this decided?

On Dec 18, 2013, at 9:03 AM, Barry Smith <phis...@buffalo.edu>

 wrote:

 

RW: Yes, 'species as a collection of organisms' does refer to all individuals of a species. Therefor, you are correct that 'collection of organisms of the same species' should be part of 'species as a collection of organisms'. It is also still true that 'species of collection of organisms' is a subclass of 'collection of organisms of the same species' (the maximal subclass, as it were), which seems a little circular to me. I will need to think more about the relationships between these two classes.

Since species is an independent continuant, then it follows that species is a maximal collection of organisms understood as meaning: maximal collection of organisms existing at a given time. This is in keeping with the Mayrian population view of species. And also in keeping with the view that species evolve over time.

This may be obvious to all, but I am mentioning it for clarity.

--
You received this message because you are subscribed to the Google Groups "popcomm-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to popcomm-ontolo...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library

www.ohsu.edu/library/ontology

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

--
You received this message because you are subscribed to the Google Groups "popcomm-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to popcomm-ontolo...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

--
You received this message because you are subscribed to the Google Groups "popcomm-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to popcomm-ontolo...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library

www.ohsu.edu/library/ontology

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[Melissa Haendel]

that sounds better to me, lets hear from Peter.

Cheers,

Melissa

On Dec 18, 2013, at 10:01 AM, Ramona Walls <rlwal...@gmail.com>

 wrote:

I think it will certainly be easier to define PCO:species as collection of organisms and not so circular if we also have a term for the concept of species as a taxonomic rank. I think that is what "species" in David's proposed definition is desribing. If that can come from the obo-taxonomy ontology, great.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Scientific Analyst, The iPlant Collaborative, University of Arizona
Laboratory Research Associate, New York Botanical Garden

[Peter Midford]

Agree that species, as a type of clade is different from species as a taxonomic rank.  The latter is an individual information artifact, and that is independent of on'e position on the question of whether species and other taxa are individuals or not.

-Peter

On Dec 18, 2013, at 1:01 PM, Ramona Walls <rlwal...@gmail.com> wrote:

I think it will certainly be easier to define PCO:species as collection of organisms and not so circular if we also have a term for the concept of species as a taxonomic rank. I think that is what "species" in David's proposed definition is desribing. If that can come from the obo-taxonomy ontology, great.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Scientific Analyst, The iPlant Collaborative, University of Arizona
Laboratory Research Associate, New York Botanical Garden

On Wed, Dec 18, 2013 at 10:58 AM, Melissa Haendel <hae...@ohsu.edu> wrote:

[Peter Midford]

To clarify this a bit: the way the taxonomic rank vocabulary is used, rank terms serve as annotations to terms denoting taxonomic groups.   So far, we have avoided dragging in the various competing definitions for what a species is.  Part of the reason for this is that species are delimited differently from taxonomic groups at other levels There are no competing definitions of what a genus or a family is, apart from the question of whether a particular group should be recognized at a particular level, which mostly has consequences for taxonomic practice (e.g. rules for name formation).  So when a taxonomic author declares something to be a group of a particular rank, we currently treat it as just a label, subject to change.

-Peter

[Chris Mungall]

"species" can denote different things in different valid formalisms.

I would prefer to avoid the more outre of these - e.g. species as qualities - and focus on a few compatible interpretations.

1. "species" as a logically silent (at least at the owl level) annotation on classes whose members are PCO/CARO:organisms. This is what is followed in NCBITaxonomy and taxrank. I would suggest this is formally analagous to the annotations on PRO classes indicating whether the class is at the gene, family, superfamily etc level

2. species as a type of collection. E.g. Homo sapiens instanceOf species. There are different ways to formalize collections. (a) One is as a BFO independent continuant (as in PCO), which necessarily changes its members over time. Thus Akhenaten is a member of Hs-as-a-population-of-organisms in 1350 CE, but no more. An atemporal collection may be the more useful formalization for non-PCO purposes. In BFO this atemporal collection would be an occurrent, which may seem counterintuitive (Hs as a process?) but perhaps not if you think of this as a history. I think this atemporal notion may be the more useful one for modeling sequence-bearing entities such as genes and proteins.

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Obo-taxonomy mailing list
Obo-ta...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/obo-taxonomy

[Ramona Walls]

I think it will certainly be easier to define PCO:species as collection of organisms and not so circular if we also have a term for the concept of species as a taxonomic rank. I think that is what "species" in David's proposed definition is desribing. If that can come from the obo-taxonomy ontology, great.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Scientific Analyst, The iPlant Collaborative, University of Arizona
Laboratory Research Associate, New York Botanical Garden

[Ramona Walls]

So, perhaps the way to define PCO:species as collection of organisms (PCO:0000017) is something like:

The maximal collection of organisms that all share the same name of the rank TAXRANK:species

Note that PCO (like the taxonomic rank vocabulary) is neutral with respect to how the boundaries of a species are delimited, that is, who the name gets applied to. Thus there is a comment on PCO:0000017 that "This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user."

------------------------------------------------------
Ramona L. Walls, Ph.D.
Scientific Analyst, The iPlant Collaborative, University of Arizona
Laboratory Research Associate, New York Botanical Garden

[Barry Smith]

On Fri, Dec 20, 2013 at 7:07 PM, Ramona Walls <rlwal...@gmail.com> wrote:

So, perhaps the way to define PCO:species as collection of organisms (PCO:0000017) is something like:

The maximal collection of organisms that all share the same name of the rank TAXRANK:species

A consequence of this is that species did not exist until there were names.

Not a good consequence, I think.

BS