DwC Occurrence [SEC=UNCLASSIFIED]
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact. The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?). To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less. To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that. If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.
I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow. Nico On May 31, 2011, at 3:44 AM, Paul Murray wrote:
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact.
The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?).
To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less.
To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that.
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.
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Hi Nico, Wouldn't the individual be asserted to be an instance of a species "concept" For instance: The species concept http://lod.taxonconcept.org/ses/ICmLC#Species <http://lod.taxonconcept.org/ses/ICmLC#Species>An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual <http://lod.taxonconcept.org/ses/ICmLC#Individual>An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre... <http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurrence>Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html <http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html>Relationships between these entities can be browsed via the Knowledge Base view. < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5...
bit.ly http://bit.ly/jgRUxv <http://bit.ly/jgRUxv>* Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base. Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or with a different predicate. Note the hypothetical links below don't work. The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ... < http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individual> <bioimages:individualHasStevesSpeciesConcept> < http://lod.bioimages.org/ses/123123#Species> * We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept. For instance those that are linked to a specific name or classification hierarchy. Respectfully, - Pete On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu>wrote:
I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow.
Nico
On May 31, 2011, at 3:44 AM, Paul Murray wrote:
* An Occurrence is a combination of an Individual and an Event.*>* An Occurrence is a coupling of an Individual and an Event.*>* An Occurrence is a pairing of an Individual and an Event.*
* * How about: An Occurrence is the *reification* of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact.
The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?).
To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less.
To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You *could* simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that.
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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-- ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project --------------------------------------------------------------------------------------
I'm glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc. I'm on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a "species" (or any taxon concept) at a place/time. I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time). However, I think these should all be framed as "Individual-at-Event", even if "Individual" is nothing more than a GUID to which Taxon identifications can be linked. I think the hardest part will be to define the allowable scope of "Individual". In my mind, it should at least span from single organism to multiple organisms up to colony and population; and can be circumscribed by any taxon concept (including "Life"). I have been re-thinking whether "part" should be treated as a separate individual. I used to think yes, but lately I've been thinking no. Aloha, Rich From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Peter DeVries Sent: Tuesday, May 31, 2011 9:24 AM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org List; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED] Hi Nico, Wouldn't the individual be asserted to be an instance of a species "concept" For instance: The species concept http://lod.taxonconcept.org/ses/ICmLC#Species An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre nce Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html Relationships between these entities can be browsed via the Knowledge Base view. < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5 22444a-2dd9-400e-be59-47213ef38cb9%23Occurrence > bit.ly http://bit.ly/jgRUxv * Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base. Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or with a different predicate. Note the hypothetical links below don't work. The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ ual <http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Indivi dual> <bioimages:individualHasStevesSpeciesConcept> <http://lod.bioimages.org/ses/123123#Species> * We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept. For instance those that are linked to a specific name or classification hierarchy. Respectfully, - Pete On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu> wrote: I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow. Nico On May 31, 2011, at 3:44 AM, Paul Murray wrote:
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact. The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?). To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less. To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that. If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content -- ---------------------------------------------------------------------------- -------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies <http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project ---------------------------------------------------------------------------- ----------
Hi Rich, The devil is in the expected use cases which I realized when I started to create useful queries. In theory, you could have the occurrence record marked up with only an individual ID, no asserted identification. Then in a separate file, map those ID's to species concepts. Merge those in a knowledge base and you can run useful queries. Look at this page: http://ocs.taxonconcept.org/ocs/index.html or this http://ocs.taxonconcept.org/ocs/fbdc4c11-25d4-4f47-91b8-99c649b9f0b9.html Think about how many people would find these usable if they had no species or classification attached to them. How would you know what to click on? You also want to be able to make statements about how this individual relates to other individuals and other species. Populations and colonies relate in different ways. You will find that records marked up with identifiers where one instance is an individual organism and the next record is a colony will give you very strange results. For instance a colony at any given time has individuals of different sexes and ages. An individual at any given time "usually" has one sex classification and one age. There will be cases where you have a fungus that spans three counties. Different people will assume that observations of that same individual in three counties are different. If I thought what you are proposing would work I would use it for some mosquito collections consisting of 10,000 individuals but treating that record as the same kind of thing as a record of one mosquito will cause problems. I think it is best to create a separate but linked entity to represent things liks a population or colony and keep those kinds of things represented as different kinds of things. There should be some way to relate a population of mosquitoes to both a species concept and individuals that exist within that population. Respectfully, - Pete On Tue, May 31, 2011 at 3:02 PM, Richard Pyle <deepreef@bishopmuseum.org>wrote:
I’m glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc. I’m on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a “species” (or any taxon concept) at a place/time. I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time). However, I think these should all be framed as “Individual-at-Event”, even if “Individual” is nothing more than a GUID to which Taxon identifications can be linked.
I think the hardest part will be to define the allowable scope of “Individual”. In my mind, it should at least span from single organism to multiple organisms up to colony and population; and can be circumscribed by any taxon concept (including “Life”). I have been re-thinking whether “part” should be treated as a separate individual. I used to think yes, but lately I’ve been thinking no.
Aloha,
Rich
*From:* tdwg-content-bounces@lists.tdwg.org [mailto: tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Peter DeVries *Sent:* Tuesday, May 31, 2011 9:24 AM *To:* Nico Cellinese *Cc:* tdwg-content@lists.tdwg.org List; Paul Murray *Subject:* Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]
Hi Nico,
Wouldn't the individual be asserted to be an instance of a species "concept"
For instance:
The species concept http://lod.taxonconcept.org/ses/ICmLC#Species
An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual
An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre...
Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html
Relationships between these entities can be browsed via the Knowledge Base view.
< http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5...
bit.ly http://bit.ly/jgRUxv
* Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base.
Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or
with a different predicate. Note the hypothetical links below don't work.
The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ...
< http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individual> <bioimages:individualHasStevesSpeciesConcept> < http://lod.bioimages.org/ses/123123#Species>
* We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept.
For instance those that are linked to a specific name or classification hierarchy.
Respectfully,
- Pete
On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu> wrote:
I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow.
Nico
On May 31, 2011, at 3:44 AM, Paul Murray wrote:
* An Occurrence is a combination of an Individual and an Event.*
* An Occurrence is a coupling of an Individual and an Event.*
* An Occurrence is a pairing of an Individual and an Event.*
How about:
An Occurrence is the *reification* of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact.
The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?).
To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less.
To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You *could* simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that.
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
--
------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project
--------------------------------------------------------------------------------------
-- ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project --------------------------------------------------------------------------------------
I think you could require a minimum of at leats one identification for every individual - even if that identification is simply "life". I think in the vast, vast majority of cases, you would have something more finely resolved than "life" (e.g., at least a kingdom, probably usually at least a family, and often a species). So if "Individual" is defined as having at least some taxonomic scope, then you wouldn't have any individuals without asserted identifications. It's just that you need to accommodate identifications at ranks above species. More later, after I digest your full message below (on another coffee break now). Rich From: Peter DeVries [mailto:pete.devries@gmail.com] Sent: Tuesday, May 31, 2011 10:39 AM To: Richard Pyle Cc: Nico Cellinese; tdwg-content@lists.tdwg.org; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED] Hi Rich, The devil is in the expected use cases which I realized when I started to create useful queries. In theory, you could have the occurrence record marked up with only an individual ID, no asserted identification. Then in a separate file, map those ID's to species concepts. Merge those in a knowledge base and you can run useful queries. Look at this page: http://ocs.taxonconcept.org/ocs/index.html or this http://ocs.taxonconcept.org/ocs/fbdc4c11-25d4-4f47-91b8-99c649b9f0b9.html Think about how many people would find these usable if they had no species or classification attached to them. How would you know what to click on? You also want to be able to make statements about how this individual relates to other individuals and other species. Populations and colonies relate in different ways. You will find that records marked up with identifiers where one instance is an individual organism and the next record is a colony will give you very strange results. For instance a colony at any given time has individuals of different sexes and ages. An individual at any given time "usually" has one sex classification and one age. There will be cases where you have a fungus that spans three counties. Different people will assume that observations of that same individual in three counties are different. If I thought what you are proposing would work I would use it for some mosquito collections consisting of 10,000 individuals but treating that record as the same kind of thing as a record of one mosquito will cause problems. I think it is best to create a separate but linked entity to represent things liks a population or colony and keep those kinds of things represented as different kinds of things. There should be some way to relate a population of mosquitoes to both a species concept and individuals that exist within that population. Respectfully, - Pete On Tue, May 31, 2011 at 3:02 PM, Richard Pyle <deepreef@bishopmuseum.org> wrote: I'm glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc. I'm on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a "species" (or any taxon concept) at a place/time. I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time). However, I think these should all be framed as "Individual-at-Event", even if "Individual" is nothing more than a GUID to which Taxon identifications can be linked. I think the hardest part will be to define the allowable scope of "Individual". In my mind, it should at least span from single organism to multiple organisms up to colony and population; and can be circumscribed by any taxon concept (including "Life"). I have been re-thinking whether "part" should be treated as a separate individual. I used to think yes, but lately I've been thinking no. Aloha, Rich From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Peter DeVries Sent: Tuesday, May 31, 2011 9:24 AM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org List; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED] Hi Nico, Wouldn't the individual be asserted to be an instance of a species "concept" For instance: The species concept http://lod.taxonconcept.org/ses/ICmLC#Species An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre nce Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html Relationships between these entities can be browsed via the Knowledge Base view. < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5 22444a-2dd9-400e-be59-47213ef38cb9%23Occurrence > bit.ly http://bit.ly/jgRUxv * Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base. Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or with a different predicate. Note the hypothetical links below don't work. The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ ual <http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Indivi dual> <bioimages:individualHasStevesSpeciesConcept> <http://lod.bioimages.org/ses/123123#Species> * We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept. For instance those that are linked to a specific name or classification hierarchy. Respectfully, - Pete On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu> wrote: I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow. Nico On May 31, 2011, at 3:44 AM, Paul Murray wrote:
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact. The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?). To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less. To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that. If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content -- ---------------------------------------------------------------------------- -------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies <http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project ---------------------------------------------------------------------------- ---------- -- ---------------------------------------------------------------------------- -------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies <http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project ---------------------------------------------------------------------------- ----------
Still waiting for the coffee break to end, so a couple more comments. A lot of this stuff is semantics (sensu lato, but also sensu stricto). Most people think of a coral head as an "individual", but it's really a colony of polyps. Ants are usually curated as individual organisms, but can also be useful to collapse to colonies. So yes - different occurrences relate in different ways -nothing new about that. Oops, conference starting again. Aloha, Rich From: Peter DeVries [mailto:pete.devries@gmail.com] Sent: Tuesday, May 31, 2011 10:39 AM To: Richard Pyle Cc: Nico Cellinese; tdwg-content@lists.tdwg.org; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED] Hi Rich, The devil is in the expected use cases which I realized when I started to create useful queries. In theory, you could have the occurrence record marked up with only an individual ID, no asserted identification. Then in a separate file, map those ID's to species concepts. Merge those in a knowledge base and you can run useful queries. Look at this page: http://ocs.taxonconcept.org/ocs/index.html or this http://ocs.taxonconcept.org/ocs/fbdc4c11-25d4-4f47-91b8-99c649b9f0b9.html Think about how many people would find these usable if they had no species or classification attached to them. How would you know what to click on? You also want to be able to make statements about how this individual relates to other individuals and other species. Populations and colonies relate in different ways. You will find that records marked up with identifiers where one instance is an individual organism and the next record is a colony will give you very strange results. For instance a colony at any given time has individuals of different sexes and ages. An individual at any given time "usually" has one sex classification and one age. There will be cases where you have a fungus that spans three counties. Different people will assume that observations of that same individual in three counties are different. If I thought what you are proposing would work I would use it for some mosquito collections consisting of 10,000 individuals but treating that record as the same kind of thing as a record of one mosquito will cause problems. I think it is best to create a separate but linked entity to represent things liks a population or colony and keep those kinds of things represented as different kinds of things. There should be some way to relate a population of mosquitoes to both a species concept and individuals that exist within that population. Respectfully, - Pete On Tue, May 31, 2011 at 3:02 PM, Richard Pyle <deepreef@bishopmuseum.org> wrote: I'm glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc. I'm on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a "species" (or any taxon concept) at a place/time. I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time). However, I think these should all be framed as "Individual-at-Event", even if "Individual" is nothing more than a GUID to which Taxon identifications can be linked. I think the hardest part will be to define the allowable scope of "Individual". In my mind, it should at least span from single organism to multiple organisms up to colony and population; and can be circumscribed by any taxon concept (including "Life"). I have been re-thinking whether "part" should be treated as a separate individual. I used to think yes, but lately I've been thinking no. Aloha, Rich From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Peter DeVries Sent: Tuesday, May 31, 2011 9:24 AM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org List; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED] Hi Nico, Wouldn't the individual be asserted to be an instance of a species "concept" For instance: The species concept http://lod.taxonconcept.org/ses/ICmLC#Species An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre nce Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html Relationships between these entities can be browsed via the Knowledge Base view. < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5 22444a-2dd9-400e-be59-47213ef38cb9%23Occurrence > bit.ly http://bit.ly/jgRUxv * Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base. Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or with a different predicate. Note the hypothetical links below don't work. The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ ual <http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Indivi dual> <bioimages:individualHasStevesSpeciesConcept> <http://lod.bioimages.org/ses/123123#Species> * We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept. For instance those that are linked to a specific name or classification hierarchy. Respectfully, - Pete On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu> wrote: I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow. Nico On May 31, 2011, at 3:44 AM, Paul Murray wrote:
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact. The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?). To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less. To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that. If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content -- ---------------------------------------------------------------------------- -------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies <http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project ---------------------------------------------------------------------------- ---------- -- ---------------------------------------------------------------------------- -------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies <http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project ---------------------------------------------------------------------------- ----------
I’m glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc. I’m on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a “species” (or any taxon concept) at a place/time. I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time). However, I think these should all be framed as “Individual-at-Event”, even if “Individual” is nothing more than a GUID to which Taxon identifications can be linked.
I totally agree! An individual is NOT a taxon. It just belongs to one so we need to focus our attention on individual-at-event type of assertions. That individual is linked to a TaxonName which represents a TaxonConcept. Why do we need to talk about species at all? All we have to deal with is individuals, taxon names, and taxon concepts.
I think the hardest part will be to define the allowable scope of “Individual”. In my mind, it should at least span from single organism to multiple organisms up to colony and population; and can be circumscribed by any taxon concept (including “Life”). I have been re-thinking whether “part” should be treated as a separate individual. I used to think yes, but lately I’ve been thinking no.
I also agreed that an individual doesn't have to be whole, so in my opinion "parts" can also be considered 'the individual in question'. Similarly, I also agree that up to populations we can still talk about individuals. However, it is important to be able to link "parts" to the whole individuals if needed, e.g. is_part_of. Nico
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Peter DeVries Sent: Tuesday, May 31, 2011 9:24 AM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org List; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]
Hi Nico,
Wouldn't the individual be asserted to be an instance of a species "concept"
For instance:
The species concept http://lod.taxonconcept.org/ses/ICmLC#Species
An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual
An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre...
Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html
Relationships between these entities can be browsed via the Knowledge Base view.
< http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5... >
bit.ly http://bit.ly/jgRUxv
* Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base.
Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or with a different predicate. Note the hypothetical links below don't work.
The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ...
<http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individual> <bioimages:individualHasStevesSpeciesConcept> <http://lod.bioimages.org/ses/123123#Species>
* We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept. For instance those that are linked to a specific name or classification hierarchy.
Respectfully,
- Pete
On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu> wrote: I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow.
Nico
On May 31, 2011, at 3:44 AM, Paul Murray wrote:
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact.
The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?).
To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less.
To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. Youcould simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that.
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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-- ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept & GeoSpecies Knowledge Bases A Semantic Web, Linked Open Data Project --------------------------------------------------------------------------------------
I totally agree! An individual is NOT a taxon. It just belongs to one
I would refine that to "It just is asserted to belong to one..."
so we need to focus our attention on individual-at-event type of assertions.
I would classify individual-at-event instances as "instances", rather than assertions. I think they represent what most of us would treat as "facts". "Assertions" are more like opinions -- like "what taxon concept this individual falls within".
That individual is linked to a TaxonName which represents a TaxonConcept. Why do we need to talk about species at all? All we have to deal with is individuals, taxon names, and taxon concepts.
I think of "species" as the most popular kind of "taxon concept". Not like strict Linnean rank sort-of species.
I also agreed that an individual doesn't have to be whole, so in my opinion "parts" can also be considered 'the individual in question'.
That is my old thinking. My new thinking is that you abstract up to an whole organism when you have a part (e.g., tissue sample), when representing an Occurrence; just as you would abstract down to "Indidividual", when you what to represent Taxon-at-Event for an Occurrence.
Similarly, I also agree that up to populations we can still talk about individuals. However, it is important to be able to link "parts" to the whole individuals if needed, e.g. is_part_of.
Agreed! The link needs to be there. We just need to figure out which links are within-class (e.g., parent-child), and which are across classes. In haste, but still with Aloha, Rich
I think of "species" as the most popular kind of "taxon concept". Not like strict Linnean rank sort-of species.
Good gods!! Now you send me straight to the bar! Doing so you are indeed treating 'species' as ranks, unless I am completely missing your point. If you think of species as taxa, the 'most popular' according tho whom? nico <><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/
Let me rephrase that: I think of species in this context the same way that Phylocode thinks of species.
-----Original Message----- From: Nico Cellinese [mailto:ncellinese@flmnh.ufl.edu] Sent: Tuesday, May 31, 2011 11:43 AM To: Richard Pyle Cc: 'Peter DeVries'; tdwg-content@lists.tdwg.org; 'Paul Murray' Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]
I think of "species" as the most popular kind of "taxon concept". Not like strict Linnean rank sort-of species.
Good gods!! Now you send me straight to the bar! Doing so you are indeed treating 'species' as ranks, unless I am completely missing your point. If you think of species as taxa, the 'most popular' according tho whom?
nico
<><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology
Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/
In other words, by "most popular" I mean that they tend to be the most-heavily cited taxon concept in exiting biodiversity literature/datasets/information -- more so than any other Linnean rank -- so much so that even the non-Linnean-rank naming system (Phylocode) acknowledges them.
-----Original Message----- From: Nico Cellinese [mailto:ncellinese@flmnh.ufl.edu] Sent: Tuesday, May 31, 2011 11:43 AM To: Richard Pyle Cc: 'Peter DeVries'; tdwg-content@lists.tdwg.org; 'Paul Murray' Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]
I think of "species" as the most popular kind of "taxon concept". Not like strict Linnean rank sort-of species.
Good gods!! Now you send me straight to the bar! Doing so you are indeed treating 'species' as ranks, unless I am completely missing your point. If you think of species as taxa, the 'most popular' according tho whom?
nico
<><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology
Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/
Hi Rich - So you're saying that it would be dangerous to frame an occurrence as a taxon concept at a place/time and should be an Individual at a place/time instead (with which I would agree), but then you go on to say that the scope of Individual should be wide enough to accommodate anything that can be circumscribed as a taxon concept. Does that mean that you view a taxon concept and something that can be circumscribed aa a taxon concept as two very different things? In ontological terms, the set of things (a class) that can be sufficiently circumscribed with a taxon concept (a class) and the taxon concept would seem semantically the same to me. I think it's important here to distinguish between instances of (individuals that are a members of) the taxon concept class (but never comprise of all members of the class), and the taxon concept itself as a class. But perhaps that is what you had in mind anyway? -hilmar Sent with a tap. On May 31, 2011, at 4:02 PM, Richard Pyle <deepreef@bishopmuseum.org> wrote:
I’m glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc. I’m on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a “species” (or any taxon concept) at a place/time. I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time). However, I think these should all be framed as “Individual-at-Event”, even if “Individual” is nothing more than a GUID to which Taxon identifications can be linked.
I think the hardest part will be to define the allowable scope of “Individual”. In my mind, it should at least span from single organism to multiple organisms up to colony and population; and can be circumscribed by any taxon concept (including “Life”). I have been re-thinking whether “part” should be treated as a separate individual. I used to think yes, but lately I’ve been thinking no.
Aloha,
Rich
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Peter DeVries Sent: Tuesday, May 31, 2011 9:24 AM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org List; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED]
Hi Nico,
Wouldn't the individual be asserted to be an instance of a species "concept"
For instance:
The species concept http://lod.taxonconcept.org/ses/ICmLC#Species
An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual
An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre...
Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html
Relationships between these entities can be browsed via the Knowledge Base view.
< http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5... >
bit.ly http://bit.ly/jgRUxv
* Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base.
Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or
with a different predicate. Note the hypothetical links below don't work.
The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ...
<http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individual> <bioimages:individualHasStevesSpeciesConcept> <http://lod.bioimages.org/ses/123123#Species>
* We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept.
For instance those that are linked to a specific name or classification hierarchy.
Respectfully,
- Pete
On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu> wrote:
I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow.
Nico
On May 31, 2011, at 3:44 AM, Paul Murray wrote:
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about:
An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact.
The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?).
To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less.
To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that.
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept & GeoSpecies Knowledge Bases A Semantic Web, Linked Open Data Project --------------------------------------------------------------------------------------
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
So you're saying that it would be dangerous to frame an occurrence as a taxon concept at a place/time and should be an Individual at a place/time instead (with which I would agree),
Yes.
but then you go on to say that the scope of Individual should be wide enough to accommodate anything that can be circumscribed as a taxon concept.
Not quite. See the long discussions of this topic on this list last fall. Obviously, "Population" is simply one step along the continuum between "Individual organism" and "taxon" -- so in that sense, I can only say "not quite", rather than "no". But when you frame it that way, there is no fundamental difference (conceptually) between an individual organism and a taxon -- they are just different extremes of the same continuum. Indeed, an "Individual Organism" is not even at the extreme -- it's closer to the middle (when you consider how many "individual organisms" are comprised of multitudes of individual cells, each of which is comprised of multiple organelles, etc.) So, if we are going to make a distinction between "Individual" and "taxon", then it is necessarily an arbitrary distinction. I think that we, in the biodiversity informatics world, see value in distinguishing between "Individual" and "Taxon Concept", because each tends to have different properties, and it's also much more intuitive for us to model it that way. All I'm saying is that, in my opinion, the arbitrary line between "Individual" and "Taxon Concept" is better drawn somewhere in the realm of "population", rather than what I think a lot of people would define as "individual organism". My reasons for having this opinion are documented in part in the earlier thread (and I have no time to go into it now). But I'll be happy to elaborate later.
Does that mean that you view a taxon concept and something that can be circumscribed aa a taxon concept as two very different things?
No.
In ontological terms, the set of things (a class) that can be sufficiently circumscribed with a taxon concept (a class) and the taxon concept would seem semantically the same to me.
To me as well.
I think it's important here to distinguish between instances of (individuals that are a members of) the taxon concept class (but never comprise of all members of the class), and the taxon concept itself as a class. But perhaps that is what you had in mind anyway?
No, but I don't think it's as simple as you make it seem. It is at face-value, but not when you really dissect it. For example, to what taxon concept does the thing typing this email message belong? Presumably, Homo sapiens L. sec. L. But >90% of the cells encapsulated within the boundaries (skin) of that thing are non-human. Sure, the majority of the *mass* is represented by human cells, but by that logic, the majority of the mass is non-living H2O. We abstract the sack of matter within the boundaries of my skin as an "individual organism", because it's intuitive and convenient to do so. But there are other kinds of organisms for with it is much less intuitive or obvious where "individual organism" ends and "small set of individual organisms" begins -- even if the "small set" is implied to refer to the organisms sharing the same genome (i.e., excluding the endo parasites alluded to previously). So, if there are pragmatic reasons why the scope of "Individual" should extend beyond "single organism" (and I think there are several), then we need to know where the scope of "Individual" ends, and "Taxon Concept" begins. If I had to come up with a more ontologically-friendly(?) distinction, I guess I would say that the scope of "Individual" should be limited to cases where the instances can (effectively) be enumerated; whereas "Taxon Concept" would encompass instances both enumerated and implied. Aloha, Rich -hilmar Sent with a tap. On May 31, 2011, at 4:02 PM, Richard Pyle <deepreef@bishopmuseum.org> wrote: I’m glad to see this conversation re-vitalized, as we (Rob Whitton & I) have been thinking a lot about this in our recent discussions concerning BiSciCol, GNUB, etc. I’m on coffee break from virtual attendance at a conference right now, so no time to elaborate, except I think it would be dangerous to accommodate an occurrence as a “species” (or any taxon concept) at a place/time. I know there are plenty of data that effectively are represented as Taxon-at-Event (i.e., occurrence of a taxon at a place and time). However, I think these should all be framed as “Individual-at-Event”, even if “Individual” is nothing more than a GUID to which Taxon identifications can be linked. I think the hardest part will be to define the allowable scope of “Individual”. In my mind, it should at least span from single organism to multiple organisms up to colony and population; and can be circumscribed by any taxon concept (including “Life”). I have been re-thinking whether “part” should be treated as a separate individual. I used to think yes, but lately I’ve been thinking no. Aloha, Rich From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Peter DeVries Sent: Tuesday, May 31, 2011 9:24 AM To: Nico Cellinese Cc: tdwg-content@lists.tdwg.org List; Paul Murray Subject: Re: [tdwg-content] DwC Occurrence [SEC=UNCLASSIFIED] Hi Nico, Wouldn't the individual be asserted to be an instance of a species "concept" For instance: The species concept http://lod.taxonconcept.org/ses/ICmLC#Species An individual of that species concept http://lod.taxonconcept.org/ses/ICmLC#Individual An occurrence that has been asserted to be an occurrence of that species http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre... Which is documented by this page http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html Relationships between these entities can be browsed via the Knowledge Base view. < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f5... > bit.ly http://bit.ly/jgRUxv * Note that links on the HTML page will also take you to the views of the different entities in the Knowledge Base. Also note that someone else could assert that the individual butterfly is actually an instance of a different species concept. One could simply replace these assertions with their own in a separate mapping file, or with a different predicate. Note the hypothetical links below don't work. The individual http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individ... <http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Individual> <bioimages:individualHasStevesSpeciesConcept> <http://lod.bioimages.org/ses/123123#Species> * We might miss some species occurrence records when we do this, so it would be best to avoid creating a number of basically duplicate concepts especially if they not the same "kind" of concept. For instance those that are linked to a specific name or classification hierarchy. Respectfully, - Pete On Tue, May 31, 2011 at 6:10 AM, Nico Cellinese <ncellinese@flmnh.ufl.edu> wrote: I personally like this nicely refined suggestion but to be honest, I can also live with the others previously made. What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow. Nico On May 31, 2011, at 3:44 AM, Paul Murray wrote:
An Occurrence is a combination of an Individual and an Event. An Occurrence is a coupling of an Individual and an Event. An Occurrence is a pairing of an Individual and an Event.
How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact. The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?). To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less. To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that. If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email. _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content -- ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept & GeoSpecies Knowledge Bases A Semantic Web, Linked Open Data Project -------------------------------------------------------------------------------------- _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
On 31/05/2011, at 9:10 PM, Nico Cellinese wrote:
What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow.
Is this do do with type specimens? Or are we talking about the OWL class vs. OWL individual problem? With respect to taxa, it seems to me that a taxon is a rule that can decide whether or not an individual is part of the taxon or not. This can be done with a description, by specifying a list of included and excluded other taxa, or by various other ways. If two taxa defined differently select the same subset of real-world individuals, then the taxa are synonymous. This is to say: the truth of assertions about taxonomic relationships can be contingent on what is out there in the real world. (The taxa "organisms that have the front half of a horse" and "organisms that have the back half of a horse" would be synonymous if not for the occasional zebra/horse hybrid. Actually ... this is a stickier point than it seems: is a taxon a subset of all potential individuals, or a subset of all actual individuals? Or a subset of all actual individuals ... including the ones that aren't currently alive, and that we don't happen to know about? Is a taxon the *rule*, or is it the *subset* of individuals? Is the rule - the definition or circumscription of the taxon - the "taxon concept", and the actual subset of individuals the "taxon"?) Anyway - to return to "species = individual": Since a taxon is simply some rule for selecting individuals out of the set of all individuals, you could quite happily define a taxon "the set of all individuals whose tokens are the type specimens of Vombatus ursinus". This is not the same as the species, or the nominal concept - it's a "concept" containing one individual. I suppose it might be called the "type taxon" of a name. Interestingly, this taxon of one individual is not an entirely useless idea. All taxa that are named "Vombatus ursinus" by definition contain the type taxon as a subset (except in cases of misattribution). From this, and the rule "if two taxa have a common nonempty subtaxon then they overlap", we can infer "if two taxa have the same (not misattributed) name, then they overlap". This is not something that could otherwise be inferred, because in general "a overlaps b" and "b overlaps c" does *not* allow us in infer "a overlaps c". It's the existence of the common subtaxon - the type taxon - that does. It's the existence of this overlap - even of just one individual - that gives meaning to different authors using the same name to label their concepts. (I am not sure that I am not repeating myself - I may have brought this up on this list previously) If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.
On Tue, May 31, 2011 at 11:09 PM, Paul Murray <pmurray@anbg.gov.au> wrote:
On 31/05/2011, at 9:10 PM, Nico Cellinese wrote:
[...]
(The taxa "organisms that have the front half of a horse" and "organisms that have the back half of a horse" would be synonymous if not for the occasional zebra/horse hybrid. [...]
Oooh, No, No, Nooooo: "The great roe is a mythological beast with the head of a lion and the body of a lion, though not the same lion." Widely attributed to Woody Allen, and quoted in one or both of Robert Willensky's magnificent Lisp books, "LispCraft" and "Common LISPcraft" in the material---surprise!---on namespaces. Oh, wait, that's an argument about individuals. Sorry. Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob@gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)
Hi Paul, One problem with the type system and many species descriptions is that they don't provide much insight or guidance as to where one species ends and the other begins. We need some system of documented concepts that makes the process of matching an individual to a concept clearer and more repeatable. So that someone can determine the *most appropriate* concept for their individual. It should also be designed so there is high repeatability across different expert identifiers. (Same specimens matched to the same concepts with high repeatability) - Pete On Tue, May 31, 2011 at 10:09 PM, Paul Murray <pmurray@anbg.gov.au> wrote:
On 31/05/2011, at 9:10 PM, Nico Cellinese wrote:
What I don't seem to be able to digest is the notion that same individual will later be equaled by some to a species. That assertion is hard to swallow.
Is this do do with type specimens? Or are we talking about the OWL class vs. OWL individual problem?
With respect to taxa, it seems to me that a taxon is a rule that can decide whether or not an individual is part of the taxon or not. This can be done with a description, by specifying a list of included and excluded other taxa, or by various other ways. If two taxa defined differently select the same subset of real-world individuals, then the taxa are synonymous. This is to say: the truth of assertions about taxonomic relationships can be contingent on what is out there in the real world.
(The taxa "organisms that have the front half of a horse" and "organisms that have the back half of a horse" would be synonymous if not for the occasional zebra/horse hybrid. Actually ... this is a stickier point than it seems: is a taxon a subset of all potential individuals, or a subset of all actual individuals? Or a subset of all actual individuals ... including the ones that aren't currently alive, and that we don't happen to know about? Is a taxon the *rule*, or is it the *subset* of individuals? Is the rule - the definition or circumscription of the taxon - the "taxon concept", and the actual subset of individuals the "taxon"?)
Anyway - to return to "species = individual":
Since a taxon is simply some rule for selecting individuals out of the set of all individuals, you could quite happily define a taxon "the set of all individuals whose tokens are the type specimens of *Vombatus ursinus*". This is not the same as the species, or the nominal concept - it's a "concept" containing one individual. I suppose it might be called the "type taxon" of a name.
Interestingly, this taxon of one individual is not an entirely useless idea. All taxa that are named "V*ombatus ursinus"* by definition contain the type taxon as a subset (except in cases of misattribution). From this, and the rule "if two taxa have a common nonempty subtaxon then they overlap", we can infer "if two taxa have the same (not misattributed) name, then they overlap". This is not something that could otherwise be inferred, because in general "a overlaps b" and "b overlaps c" does *not* allow us in infer "a overlaps c". It's the existence of the common subtaxon - the type taxon - that does. It's the existence of this overlap - even of just one individual - that gives meaning to different authors using the same name to label their concepts.
(I am not sure that I am not repeating myself - I may have brought this up on this list previously)
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.
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-- ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project --------------------------------------------------------------------------------------
Comments inline Paul Murray wrote: ...
How about: An Occurrence is the /reification/ of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact.
The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?).
To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less.
Yes and I would add "=RDF graph node" to your list above. It is a relationship made into something onto which we can slap an identifier and link other resources via object properties. I would add that its nature is similar to that of dwc:Event (which you could say is a reification of an Occurrence's relationship to a Location and time) and a dwc:Identification (which you could say is a reification of the relationship between an "Individual" and the Taxon that somebody asserts that it represents). None of these things (Occurrence, Event, or Identification) have a physical existence. They exist because we need them to connect instances of other classes of resources. We give them names that have something to do with the nature of the connection, but they really are just connections (or nodes if you wish). Peter DeVries wrote:
Wouldn't the individual be asserted to be an instance of a species "concept" Defining an Individual this way assumes that one knows what taxon the Individual represents. What about the Individual I've assigned the GUID http://bioimages.vanderbilt.edu/ind-baskauf/70858 ? I don't really have any idea what it is. That really shouldn't prevent me from assigning it a GUID and an rdf:type. I suppose that you could do what Rich suggested which was to require at least one dwc:Identification at a level as high as "Life" but I would prefer to say that an Individual could have 0 to many dwc:Identifications, with "many" being the number of Taxa that people wish to assert that it represents. That number is never fixed because somebody could always come along later and assert that it was something else, or even assert that it is the same taxon that somebody else previously had asserted.
Richard Pyle wrote:
I think the hardest part will be to define the allowable scope of
"Individual". In my mind, it should at least span from single organism to multiple organisms up to
colony and population; and can be circumscribed by any taxon concept (including "Life"). I have been re-thinking whether "part" should be treated as a separate individual. I used to think yes, but lately I've been thinking no.
I think that the answer to this question is related to the original definition of Paul's that started this thread (i.e. reification of relationships to create identifiable/linkable entities). Back in October when you and I were butting heads on this topic, I think that the mistake was to try to demand that an Individual represent both a physical individual organism and the "reification" (my new favorite word) of an conceptual entity that connects an Identification to an Occurrence (a so-called TaxonomicallyHomogeneousUnit) [see Kevin Richard's comment at http://lists.tdwg.org/pipermail/tdwg-content/2010-November/001956.html which first made this distinction clearly]. In some cases, it is easy to define a resource as being both things (e.g. discrete organisms) but in others it's not (colonial organisms, clones, herds, tissue cultures, etc.). After thinking about this for a long time I felt that the best thing to do was to cleanly separate the physical thing (a.k.a. a "token") from the conceptual thing (the reified entity onto which we can hang Identifications and Occurrence records). If one wishes or if it is convenient, one could describe a particular resource as both the token and the conceptual thing (e.g. in the case of a discrete organism) but if it is more convenient one can identify the conceptual entity as a separate thing and identify any number of related tokens associated with this entity. These related tokens could span the range from individual cells to tissues to discrete organisms to herds to populations and the relationships among them could be described using dcterms:hasPart or other appropriate object properties. This was the approach we decided to take with darwin-sw (see http://code.google.com/p/darwin-sw/wiki/ClassIndividual http://code.google.com/p/darwin-sw/wiki/TokenIssues and http://code.google.com/p/darwin-sw/wiki/ClassToken for a more detailed description of the approach with diagrams and references). This approach can handle these situations: Richard Pyle wrote:
Most people think of a coral head as an "individual", but it's really a colony of polyps. Ants are usually curated as individual organisms, but can also be useful to collapse to colonies. Nico Cellinese wrote: I also agreed that an individual doesn't have to be whole, so in my opinion "parts" can also be considered 'the individual in question'. Similarly, I also agree that up to populations we can still talk about individuals. However, it is important to be able to link "parts" to the whole individuals if needed, e.g. is_part_of.
Separate the abstract TaxonomicallyHomogeneousUnit from the physical tokens and this issue goes away: Richard Pyle wrote:
That is my old thinking. My new thinking is that you abstract up to an whole organism when you have a part (e.g., tissue sample), when representing an Occurrence; just as you would abstract down to "Indidividual", when you what to represent Taxon-at-Event for an Occurrence.
In darwin-sw we did not attempt to define a real ontology of tokens that are physical parts or conglomerations of organisms (cells/tissues/discrete organisms/herds/populations/colonies/clones/etc.), but that would be a good thing to do. It could be done in isolation from the definition of the "reified" TaxonomicallyHomogeneousUnit. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu
There are too many ideas here for me to digest at once, but I have some comments. One of the problems with my examples is that I have to make a separate code base to fully support each "thing" I try to include In my occurrence examples I simply stub out an "individual", it would have been better to have these exist as a separate table. One data set might make statements about a specific individual and coin their own URI for that individual, that is later observed and recorded in a different data set. Since it is difficult to determine ahead of time what other studies might have data about that same individual, it would be easiest to create the following triple after verifying that it is true. IndividualDataSetA owl:sameAs IndividualDataSetB Also I have no examples for unknown or partially identified taxa. My thinking is that this is still a kind of species concept but one that is unspecified. I don't think it would be good to mark it up as only an instance of a genus. So something like <SpeciesConceptUnspecifiedInsect_Culex> This would indicate that the individual has been identified as some Insect in the genus Culex, This can be interpreted as as asserting that the individual is an instance of some species concept within the Insect genus Culex. The way to deal with observations of multi-individual groups might be handled with "something like" the following: A swarm of bees http://lod.taxonconcept.org/ses/z9oqP#MultipleIndividualGroup This has different allowed properties than an individual. For instance it could have a count for each sex. male:2 female:1000 immature:0 #Swarm could be a subproperty of #MultipleIndividualGroup This is somewhat like a #Population, but I can think of instances where the #Population and #MultipleIndividualGroup are different things. - Pete <http://en.wikipedia.org/wiki/Provenance> On Mon, Jun 6, 2011 at 5:09 PM, Steve Baskauf <steve.baskauf@vanderbilt.edu>wrote:
Comments inline
Paul Murray wrote: ...
How about: An Occurrence is the *reification* of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact.
The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?).
To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less.
Yes and I would add "=RDF graph node" to your list above. It is a relationship made into something onto which we can slap an identifier and link other resources via object properties. I would add that its nature is similar to that of dwc:Event (which you could say is a reification of an Occurrence's relationship to a Location and time) and a dwc:Identification (which you could say is a reification of the relationship between an "Individual" and the Taxon that somebody asserts that it represents). None of these things (Occurrence, Event, or Identification) have a physical existence. They exist because we need them to connect instances of other classes of resources. We give them names that have something to do with the nature of the connection, but they really are just connections (or nodes if you wish).
Peter DeVries wrote:
Wouldn't the individual be asserted to be an instance of a species "concept" Defining an Individual this way assumes that one knows what taxon the Individual represents. What about the Individual I've assigned the GUID http://bioimages.vanderbilt.edu/ind-baskauf/70858 ? I don't really have any idea what it is. That really shouldn't prevent me from assigning it a GUID and an rdf:type. I suppose that you could do what Rich suggested which was to require at least one dwc:Identification at a level as high as "Life" but I would prefer to say that an Individual could have 0 to many dwc:Identifications, with "many" being the number of Taxa that people wish to assert that it represents. That number is never fixed because somebody could always come along later and assert that it was something else, or even assert that it is the same taxon that somebody else previously had asserted.
Richard Pyle wrote:
I think the hardest part will be to define the allowable scope of
“Individual”. In my mind, it should at least span from single organism to multiple organisms up to
colony and population; and can be circumscribed by any taxon concept (including “Life”). I have been re-thinking whether “part” should be treated as a separate individual. I used to think yes, but lately I’ve been thinking no.
I think that the answer to this question is related to the original definition of Paul's that started this thread (i.e. reification of relationships to create identifiable/linkable entities). Back in October when you and I were butting heads on this topic, I think that the mistake was to try to demand that an Individual represent both a physical individual organism and the "reification" (my new favorite word) of an conceptual entity that connects an Identification to an Occurrence (a so-called TaxonomicallyHomogeneousUnit) [see Kevin Richard's comment at http://lists.tdwg.org/pipermail/tdwg-content/2010-November/001956.htmlwhich first made this distinction clearly]. In some cases, it is easy to define a resource as being both things (e.g. discrete organisms) but in others it's not (colonial organisms, clones, herds, tissue cultures, etc.). After thinking about this for a long time I felt that the best thing to do was to cleanly separate the physical thing (a.k.a. a "token") from the conceptual thing (the reified entity onto which we can hang Identifications and Occurrence records). If one wishes or if it is convenient, one could describe a particular resource as both the token and the conceptual thing (e.g. in the case of a discrete organism) but if it is more convenient one can identify the conceptual entity as a separate thing and identify any number of related tokens associated with this entity. These related tokens could span the range from individual cells to tissues to discrete organisms to herds to populations and the relationships among them could be described using dcterms:hasPart or other appropriate object properties. This was the approach we decided to take with darwin-sw (see http://code.google.com/p/darwin-sw/wiki/ClassIndividual http://code.google.com/p/darwin-sw/wiki/TokenIssues and http://code.google.com/p/darwin-sw/wiki/ClassToken for a more detailed description of the approach with diagrams and references). This approach can handle these situations:
Richard Pyle wrote:
Most people think of a coral head as an “individual”, but it’s really a colony of polyps. Ants are usually curated as individual organisms, but can also be useful to collapse to colonies. Nico Cellinese wrote: I also agreed that an individual doesn't have to be whole, so in my opinion "parts" can also be considered 'the individual in question'. Similarly, I also agree that up to populations we can still talk about individuals. However, it is important to be able to link "parts" to the whole individuals if needed, e.g. is_part_of.
Separate the abstract TaxonomicallyHomogeneousUnit from the physical tokens and this issue goes away:
Richard Pyle wrote:
That is my old thinking. My new thinking is that you abstract up to an whole organism when you have a part (e.g., tissue sample), when representing an Occurrence; just as you would abstract down to "Indidividual", when you what to represent Taxon-at-Event for an Occurrence.
In darwin-sw we did not attempt to define a real ontology of tokens that are physical parts or conglomerations of organisms (cells/tissues/discrete organisms/herds/populations/colonies/clones/etc.), but that would be a good thing to do. It could be done in isolation from the definition of the "reified" TaxonomicallyHomogeneousUnit.
Steve
-- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences
postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A.
delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235
office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707http://bioimages.vanderbilt.edu
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries@wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project --------------------------------------------------------------------------------------
participants (7)
-
Bob Morris -
Hilmar Lapp -
Nico Cellinese -
Paul Murray -
Peter DeVries -
Richard Pyle -
Steve Baskauf