Re: [tdwg-content] New terms need resolution: "Individual"
On 11 July 2011 02:51, Paul Murray pmurray@anbg.gov.au wrote:
What happened to 'Organism'?
Would exclude viruses. -- Gregor
Personally, I don't really care what the term is -- as long as it's well-defined, appropriate, reasonably unambiguous, and used consistently. Of the options John listed, I personally prefer "Biological Entity", but I also see Gregor's point that it may be too generic. I don't like the word "Individual", because I would like to see it applied up to at least the level of a group of individuals, if not a population (I would be very happy if the "entity" covered by the term included subtypes of "Population", "Group", "IndividualOrganism", and perhaps even "OrganismPart"; as well as whatever terms in-between this spectrum are deemed useful).
I guess "Organism" comes closest, and I don't think the definition needs to be so "pure" that it excludes viruses. But whatever term is selected, please try to pick something that introduces as little ambiguity as possible.
Aloha, Rich
-----Original Message----- From: Gregor Hagedorn [mailto:g.m.hagedorn@gmail.com] Sent: Monday, July 11, 2011 11:07 AM To: Paul Murray Cc: Richard Pyle; TDWG Content Mailing List; biscicol@googlegroups.com Subject: Re: [tdwg-content] New terms need resolution: "Individual"
On 11 July 2011 02:51, Paul Murray pmurray@anbg.gov.au wrote:
What happened to 'Organism'?
Would exclude viruses. -- Gregor
I agree with Rich. All the standard terms need clear definitions to reduce the variation in usage. Single or double words will never be sufficient to clarify all the permutations that seem to crop up when applying the terms to actual data sets. Clear definitions with multiple examples are necessary to minimize the GIGO problem.
I think we also have some terms that may have different meanings when used in context with other terms. The "source" term has been discussed this week and its alternatives. But, the meaning of source or ReferencedBy or related terms, can vary depending upon the other term with which it is being associated. These contextually-varying meanings could also be included in the definitions and examples.
Chuck
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle Sent: Monday, July 11, 2011 8:59 AM To: 'Gregor Hagedorn'; 'Paul Murray' Cc: 'TDWG Content Mailing List'; biscicol@googlegroups.com Subject: Re: [tdwg-content] New terms need resolution: "Individual"
Personally, I don't really care what the term is -- as long as it's well-defined, appropriate, reasonably unambiguous, and used consistently. Of the options John listed, I personally prefer "Biological Entity", but I also see Gregor's point that it may be too generic. I don't like the word "Individual", because I would like to see it applied up to at least the level of a group of individuals, if not a population (I would be very happy if the "entity" covered by the term included subtypes of "Population", "Group", "IndividualOrganism", and perhaps even "OrganismPart"; as well as whatever terms in-between this spectrum are deemed useful).
I guess "Organism" comes closest, and I don't think the definition needs to be so "pure" that it excludes viruses. But whatever term is selected, please try to pick something that introduces as little ambiguity as possible.
Aloha, Rich
-----Original Message----- From: Gregor Hagedorn [mailto:g.m.hagedorn@gmail.com] Sent: Monday, July 11, 2011 11:07 AM To: Paul Murray Cc: Richard Pyle; TDWG Content Mailing List; biscicol@googlegroups.com Subject: Re: [tdwg-content] New terms need resolution: "Individual"
On 11 July 2011 02:51, Paul Murray pmurray@anbg.gov.au wrote:
What happened to 'Organism'?
Would exclude viruses. -- Gregor
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
I made up the outline below to get a better idea of what things each of the classes "needs" to have defined.
Another way to think of this is what do these need to be linked to.
To some extent this is structured based on how these records will be used.
For instance, you could simply link from an Occurrence to a Indentification, but you will probably want to display the scientificName without having to do a separate subquery.
Although some want to include all the identifications in the Occurrence record without stating which is the preferred identification; I see the need to view the identification history as a much rarer event and is therefore best accessed via the record for Individual.
The individual has an identification history, while it would work best if the Occurrence had one preferred identification.
The use of a taxonConceptID allows all occurrences of the Mountain Lion to be found even if they have the scientific name "*Felis concolor*", "*Puma concolor"*, "*Puma concolor cougari*"
An observation of "*Puma concolor cougari*" counts as an observation of "*Puma concolor" *or of the concept http://lod.taxonconcept.org/ses/v6n7p#Species
The names used below are mainly descriptive and should not be interpreted as proposed DWC names.
Occurrence is a subclass of Event
an instanceOf:Occurrence has the following attributes ( modeled based on what users will want from them)
instanceOf:Event instanceOf:Location instanceOf:TimeInterval instanceOf:Individual instanceOf:SpeciesConcept (taxonConceptID) instanceOf:ScientificName (could also include the full classification) instanceOf:IdentificationCurrent instanceOf:IdentificationPrevious ?? instanceOf:Observer (a Person) instanceOf:Identifier (a Person)
* Note that Event is the combination of a Location a TimeInterval
instanceOf:Identification has the following attributes
instanceOf:Time (date?, year?) instanceOf:Individual instanceOf:Identifier (a Person) instanceOf:ScientificName instanceOf:SpeciesConcept (taxonConceptID) instanceOf:Occurrence
* Note that IdentificationCurrent, IdentificationPrevious is are subclasses of Identification
instanceOf:Individual has the following attributes
instanceOf:Occurrence (multiple) instanceOf:Identifier (a Person) instanceOf:ScientificName instanceOf:SpeciesConcept (taxonConceptID) instanceOf:IdentificationCurrent instanceOf:IdentificationHistory
Respectfully,
- Pete
On Mon, Jul 11, 2011 at 8:58 AM, Richard Pyle deepreef@bishopmuseum.orgwrote:
Personally, I don't really care what the term is -- as long as it's well-defined, appropriate, reasonably unambiguous, and used consistently. Of the options John listed, I personally prefer "Biological Entity", but I also see Gregor's point that it may be too generic. I don't like the word "Individual", because I would like to see it applied up to at least the level of a group of individuals, if not a population (I would be very happy if the "entity" covered by the term included subtypes of "Population", "Group", "IndividualOrganism", and perhaps even "OrganismPart"; as well as whatever terms in-between this spectrum are deemed useful).
I guess "Organism" comes closest, and I don't think the definition needs to be so "pure" that it excludes viruses. But whatever term is selected, please try to pick something that introduces as little ambiguity as possible.
Aloha, Rich
-----Original Message----- From: Gregor Hagedorn [mailto:g.m.hagedorn@gmail.com] Sent: Monday, July 11, 2011 11:07 AM To: Paul Murray Cc: Richard Pyle; TDWG Content Mailing List; biscicol@googlegroups.com Subject: Re: [tdwg-content] New terms need resolution: "Individual"
On 11 July 2011 02:51, Paul Murray pmurray@anbg.gov.au wrote:
What happened to 'Organism'?
Would exclude viruses. -- Gregor
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
On 11/07/2011, at 11:58 PM, Richard Pyle wrote:
I don't like the word "Individual", because I would like to see it applied up to at least the level of a group of individuals, if not a population
Another difficulty is that "Individual" is a term-of-art in RDF/OWL: an individual is any instance of a class. "Individual", in OWL, means pretty much the same thing as "entity" or "object" in other spaces. 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 forgot to mention in my earlier email that I would like to see the definition of BiologicalEntity include clarification of whether the "single taxon" is required to be taxonomically homogeneous or if it is allowed to be taxonomically heterogeneous. I have expressed a preference in the past that it be restricted to taxonomically homogeneous entities, but I believe that in the extended discussion that took place about six months ago, a definition such as the one currently on the table was understood to allow taxonomic heterogeneity. I believe that as a practical matter, allowing taxonomic hetergeneity introduces some significant complications, but I'm willing to live with it if that's what it takes to get this issue resolved. See http://code.google.com/p/darwin-sw/wiki/ClassIndividual and http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity for my attempt to summarize the history of the extended discussion which took place on this subject and what I believe to be the implications of allowing "individuals" to be taxonomically heterogeneous or not.
Steve
On 7/11/2011 9:03 PM, Paul Murray wrote:
On 11/07/2011, at 11:58 PM, Richard Pyle wrote:
I don't like the word "Individual", because I would like to see it applied up to at least the level of a group of individuals, if not a population
Another difficulty is that "Individual" is a term-of-art in RDF/OWL: an individual is any instance of a class. "Individual", in OWL, means pretty much the same thing as "entity" or "object" in other spaces. 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
Very briefly: I support taxonomic homogeneity as well. It's just that I don't think there should be a restriction on the taxonomic rank of the implied taxon. In my mind, a group of sponges attached to a single rock can be taxonomically homogeneous as "Porifera", and be represented as an instanbce of this class. As soon as someone wants to put a more specific taxonomic identity on the different sponges (taxonomic heterogeneity), then there should be N-number of instances corresponding to N-number of taxa represented.
In haste, Rich
-----Original Message----- From: Steven J. Baskauf [mailto:steve.baskauf@vanderbilt.edu] Sent: Tuesday, July 12, 2011 2:36 PM To: Paul Murray Cc: Richard Pyle; 'TDWG Content Mailing List'; biscicol@googlegroups.com Subject: Re: [tdwg-content] New terms need resolution: "Individual" [SEC=UNCLASSIFIED]
I forgot to mention in my earlier email that I would like to see the
definition
of BiologicalEntity include clarification of whether the "single taxon" is required to be taxonomically homogeneous or if it is allowed to be taxonomically heterogeneous. I have expressed a preference in the past that it be restricted to taxonomically homogeneous entities, but I believe that in the extended discussion that took place about six months ago, a definition such as the one currently on the table was understood to allow taxonomic heterogeneity. I believe that as a practical matter, allowing taxonomic hetergeneity introduces some significant complications, but I'm willing to live with it if that's what it takes to get this issue
resolved. See
http://code.google.com/p/darwin-sw/wiki/ClassIndividual and http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity for my attempt to summarize the history of the extended discussion which took place on this subject and what I believe to be the implications of allowing "individuals" to be taxonomically heterogeneous or not.
Steve
On 7/11/2011 9:03 PM, Paul Murray wrote:
On 11/07/2011, at 11:58 PM, Richard Pyle wrote:
I don't like the word "Individual", because I would like to see it applied up to at least the level of a group of individuals, if not a population
Another difficulty is that "Individual" is a term-of-art in RDF/OWL: an
individual is any instance of a class. "Individual", in OWL, means pretty
much
the same thing as "entity" or "object" in other spaces.
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
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
-- 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.
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participants (6)
-
Chuck Miller -
Gregor Hagedorn -
Paul Murray -
Peter DeVries -
Richard Pyle -
Steven J. Baskauf