Comments on Darwin Core Issue 205 (the proposed Organism term)
Everyone,
I'd like to comment on the proposed addition to Darwin Core of an "organism" class (https://code.google.com/p/darwincore/issues/detail?id=205). I am one of the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." This definition is not internally consistent, since it delineates organisms as being either unicellular or multi-cellular, while at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC definition, since the DwC definition goes on to include the clarifying aspects of the OBI definition (viruses and lichens are organsims), while leaving out the muddying aspects of the OBI definition (organisms are unicellular or multicellular). The DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic Formal Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to any particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have deliberately chosen to use none at all.) In general, I like the notion of Darwin Core as a glossary of terms, on top of which various data models can be built. When we import terms that carry with them an abundance of ontological commitment, it raises the stakes for those who choose to use TDWG vocabularies. (In contrast, when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to any particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and there was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus name, but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and is not a requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers in our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
On The Name:
I'd prefer dwc:2357. Oh, wait maybe that's not so opaque...
On Wed, Sep 17, 2014 at 1:34 PM, joel sachs jsachs@csee.umbc.edu wrote:
Everyone,
I'd like to comment on the proposed addition to Darwin Core of an "organism" class (https://code.google.com/p/darwincore/issues/detail?id=205). I am one of the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." This definition is not internally consistent, since it delineates organisms as being either unicellular or multi-cellular, while at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC definition, since the DwC definition goes on to include the clarifying aspects of the OBI definition (viruses and lichens are organsims), while leaving out the muddying aspects of the OBI definition (organisms are unicellular or multicellular). The DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic Formal Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to any particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have deliberately chosen to use none at all.) In general, I like the notion of Darwin Core as a glossary of terms, on top of which various data models can be built. When we import terms that carry with them an abundance of ontological commitment, it raises the stakes for those who choose to use TDWG vocabularies. (In contrast, when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to any particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and there was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus name, but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and is not a requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers in our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Hi Joel,
As I fellow submitter and strong supporter of the Organism class for DwC, I, like you, have been uneasy with the cross-reference to OBI:0100026 in the definition. It may be appropriate to include this in some sort of qualifying remarks about the class, but it doesn't seem to be appropriate to include the reference in the definition. Even though it is somewhat softened by the phrase "in the sense" (as opposed to some sort of "same as" assertion), I would support the removal of the sentence "An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026)." from the definition of dwc:Organism.
I still believe that a human-friendly name is very helpful. The barrier is not the standard or how it's named. The barrier is how humans interpret and implement the standard. Giving the class an opaque identifier (I would, of course, vote in favor of a UUID!) would probably create a barrier to progress through opacity that is greater than the barrier of confusion through mis-interpretation of an imperfect human-friendly name like "Organism".
Of course, you didn't even indicate the term that we have been using for years, and which I prefer, which is "IndividualOrganism". However, in the interest of progress, I strongly oppose re-opening the "name" can of worms. DwC is riddled with mis-applied names of things, and we can still manage to muddle our way through it (provided the definitions are clear). For example, the term "Occurrence" has been used to represent "things" that range from actual occurrence instances (e.g., observations of organisms at a place and time), to individual organisms (e.g. specimens as a proxy to the occurrence of an organism at the time it was extracted from nature), to evidence (e.g. photographs of organisms), to occurrence-evidence instances (photographs of organism in nature). Yet we still manage to exchange data (perhaps less efficiently than we could).
Anyway, I support the removal of the OBI reference in the definition of "Occurrence", and I oppose re-visiting the issue of the label we apply to the proposed new dwc class.
Aloha, Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of joel sachs Sent: Wednesday, September 17, 2014 9:34 AM To: tdwg-content@lists.tdwg.org Subject: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)
Everyone,
I'd like to comment on the proposed addition to Darwin Core of an
"organism"
class (https://code.google.com/p/darwincore/issues/detail?id=205). I am
one of
the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined
as
OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of
the
Organism class are intended to facilitate linking of one or more
Identification
instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and
lichens) and
aggregates whose occurrences are typically recorded (such as packs,
clones,
and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an
individual living
system, such as animal, plant, bacteria or virus, that is capable of
replicating or
reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells
divided
into specialized tissues and organs." This definition is not internally
consistent,
since it delineates organisms as being either unicellular or
multi-cellular, while
at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC
definition,
since the DwC definition goes on to include the clarifying aspects of the
OBI
definition (viruses and lichens are organsims), while leaving out the
muddying
aspects of the OBI definition (organisms are unicellular or
multicellular). The
DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic
Formal
Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to
any
particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have
deliberately
chosen to use none at all.) In general, I like the notion of Darwin Core
as a
glossary of terms, on top of which various data models can be built. When
we
import terms that carry with them an abundance of ontological commitment,
it
raises the stakes for those who choose to use TDWG vocabularies. (In
contrast,
when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to
any
particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and
there
was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus
name,
but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and
is not a
requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers
in
our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Rich- You might peruse
http://www.w3.org/DesignIssues/Axioms.html#opaque
In truth, I don't know whether Sir Tim has changed his view, but I'll be surprised and disappointed if so.
I support removal of the OBI reference. I support an opaque reference.
Bob
On Wed, Sep 17, 2014 at 2:06 PM, Richard Pyle deepreef@bishopmuseum.org wrote:
Hi Joel,
As I fellow submitter and strong supporter of the Organism class for DwC, I, like you, have been uneasy with the cross-reference to OBI:0100026 in the definition. It may be appropriate to include this in some sort of qualifying remarks about the class, but it doesn't seem to be appropriate to include the reference in the definition. Even though it is somewhat softened by the phrase "in the sense" (as opposed to some sort of "same as" assertion), I would support the removal of the sentence "An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026)." from the definition of dwc:Organism.
I still believe that a human-friendly name is very helpful. The barrier is not the standard or how it's named. The barrier is how humans interpret and implement the standard. Giving the class an opaque identifier (I would, of course, vote in favor of a UUID!) would probably create a barrier to progress through opacity that is greater than the barrier of confusion through mis-interpretation of an imperfect human-friendly name like "Organism".
Of course, you didn't even indicate the term that we have been using for years, and which I prefer, which is "IndividualOrganism". However, in the interest of progress, I strongly oppose re-opening the "name" can of worms. DwC is riddled with mis-applied names of things, and we can still manage to muddle our way through it (provided the definitions are clear). For example, the term "Occurrence" has been used to represent "things" that range from actual occurrence instances (e.g., observations of organisms at a place and time), to individual organisms (e.g. specimens as a proxy to the occurrence of an organism at the time it was extracted from nature), to evidence (e.g. photographs of organisms), to occurrence-evidence instances (photographs of organism in nature). Yet we still manage to exchange data (perhaps less efficiently than we could).
Anyway, I support the removal of the OBI reference in the definition of "Occurrence", and I oppose re-visiting the issue of the label we apply to the proposed new dwc class.
Aloha, Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of joel sachs Sent: Wednesday, September 17, 2014 9:34 AM To: tdwg-content@lists.tdwg.org Subject: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)
Everyone,
I'd like to comment on the proposed addition to Darwin Core of an
"organism"
class (https://code.google.com/p/darwincore/issues/detail?id=205). I am
one of
the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the
name.
Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined
as
OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of
the
Organism class are intended to facilitate linking of one or more
Identification
instances to one or more Occurrence instances. Therefore, things that
are
typically assigned scientific names (such as viruses, hybrids, and
lichens) and
aggregates whose occurrences are typically recorded (such as packs,
clones,
and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an
individual living
system, such as animal, plant, bacteria or virus, that is capable of
replicating or
reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells
divided
into specialized tissues and organs." This definition is not internally
consistent,
since it delineates organisms as being either unicellular or
multi-cellular, while
at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC
definition,
since the DwC definition goes on to include the clarifying aspects of the
OBI
definition (viruses and lichens are organsims), while leaving out the
muddying
aspects of the OBI definition (organisms are unicellular or
multicellular). The
DwC definition also extends the the OBI defintion (to include wolf
packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic
Formal
Ontology (BFO). I've long argued that it's a mistake for TDWG to commit
to any
particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have
deliberately
chosen to use none at all.) In general, I like the notion of Darwin Core
as a
glossary of terms, on top of which various data models can be built. When
we
import terms that carry with them an abundance of ontological commitment,
it
raises the stakes for those who choose to use TDWG vocabularies. (In
contrast,
when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to
any
particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and
there
was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus
name,
but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and
is not a
requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque
identifiers in
our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
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
Thanks, Bob. Of course, Identifiers > URIs. URIs fail my own Opacity Axiom, in that most of them start with “http://”, which temps people into inferring that they can be dereferenced via the HTTP protocol.
Aloha,
Rich
(confessed mental self-fornicator)
From: Bob Morris [mailto:morris.bob@gmail.com] Sent: Wednesday, September 17, 2014 10:20 AM To: Richard Pyle Cc: joel sachs; tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)
Rich- You might peruse
http://www.w3.org/DesignIssues/Axioms.html#opaque
In truth, I don't know whether Sir Tim has changed his view, but I'll be surprised and disappointed if so.
I support removal of the OBI reference. I support an opaque reference.
Bob
On Wed, Sep 17, 2014 at 2:06 PM, Richard Pyle deepreef@bishopmuseum.org wrote:
Hi Joel,
As I fellow submitter and strong supporter of the Organism class for DwC, I, like you, have been uneasy with the cross-reference to OBI:0100026 in the definition. It may be appropriate to include this in some sort of qualifying remarks about the class, but it doesn't seem to be appropriate to include the reference in the definition. Even though it is somewhat softened by the phrase "in the sense" (as opposed to some sort of "same as" assertion), I would support the removal of the sentence "An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026)." from the definition of dwc:Organism.
I still believe that a human-friendly name is very helpful. The barrier is not the standard or how it's named. The barrier is how humans interpret and implement the standard. Giving the class an opaque identifier (I would, of course, vote in favor of a UUID!) would probably create a barrier to progress through opacity that is greater than the barrier of confusion through mis-interpretation of an imperfect human-friendly name like "Organism".
Of course, you didn't even indicate the term that we have been using for years, and which I prefer, which is "IndividualOrganism". However, in the interest of progress, I strongly oppose re-opening the "name" can of worms. DwC is riddled with mis-applied names of things, and we can still manage to muddle our way through it (provided the definitions are clear). For example, the term "Occurrence" has been used to represent "things" that range from actual occurrence instances (e.g., observations of organisms at a place and time), to individual organisms (e.g. specimens as a proxy to the occurrence of an organism at the time it was extracted from nature), to evidence (e.g. photographs of organisms), to occurrence-evidence instances (photographs of organism in nature). Yet we still manage to exchange data (perhaps less efficiently than we could).
Anyway, I support the removal of the OBI reference in the definition of "Occurrence", and I oppose re-visiting the issue of the label we apply to the proposed new dwc class.
Aloha, Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of joel sachs Sent: Wednesday, September 17, 2014 9:34 AM To: tdwg-content@lists.tdwg.org Subject: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)
Everyone,
I'd like to comment on the proposed addition to Darwin Core of an
"organism"
class (https://code.google.com/p/darwincore/issues/detail?id=205). I am
one of
the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined
as
OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of
the
Organism class are intended to facilitate linking of one or more
Identification
instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and
lichens) and
aggregates whose occurrences are typically recorded (such as packs,
clones,
and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an
individual living
system, such as animal, plant, bacteria or virus, that is capable of
replicating or
reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells
divided
into specialized tissues and organs." This definition is not internally
consistent,
since it delineates organisms as being either unicellular or
multi-cellular, while
at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC
definition,
since the DwC definition goes on to include the clarifying aspects of the
OBI
definition (viruses and lichens are organsims), while leaving out the
muddying
aspects of the OBI definition (organisms are unicellular or
multicellular). The
DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic
Formal
Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to
any
particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have
deliberately
chosen to use none at all.) In general, I like the notion of Darwin Core
as a
glossary of terms, on top of which various data models can be built. When
we
import terms that carry with them an abundance of ontological commitment,
it
raises the stakes for those who choose to use TDWG vocabularies. (In
contrast,
when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to
any
particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and
there
was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus
name,
but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and
is not a
requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers
in
our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
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
On Wed, Sep 17, 2014 at 5:06 PM, Richard Pyle deepreef@bishopmuseum.org wrote:
I still believe that a human-friendly name is very helpful. The barrier is not the standard or how it's named. The barrier is how humans interpret and implement the standard.
I agree.
Giving the class an opaque identifier (I would, of course, vote in favor of a UUID!) would probably create a barrier to progress through opacity that is greater than the barrier of confusion through mis-interpretation of an imperfect human-friendly name like "Organism".
I think this is a false conclusion. The Gene Ontology has been widely adopted, as have been other OBO ontologies, despite (or perhaps because?) opaque identifiers.
I say parenthetically "perhaps because" because having opaque identifiers actually allows you to evolve and change labels so that they make the most sense, rather than being stuck with choices made early on because now all kinds of data uses those identifiers.
-hilmar
Hi Hilmar,
I was not clear in my statement. I should have said “Giving the class *only* an opaque identifier…”. In other words, my point was something along the lines of:
“As for the name, although using opaque identifiers in DwC is something I would wholeheartedly welcome, in this case all it accomplishes is buying time rather than a solution. Opaquely identified terms still need a human-readable label that's succinct, precise, and accurate, and arguably more so, not less, if the identifier is opaque.”
Aloha,
Rich
From: hilmar.lapp@gmail.com [mailto:hilmar.lapp@gmail.com] On Behalf Of Hilmar Lapp Sent: Wednesday, September 17, 2014 10:38 AM To: deepreef@bishopmuseum.org Cc: joel sachs; TDWG Content Mailing List Subject: Re: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)
On Wed, Sep 17, 2014 at 5:06 PM, Richard Pyle deepreef@bishopmuseum.org wrote:
I still believe that a human-friendly name is very helpful. The barrier is not the standard or how it's named. The barrier is how humans interpret and implement the standard.
I agree.
Giving the class an opaque identifier (I would, of course, vote in favor of a UUID!) would probably create a barrier to progress through opacity that is greater than the barrier of confusion through mis-interpretation of an imperfect human-friendly name like "Organism".
I think this is a false conclusion. The Gene Ontology has been widely adopted, as have been other OBO ontologies, despite (or perhaps because?) opaque identifiers.
I say parenthetically "perhaps because" because having opaque identifiers actually allows you to evolve and change labels so that they make the most sense, rather than being stuck with choices made early on because now all kinds of data uses those identifiers.
-hilmar
I think the case for opaque identifiers can be argued both ways. See, e.g. discussion here [1]. Further to Hilmar's point about offering flexibility around defining labels, I also like them because, especially for new-comers, they help distinguish the concept from the label we apply to the concept and do not give preeminence to the English label. Éamonn
[1] http://ontolog.cim3.net/forum/ontology-summit/2014-02/msg00028.html
On Wed, Sep 17, 2014 at 5:06 PM, Richard Pyle deepreef@bishopmuseum.org wrote:
I still believe that a human-friendly name is very helpful. The barrier is not the standard or how it's named. The barrier is how humans interpret and implement the standard.
I agree.
Giving the class an opaque identifier (I would, of course, vote in favor of a UUID!) would probably create a barrier to progress through opacity that is greater than the barrier of confusion through mis-interpretation of an imperfect human-friendly name like "Organism".
I think this is a false conclusion. The Gene Ontology has been widely adopted, as have been other OBO ontologies, despite (or perhaps because?) opaque identifiers.
I say parenthetically "perhaps because" because having opaque identifiers actually allows you to evolve and change labels so that they make the most sense, rather than being stuck with choices made early on because now all kinds of data uses those identifiers.
-hilmar _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Just to let readers of the broader list know a bit of the history on this, the ad hoc group who hammered out the definitions could find no name for this class that satisfied everyone. So we agreed to a name that was not adamantly opposed even if most people weren't completely happy about it. I think it is more important to HAVE the term than for it to have a name that makes everyone happy.
In an attempt to avoid another rehashing of the debate that is referenced in the proposal [1], I want to note that I believe that the purpose for creating this class is NOT to try to come up with a clear definition for "organism", but rather to create a term that can be used for typing things that would be referenced by the existing term dwc:individualID. That term's definition says "Meant to accommodate resampling of the same individual or group for monitoring purposes." So we don't intend to define class instances strictly as organisms, but rather as any kind of thing that is coherent enough that it could potentially be resampled and on which we could hang a taxonomic determination. We thus dodge the question of whether fungi and wolf packs are really organisms. If they can be resampled and assigned a taxonomic determination, they fall into the class. I realize that this may make some people uncomfortable, but the reality is that this class already exists - it just doesn't have a term to use for typing it. I think that discomfort is at least partly why we referenced OBI:0100026 - it gives people something more concrete to "connect" with .
I'm less concerned about mentioning OBI:010026 in a textual definition than I am making subclass declarations in the RDF. That's where we run into unintended consequences with machine processing. As Hilmar said, that horse is already out of the barn with definition of dwctype:MaterialSample - the implications of that kind of subclassing didn't get discussed very thoroughly in the run-up to dwctype:MaterialSample's addition to DwC. But I'll note that in the current proposed suite of changes to the DwC classes [2], all of the "dwctype:" namespace terms would be deprecated in favor of "dwc:" namespace analogs. The proposed definition of dwc:MaterialSample does NOT include this subclassing. See the "justification" section at [3]. So if the whole group of class term changes goes through as a package, we would no longer have any subclass relations asserted in the RDF of Darwin Core classes. If people don't like that, they should speak up now and explain their reasoning, because that's how the proposal stands now.
Steve
[1] https://code.google.com/p/darwincore/issues/detail?id=205 [2] https://code.google.com/p/darwincore/issues/detail?id=204 [3] https://code.google.com/p/darwincore/issues/detail?id=213
Richard Pyle wrote:
Hi Joel,
As I fellow submitter and strong supporter of the Organism class for DwC, I, like you, have been uneasy with the cross-reference to OBI:0100026 in the definition. It may be appropriate to include this in some sort of qualifying remarks about the class, but it doesn't seem to be appropriate to include the reference in the definition. Even though it is somewhat softened by the phrase "in the sense" (as opposed to some sort of "same as" assertion), I would support the removal of the sentence "An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026)." from the definition of dwc:Organism.
I still believe that a human-friendly name is very helpful. The barrier is not the standard or how it's named. The barrier is how humans interpret and implement the standard. Giving the class an opaque identifier (I would, of course, vote in favor of a UUID!) would probably create a barrier to progress through opacity that is greater than the barrier of confusion through mis-interpretation of an imperfect human-friendly name like "Organism".
Of course, you didn't even indicate the term that we have been using for years, and which I prefer, which is "IndividualOrganism". However, in the interest of progress, I strongly oppose re-opening the "name" can of worms. DwC is riddled with mis-applied names of things, and we can still manage to muddle our way through it (provided the definitions are clear). For example, the term "Occurrence" has been used to represent "things" that range from actual occurrence instances (e.g., observations of organisms at a place and time), to individual organisms (e.g. specimens as a proxy to the occurrence of an organism at the time it was extracted from nature), to evidence (e.g. photographs of organisms), to occurrence-evidence instances (photographs of organism in nature). Yet we still manage to exchange data (perhaps less efficiently than we could).
Anyway, I support the removal of the OBI reference in the definition of "Occurrence", and I oppose re-visiting the issue of the label we apply to the proposed new dwc class.
Aloha, Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of joel sachs Sent: Wednesday, September 17, 2014 9:34 AM To: tdwg-content@lists.tdwg.org Subject: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)
Everyone,
I'd like to comment on the proposed addition to Darwin Core of an
"organism"
class (https://code.google.com/p/darwincore/issues/detail?id=205). I am
one of
the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined
as
OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of
the
Organism class are intended to facilitate linking of one or more
Identification
instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and
lichens) and
aggregates whose occurrences are typically recorded (such as packs,
clones,
and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an
individual living
system, such as animal, plant, bacteria or virus, that is capable of
replicating or
reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells
divided
into specialized tissues and organs." This definition is not internally
consistent,
since it delineates organisms as being either unicellular or
multi-cellular, while
at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC
definition,
since the DwC definition goes on to include the clarifying aspects of the
OBI
definition (viruses and lichens are organsims), while leaving out the
muddying
aspects of the OBI definition (organisms are unicellular or
multicellular). The
DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic
Formal
Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to
any
particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have
deliberately
chosen to use none at all.) In general, I like the notion of Darwin Core
as a
glossary of terms, on top of which various data models can be built. When
we
import terms that carry with them an abundance of ontological commitment,
it
raises the stakes for those who choose to use TDWG vocabularies. (In
contrast,
when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to
any
particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and
there
was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus
name,
but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and
is not a
requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers
in
our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
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 .
Three comments:
OBI class definitions are not carved in stone. If you have issues with the definition (and the ones you express are well taken), why wouldn't you take them to OBI but to DwC? I.e., do you want to suggest that the OBI term definition won't improve in the foreseeable future such that your criticisms are addressed?
As for the BFO, I know that's been brought up repeatedly, but to me that's entirely a red herring. By having a reference to the OBI class, DwC makes no commitment whatsoever to BFO axioms; only users who assert a subclass axiom and expressly import OBI as well as BFO do. I would argue that those who do so make an explicit choice. (Also, that horse has already left the barn by reference to material sample. So even if it wasn't a red herring before, it is one now.)
As for the name, although using opaque identifiers in DwC is something I would wholeheartedly welcome, in this case all it accomplishes is buying time rather than a solution. Opaquely identified terms still need a human-readable label that's succinct, precise, and accurate, and arguably more so, not less, if the identifier is opaque.
-hilmar
On Wed, Sep 17, 2014 at 4:34 PM, joel sachs jsachs@csee.umbc.edu wrote:
Everyone,
I'd like to comment on the proposed addition to Darwin Core of an "organism" class (https://code.google.com/p/darwincore/issues/detail?id=205). I am one of the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." This definition is not internally consistent, since it delineates organisms as being either unicellular or multi-cellular, while at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC definition, since the DwC definition goes on to include the clarifying aspects of the OBI definition (viruses and lichens are organsims), while leaving out the muddying aspects of the OBI definition (organisms are unicellular or multicellular). The DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic Formal Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to any particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have deliberately chosen to use none at all.) In general, I like the notion of Darwin Core as a glossary of terms, on top of which various data models can be built. When we import terms that carry with them an abundance of ontological commitment, it raises the stakes for those who choose to use TDWG vocabularies. (In contrast, when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to any particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and there was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus name, but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and is not a requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers in our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Hope you are actively working on our paper in addition to this mental masturbation. Tree-thinking is way more orgasmic than organismic terms. I see you have not touched the draft I sent you a week ago :-)
nico
On Sep 17, 2014, at 5:18 PM, Hilmar Lapp <hlapp@nescent.orgmailto:hlapp@nescent.org> wrote:
Three comments:
OBI class definitions are not carved in stone. If you have issues with the definition (and the ones you express are well taken), why wouldn't you take them to OBI but to DwC? I.e., do you want to suggest that the OBI term definition won't improve in the foreseeable future such that your criticisms are addressed?
As for the BFO, I know that's been brought up repeatedly, but to me that's entirely a red herring. By having a reference to the OBI class, DwC makes no commitment whatsoever to BFO axioms; only users who assert a subclass axiom and expressly import OBI as well as BFO do. I would argue that those who do so make an explicit choice. (Also, that horse has already left the barn by reference to material sample. So even if it wasn't a red herring before, it is one now.)
As for the name, although using opaque identifiers in DwC is something I would wholeheartedly welcome, in this case all it accomplishes is buying time rather than a solution. Opaquely identified terms still need a human-readable label that's succinct, precise, and accurate, and arguably more so, not less, if the identifier is opaque.
-hilmar
On Wed, Sep 17, 2014 at 4:34 PM, joel sachs <jsachs@csee.umbc.edumailto:jsachs@csee.umbc.edu> wrote: Everyone,
I'd like to comment on the proposed addition to Darwin Core of an "organism" class (https://code.google.com/p/darwincore/issues/detail?id=205). I am one of the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." This definition is not internally consistent, since it delineates organisms as being either unicellular or multi-cellular, while at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC definition, since the DwC definition goes on to include the clarifying aspects of the OBI definition (viruses and lichens are organsims), while leaving out the muddying aspects of the OBI definition (organisms are unicellular or multicellular). The DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic Formal Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to any particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have deliberately chosen to use none at all.) In general, I like the notion of Darwin Core as a glossary of terms, on top of which various data models can be built. When we import terms that carry with them an abundance of ontological commitment, it raises the stakes for those who choose to use TDWG vocabularies. (In contrast, when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to any particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and there was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus name, but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and is not a requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers in our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- Hilmar Lapp -:- informatics.nescent.org/wikihttp://informatics.nescent.org/wiki -:- lappland.iohttp://lappland.io/
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
<><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Associate Curator, Botany & Informatics Joint Associate 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/
Oh shoot!! I am so sorry everyone!! That was meant for Hilmar alone! OMG, I hate 'reply to all'! Now I have to run to the bathroom! I look forward to seeing you all in Sweden and promise to enjoy every discussion there about this. Also, I will buy you a beer, Joel!
Nico
On Sep 17, 2014, at 5:34 PM, Cellinese,Nico <ncellinese@flmnh.ufl.edumailto:ncellinese@flmnh.ufl.edu> wrote:
Hope you are actively working on our paper in addition to this mental masturbation. Tree-thinking is way more orgasmic than organismic terms. I see you have not touched the draft I sent you a week ago :-)
nico
On Sep 17, 2014, at 5:18 PM, Hilmar Lapp <hlapp@nescent.orgmailto:hlapp@nescent.org> wrote:
Three comments:
OBI class definitions are not carved in stone. If you have issues with the definition (and the ones you express are well taken), why wouldn't you take them to OBI but to DwC? I.e., do you want to suggest that the OBI term definition won't improve in the foreseeable future such that your criticisms are addressed?
As for the BFO, I know that's been brought up repeatedly, but to me that's entirely a red herring. By having a reference to the OBI class, DwC makes no commitment whatsoever to BFO axioms; only users who assert a subclass axiom and expressly import OBI as well as BFO do. I would argue that those who do so make an explicit choice. (Also, that horse has already left the barn by reference to material sample. So even if it wasn't a red herring before, it is one now.)
As for the name, although using opaque identifiers in DwC is something I would wholeheartedly welcome, in this case all it accomplishes is buying time rather than a solution. Opaquely identified terms still need a human-readable label that's succinct, precise, and accurate, and arguably more so, not less, if the identifier is opaque.
-hilmar
On Wed, Sep 17, 2014 at 4:34 PM, joel sachs <jsachs@csee.umbc.edumailto:jsachs@csee.umbc.edu> wrote: Everyone,
I'd like to comment on the proposed addition to Darwin Core of an "organism" class (https://code.google.com/p/darwincore/issues/detail?id=205). I am one of the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn:
The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class."
There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." This definition is not internally consistent, since it delineates organisms as being either unicellular or multi-cellular, while at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC definition, since the DwC definition goes on to include the clarifying aspects of the OBI definition (viruses and lichens are organsims), while leaving out the muddying aspects of the OBI definition (organisms are unicellular or multicellular). The DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic Formal Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to any particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have deliberately chosen to use none at all.) In general, I like the notion of Darwin Core as a glossary of terms, on top of which various data models can be built. When we import terms that carry with them an abundance of ontological commitment, it raises the stakes for those who choose to use TDWG vocabularies. (In contrast, when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to any particular upper world-view.)
The Name There have been multiple debates about a good name for this class, and there was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus name, but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and is not a requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers in our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks, Joel.
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- Hilmar Lapp -:- informatics.nescent.org/wikihttp://informatics.nescent.org/wiki -:- lappland.iohttp://lappland.io/
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
<><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Associate Curator, Botany & Informatics Joint Associate 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/
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
<><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Associate Curator, Botany & Informatics Joint Associate 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/
participants (7)
-
Bob Morris -
Cellinese,Nico -
Eamonn O Tuama [GBIF] -
Hilmar Lapp -
joel sachs -
Richard Pyle -
Steve Baskauf