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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. <br>
<br>
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 .<br>
<br>
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.<br>
<br>
Steve <br>
<br>
[1] <a class="moz-txt-link-freetext" href="https://code.google.com/p/darwincore/issues/detail?id=205">https://code.google.com/p/darwincore/issues/detail?id=205</a><br>
[2] <a class="moz-txt-link-freetext" href="https://code.google.com/p/darwincore/issues/detail?id=204">https://code.google.com/p/darwincore/issues/detail?id=204</a><br>
[3] <a class="moz-txt-link-freetext" href="https://code.google.com/p/darwincore/issues/detail?id=213">https://code.google.com/p/darwincore/issues/detail?id=213</a><br>
<br>
Richard Pyle wrote:
<blockquote cite="mid:008f01cfd2bb$49eed560$ddcc8020$@bishopmuseum.org"
type="cite">
<pre wrap="">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
(<a class="moz-txt-link-freetext" href="http://purl.obolibrary.org/obo/OBI_0100026">http://purl.obolibrary.org/obo/OBI_0100026</a>)." 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
</pre>
<blockquote type="cite">
<pre wrap="">-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a> [<a class="moz-txt-link-freetext" href="mailto:tdwg-content">mailto:tdwg-content</a>-
<a class="moz-txt-link-abbreviated" href="mailto:bounces@lists.tdwg.org">bounces@lists.tdwg.org</a>] On Behalf Of joel sachs
Sent: Wednesday, September 17, 2014 9:34 AM
To: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>
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
</pre>
</blockquote>
<pre wrap=""><!---->"organism"
</pre>
<blockquote type="cite">
<pre wrap="">class (<a class="moz-txt-link-freetext" href="https://code.google.com/p/darwincore/issues/detail?id=205">https://code.google.com/p/darwincore/issues/detail?id=205</a>). I am
</pre>
</blockquote>
<pre wrap=""><!---->one of
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<pre wrap=""><!---->as
</pre>
<blockquote type="cite">
<pre wrap="">OBI:0100026 (<a class="moz-txt-link-freetext" href="http://purl.obolibrary.org/obo/OBI_0100026">http://purl.obolibrary.org/obo/OBI_0100026</a>). Instances of
</pre>
</blockquote>
<pre wrap=""><!---->the
</pre>
<blockquote type="cite">
<pre wrap="">Organism class are intended to facilitate linking of one or more
</pre>
</blockquote>
<pre wrap=""><!---->Identification
</pre>
<blockquote type="cite">
<pre wrap="">instances to one or more Occurrence instances. Therefore, things that are
typically assigned scientific names (such as viruses, hybrids, and
</pre>
</blockquote>
<pre wrap=""><!---->lichens) and
</pre>
<blockquote type="cite">
<pre wrap="">aggregates whose occurrences are typically recorded (such as packs,
</pre>
</blockquote>
<pre wrap=""><!---->clones,
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<pre wrap=""><!---->individual living
</pre>
<blockquote type="cite">
<pre wrap="">system, such as animal, plant, bacteria or virus, that is capable of
</pre>
</blockquote>
<pre wrap=""><!---->replicating or
</pre>
<blockquote type="cite">
<pre wrap="">reproducing, growth and maintenance in the right environment. An organism
may be unicellular or made up, like humans, of many billions of cells
</pre>
</blockquote>
<pre wrap=""><!---->divided
</pre>
<blockquote type="cite">
<pre wrap="">into specialized tissues and organs." This definition is not internally
</pre>
</blockquote>
<pre wrap=""><!---->consistent,
</pre>
<blockquote type="cite">
<pre wrap="">since it delineates organisms as being either unicellular or
</pre>
</blockquote>
<pre wrap=""><!---->multi-cellular, while
</pre>
<blockquote type="cite">
<pre wrap="">at the same time explicitly including viruses, which are acellular.
ii. The reference to OBI:0100026 does not add clarity to the DwC
</pre>
</blockquote>
<pre wrap=""><!---->definition,
</pre>
<blockquote type="cite">
<pre wrap="">since the DwC definition goes on to include the clarifying aspects of the
</pre>
</blockquote>
<pre wrap=""><!---->OBI
</pre>
<blockquote type="cite">
<pre wrap="">definition (viruses and lichens are organsims), while leaving out the
</pre>
</blockquote>
<pre wrap=""><!---->muddying
</pre>
<blockquote type="cite">
<pre wrap="">aspects of the OBI definition (organisms are unicellular or
</pre>
</blockquote>
<pre wrap=""><!---->multicellular). The
</pre>
<blockquote type="cite">
<pre wrap="">DwC definition also extends the the OBI defintion (to include wolf packs).
iii. The rdf definition of OBI:organism inherits axioms from the Basic
</pre>
</blockquote>
<pre wrap=""><!---->Formal
</pre>
<blockquote type="cite">
<pre wrap="">Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to
</pre>
</blockquote>
<pre wrap=""><!---->any
</pre>
<blockquote type="cite">
<pre wrap="">particular upper ontology, as there is no consensus upper ontology. (Some
scientific communities use Dolce, some use SUMO, and many have
</pre>
</blockquote>
<pre wrap=""><!---->deliberately
</pre>
<blockquote type="cite">
<pre wrap="">chosen to use none at all.) In general, I like the notion of Darwin Core
</pre>
</blockquote>
<pre wrap=""><!---->as a
</pre>
<blockquote type="cite">
<pre wrap="">glossary of terms, on top of which various data models can be built. When
</pre>
</blockquote>
<pre wrap=""><!---->we
</pre>
<blockquote type="cite">
<pre wrap="">import terms that carry with them an abundance of ontological commitment,
</pre>
</blockquote>
<pre wrap=""><!---->it
</pre>
<blockquote type="cite">
<pre wrap="">raises the stakes for those who choose to use TDWG vocabularies. (In
</pre>
</blockquote>
<pre wrap=""><!---->contrast,
</pre>
<blockquote type="cite">
<pre wrap="">when Darwin Core imported "Location"
from Dublin Core, it did so at no cost, since Dublin Core is not tied to
</pre>
</blockquote>
<pre wrap=""><!---->any
</pre>
<blockquote type="cite">
<pre wrap="">particular upper world-view.)
The Name
There have been multiple debates about a good name for this class, and
</pre>
</blockquote>
<pre wrap=""><!---->there
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<pre wrap=""><!---->name,
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<pre wrap=""><!---->is not a
</pre>
<blockquote type="cite">
<pre wrap="">requirement. Is it time to test the "opaque identifier" waters? Are there
potential problems with having a mix of transparent and opaque identifiers
</pre>
</blockquote>
<pre wrap=""><!---->in
</pre>
<blockquote type="cite">
<pre wrap="">our vocabularies? If not, could we call this class dwc:12345? Should we?
Thoughts on any of the above?
Many thanks,
Joel.
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</blockquote>
<pre wrap=""><!---->
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 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) 322-4942
If you fax, please phone or email so that I will know to look for it.
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
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