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Thanks to all for the clarifying comments. I think that what we are
seeing here is a manifestation of what we've seen previously on this
list in discussions about terms: that people make assumptions about
what a term means based on its label (mea culpa). The solution, as in
previous cases, is to look carefully at the definition to make sure the
term actually means what you think it does. <br>
<br>
I don't have a problem with the ENVO text definition "an environmental
system to which resident ecological communities have evolved
adaptations." if that's what ENVO wants the term ENVO:00000428 to
mean. But I'm not sure that I would necessarily have gotten a clear
picture of what ENVO wants "biome" to mean solely from the
documentation. The .obo file includes "Wikipedia:Biome" as a citation
for the ENVO definition, but the Wikipedia definition of bioime [1]
doesn't really seem to bear any resemblence to the ENVO definition.
The ENVO term description also includes "synonym: 'major habitat type'
EXACT [WWF:Biome]", but WWF [2] doesn't define biomes as ENVO does
either. Both Wikipedia and WWF talk about biomes in the traditional
sense of large geographic regions. If the ENVO definition of biome is
intended to broaden biome beyond its traditional meaning, then I think
it would be better to give the ENVO:00000428 some different label
("evolved environmental system"?) and reserve the label "biome" for
biome in the traditional sense (with the declared WWF and Wikipedia
equivalencies). Then declare "biome" rdfs:subClassOf "evolved
environmental system".<br>
<br>
Also, if the various ENVO subclasses of ENVO:00000428 are intended to
be equivalent to all or part of WWF biomes, then why not note this in
the term description. Unlike Wikipedia, which could change tomorrow,
the WWF bioimes are well-described in stable publications such as
Ricketts et al. (1999) [3].<br>
<br>
Steve<br>
<br>
[1] "Biomes are climatically and geographically defined as contiguous
areas with similar climatic conditions on the Earth, such as
communities of plants, animals, soil organisms, and viruses and are
often referred to as ecosystems. Some parts of the earth have more or
less the same kind of abiotic and biotic factors spread over a large
area, creating a typical ecosystem over that area. Such major
ecosystems are termed as biomes. Biomes are defined by factors such as
plant structures (such as trees, shrubs, and grasses), leaf types (such
as broadleaf and needleleaf), plant spacing (forest, woodland,
savanna), and climate. " <br>
<br>
[2] "Biomes are the various regions of our planet that can best be
distinguished by their climate, fauna and flora. There are different
ways of classifying biomes but the common elements are climate,
habitat, animal and plant adaptation, biodiversity and human activity."<br>
<a class="moz-txt-link-freetext" href="http://wwf.panda.org/about_our_earth/teacher_resources/webfieldtrips/major_biomes/">http://wwf.panda.org/about_our_earth/teacher_resources/webfieldtrips/major_biomes/</a><br>
<br>
[3] <a class="moz-txt-link-freetext" href="http://islandpress.org/terrestrial-ecoregions-north-america">http://islandpress.org/terrestrial-ecoregions-north-america</a><br>
<br>
Pier Luigi Buttigieg wrote:<br>
<blockquote cite="mid:e1a79af81581896f11119c6126974e79@194.95.7.50"
type="cite">
<blockquote type="cite">
<pre wrap="">The ENVO definition of biome is : "A biome is an environmental system to
which resident ecological communities have evolved adaptations." (<a class="moz-txt-link-freetext" href="http://purl.obolibrary.org/obo/ENVO_00000428">http://purl.obolibrary.org/obo/ENVO_00000428</a>)
</pre>
</blockquote>
<pre wrap=""><!---->
We try to be agnostic to spatial scale with this definition as we
encountered numerous instances of the term being used outside of
'classical' biome classification systems with reasonable rationale (e.g.
many environments - such as marine and lacustrine environments - are not
adequately covered by existing schemes). Even within classical systems,
identifying the scale threshold is hardly precise (if anyone knows of
anything that defines this, please let me know) and definitions are revised
from time to time as new technologies (e.g. remote sensing) emerge. Some
have suggested using prevailing climate as a way to stabilise 'large'
scales, but this is problematic as microclimates (e.g. near large water
bodies) can result in the emergence of different biomes (in the classical
sense) existing at comparatively small regions. The presence of an
ecological community which has adapted to a given environment seems to be
the common theme. A successful, in situ adaptation process indicates that
the environment a) can sustain viable populations over multiple generations
and b) persists long enough for these populations to undergo evolutionarily
consequential changes, distinguishing it from other environment types. If
users wish to use a 'classical' biome type, they have access to an adapted
version of the WWF classification (see below).
</pre>
<blockquote type="cite">
<pre wrap="">A resident ecological community from the perspective of a microbe likely
does not care about the large-scale plant and animal communities, so it
</pre>
</blockquote>
<pre wrap=""><!---->is
</pre>
<blockquote type="cite">
<pre wrap="">a matter of perspective taken from the point of view of the subject. To
that end, leaf litter as the biome seems entirely reasonable if the
microbes resident there have evolved adaptations to leaf litter.
</pre>
</blockquote>
<pre wrap=""><!---->[...]
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Steve Baskauf wrote:
I haven't looked at the definition given to "biome" in ENVO, but based
on what I believe is the common consensus on what a biome is (a major,
large-scale set of plant and animal communities occupying a geographic
region), it doesn't seem right to apply that term to "leaf litter".
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->[...]
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">There are a number of standard lists of the world's biomes and they
include large-scale regions like "temperate deciduous forest", not
small-scale features.
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
ENVO includes a representation of the WWF biome classification system. At
one stage, the Udvardy, WWF, and Bailey systems were all in ENVO (which was
quite confusing). We opted to use the WWF system (obsoleting the other
classes) as it was the most current and had the highest global coverage.
The WWF categories were modified to make them more suitable for an ontology
(e.g. compound classes were split).
As a microbial ecologist, I think that the position outlined by John is a
valid one. The scales used in the 'classical' definition are, ultimately, a
function of our own observational capacities and various forms of ecosystem
can be nested across scales. However, Steve's right in saying that this is
a fairly profound change in the usage of a well-established term (with a
substantial literature base behind it). Further, just because a microbial
ecologist (or anyone else, but I'm going with this example) declares
something to be a biome, doesn't make it so: the communities of microbes
living in leaf litter may not have evolved in that particular environment,
they may simply have adaptations to other environments that allow them to
colonise a one with sufficient similarities.
In our annotation guidelines
(<a class="moz-txt-link-freetext" href="http://www.environmentontology.org/annotation-guidelines">http://www.environmentontology.org/annotation-guidelines</a>) we do ask that
such "small scale" biomes are requested with reference to some form of
empirical data supporting the notion that the communities have adapted to
that particular environment. ENVO doesn't try to dictate what is "right"
here, but attempts to represent how different communities (who are creating
new conventions which reflect their phenomena they study) are talking about
environments. Whether they turn out to be correct in their usage of a given
term is a somewhat different question and we're always happy to receive
critiques and input.
I think it's best if we declare or produce subset of biome classes that are
approved by a certain body (e.g. the WWF). Conversely, classes that are
somehow 'nascent' or 'experimental' can also be marked. Plans to produce
subsets of ENVO that are relevant to specific working bodies are already
queued.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Ramona Walls wrote:
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->[...]
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap=""> -- ENVO very clearly distinguishes between a biome, a feature, and a
material. It is never the case that the same ENVO class can be use as
both a biome and a feature or a feature and a material. Although the
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->same
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">entity, depending on its role, may serve as either a biome or material
(or feature for that matter), in that case, it would be an instance of
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->two
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">different classes in ENVO. Take the leaf litter example. A correct
annotation would need to point to both a "leaf litter biome" class and a
"leaf litter material" class. It is really crucial not to confuse
material
entities in world with the roles they take on as instances of classes in
ENVO.
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
A "leaf litter biome" would, roughly, refer to the environmental system
that is determined by (~ must include) the community of organisms that have
adapted to the conditions in leaf litter. As noted above, there should be
some sort of evidence that this environment-specific adaptation occurred.
As a material, "leaf litter" is referring to some portion of 'stuff'
primarily composed of (but not necessarily limited to) fallen, dead or
dying plant material. As another example, when you use ENVO:water you
roughly mean "a volume of material primarily composed of H2O, but which is
likely to include stuff other than H2O found in some environment".
I'm not sure that leaf litter works as a feature as it doesn't seem to have
countable parts that would be called, e.g. "pieces of leaf litter" (does
it?). One would rather say "dead leaf" or "dead twig". As an alternative
example, "rock", as a mass noun, is a material, but a "piece of rock" can
be a feature.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Joel sachs wrote:
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap=""><!---->[...]
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">I have some concerns with these terms. As far as I can tell, no one
knows how to use these them.
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap=""><!---->[...]
I feel that creating interfaces for annotators to use ontologies without
delving too deeply into (the individual) ontology are sorely needed. Some
of us have discussed something like a GUI-based wizard to help people use
ENVO (gamifying it to increase 'uptake' and annotation accuracy), but
haven't had the time to put it together.
In the meantime, I can certainly help write more sets of annotation
guidelines for different communities (linking to them from the ENVO website
to show that there are multiple ways to use the ontology).
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Creating tripartite (biome/feature/material) decompositions of habitats
sometimes makes sense. Certainly, it made sense for some of the early
metagenomic assays that gave rise to ENVO. But it doesn't always make
sense, and there are often better ways to characterize an environment.
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap=""><!---->I
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">think it was a mistake for these terms to be made mandatory in
MIxS/MIMARKS.
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap=""><!---->
The main arguments for using the tripartite annotation (and its mandatory
status) were: 1) many of the better ways of describing environments (e.g.
hard data) were non-recoverable and 2) adding more than one term for each
of ENVO's main hierarchies would add too much to the already long
checklist. Even when other data is missing, there is usually enough
information around to compose a 'three-phase zoom in' (from biome to
material) on an entity's environment. This way, at least rough comparative
studies could be performed using an ontology (or, at the very least, a
controlled vocabulary). It's clear, however, that many MIxS report
submitters don't use ENVO very well, even after directed to the annotation
guidelines. Again, some sort of nifty annotation interface would probably
make this more successful.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">... I'd like to see our usage
guides differ from current ENVO/MIxS guidelines which mandate one and
only one value for each of the terms. "Environmental feature",
in particular, often merits multiple uses within the same record,
and I think disallowing such usage would impede uptake of the term
set. (As far as I can see from browsing metagenomic sampling metadata,
it *has* impeded uptake of the term set.)
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap=""><!---->ENVO's guidelines suggest that there should be *at least* one class from
each hierarchy used.
Indeed, multiple feature and material classes can and should be used to
fully characterise an entity's environment. There is certainly more than
one feature that is likely to exert a strong
causal influence on (i.e. determine) an entity's environment and all those
that are deemed relevant should all be recorded. Ideally, they would be
'ranked', but this requires some further thinking and implementation. For
materials, entities can be partially surrounded by multiple materials
(Chris' duck swimming in water example, for instance).
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">So I'm not necessarily opposed to the addition of these terms, but I do
wonder why we need them.
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap=""><!---->I think there are some good reasons to use some form of ontology in
annotations to enhance comparative power across granularities and shades of
meaning. Naturally, ontologies like ENVO are constantly developing and if
they don't meet a community's needs, there are usually ways to either
report and discuss issues (e.g.
<a class="moz-txt-link-freetext" href="https://github.com/EnvironmentOntology/envo/issues">https://github.com/EnvironmentOntology/envo/issues</a>) or become a
co-developer.
[...]
I hope this has helped rather clarify our thinking. As always, we're very
interested in insight (especially on our issue tracker) to help enhance the
usefulness of the ontology.
Best,
Pier
PS: For general interest, I'll be meeting some urban environment
specialists next week and intend to add more city-based environment classes
(e.g. "urban prairies" such as those proliferating in Detroit).
.
</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>
<a class="moz-txt-link-freetext" href="http://vanderbilt.edu/trees">http://vanderbilt.edu/trees</a>
</pre>
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