<div dir="ltr"><div>Forwarding Pier's response, because he is not on the TDWG list.<br><br></div>Thanks, Pier!<br clear="all"><div><div><div><div class="gmail_signature"><div dir="ltr">------------------------------------------------------<br>Ramona L. Walls, Ph.D.<br>Scientific Analyst, The iPlant Collaborative, University of Arizona<br>Research Associate, Bio5 Institute, University of Arizona<br>Laboratory Research Associate, New York Botanical Garden</div></div></div>
<br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Pier Luigi Buttigieg</b> <span dir="ltr"><<a href="mailto:pbuttigi@mpi-bremen.de">pbuttigi@mpi-bremen.de</a>></span><br>Date: Fri, May 15, 2015 at 7:51 PM<br>Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms (biome)<br>To: John Deck <<a href="mailto:jdeck88@gmail.com">jdeck88@gmail.com</a>><br>Cc: Steve Baskauf <<a href="mailto:steve.baskauf@vanderbilt.edu">steve.baskauf@vanderbilt.edu</a>>, Ramona Walls <<a href="mailto:rlwalls2008@gmail.com">rlwalls2008@gmail.com</a>>, TDWG Content Mailing List <<a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>>, Suzanna Lewis <<a href="mailto:suzi@berkeleybop.org">suzi@berkeleybop.org</a>>, Chris Mungall <<a href="mailto:cjmungall@lbl.gov">cjmungall@lbl.gov</a>><br><br><br>Hi all,<br>
<br>
I've restricted my responses (in line, below) to the usage of ENVO classes<br>
as I can't really comment on DwC strategy.<br>
<br>
> John Deck wrote:<br>
[...]<br>
<span class="">> The ENVO definition of biome is : "A biome is an environmental system to<br>
> which resident ecological communities have evolved adaptations." (<br>
> <a href="http://purl.obolibrary.org/obo/ENVO_00000428" target="_blank">http://purl.obolibrary.org/obo/ENVO_00000428</a>)<br>
<br>
</span>We try to be agnostic to spatial scale with this definition as we<br>
encountered numerous instances of the term being used outside of<br>
'classical' biome classification systems with reasonable rationale (e.g.<br>
many environments - such as marine and lacustrine environments - are not<br>
adequately covered by existing schemes). Even within classical systems,<br>
identifying the scale threshold is hardly precise (if anyone knows of<br>
anything that defines this, please let me know) and definitions are revised<br>
from time to time as new technologies (e.g. remote sensing) emerge. Some<br>
have suggested using prevailing climate as a way to stabilise 'large'<br>
scales, but this is problematic as microclimates (e.g. near large water<br>
bodies) can result in the emergence of different biomes (in the classical<br>
sense) existing at comparatively small regions. The presence of an<br>
ecological community which has adapted to a given environment seems to be<br>
the common theme. A successful, in situ adaptation process indicates that<br>
the environment a) can sustain viable populations over multiple generations<br>
and b) persists long enough for these populations to undergo evolutionarily<br>
consequential changes, distinguishing it from other environment types. If<br>
users wish to use a 'classical' biome type, they have access to an adapted<br>
version of the WWF classification (see below).<br>
<span class=""><br>
> A resident ecological community from the perspective of a microbe likely<br>
> does not care about the large-scale plant and animal communities, so it<br>
is<br>
> a matter of perspective taken from the point of view of the subject. To<br>
> that end, leaf litter as the biome seems entirely reasonable if the<br>
> microbes resident there have evolved adaptations to leaf litter.<br>
</span>[...]<br>
<span class="">>> Steve Baskauf wrote:<br>
>> I haven't looked at the definition given to "biome" in ENVO, but based<br>
>> on what I believe is the common consensus on what a biome is (a major,<br>
>> large-scale set of plant and animal communities occupying a geographic<br>
>> region), it doesn't seem right to apply that term to "leaf litter".<br>
</span>[...]<br>
<span class="">>> There are a number of standard lists of the world's biomes and they<br>
>> include large-scale regions like "temperate deciduous forest", not<br>
>> small-scale features.<br>
<br>
</span>ENVO includes a representation of the WWF biome classification system. At<br>
one stage, the Udvardy, WWF, and Bailey systems were all in ENVO (which was<br>
quite confusing). We opted to use the WWF system (obsoleting the other<br>
classes) as it was the most current and had the highest global coverage.<br>
The WWF categories were modified to make them more suitable for an ontology<br>
(e.g. compound classes were split).<br>
<br>
As a microbial ecologist, I think that the position outlined by John is a<br>
valid one. The scales used in the 'classical' definition are, ultimately, a<br>
function of our own observational capacities and various forms of ecosystem<br>
can be nested across scales. However, Steve's right in saying that this is<br>
a fairly profound change in the usage of a well-established term (with a<br>
substantial literature base behind it). Further, just because a microbial<br>
ecologist (or anyone else, but I'm going with this example) declares<br>
something to be a biome, doesn't make it so: the communities of microbes<br>
living in leaf litter may not have evolved in that particular environment,<br>
they may simply have adaptations to other environments that allow them to<br>
colonise a one with sufficient similarities.<br>
<br>
In our annotation guidelines<br>
(<a href="http://www.environmentontology.org/annotation-guidelines" target="_blank">http://www.environmentontology.org/annotation-guidelines</a>) we do ask that<br>
such "small scale" biomes are requested with reference to some form of<br>
empirical data supporting the notion that the communities have adapted to<br>
that particular environment. ENVO doesn't try to dictate what is "right"<br>
here, but attempts to represent how different communities (who are creating<br>
new conventions which reflect their phenomena they study) are talking about<br>
environments. Whether they turn out to be correct in their usage of a given<br>
term is a somewhat different question and we're always happy to receive<br>
critiques and input.<br>
<br>
I think it's best if we declare or produce subset of biome classes that are<br>
approved by a certain body (e.g. the WWF). Conversely, classes that are<br>
somehow 'nascent' or 'experimental' can also be marked. Plans to produce<br>
subsets of ENVO that are relevant to specific working bodies are already<br>
queued.<br>
<br>
>> Ramona Walls wrote:<br>
>><br>
[...]<br>
<span class="">>> -- ENVO very clearly distinguishes between a biome, a feature, and a<br>
>> material. It is never the case that the same ENVO class can be use as<br>
>> both a biome and a feature or a feature and a material. Although the<br>
same<br>
>> entity, depending on its role, may serve as either a biome or material<br>
>> (or feature for that matter), in that case, it would be an instance of<br>
two<br>
>> different classes in ENVO. Take the leaf litter example. A correct<br>
>> annotation would need to point to both a "leaf litter biome" class and a<br>
>> "leaf litter material" class. It is really crucial not to confuse<br>
>> material<br>
>> entities in world with the roles they take on as instances of classes in<br>
>> ENVO.<br>
<br>
</span>A "leaf litter biome" would, roughly, refer to the environmental system<br>
that is determined by (~ must include) the community of organisms that have<br>
adapted to the conditions in leaf litter. As noted above, there should be<br>
some sort of evidence that this environment-specific adaptation occurred.<br>
<br>
As a material, "leaf litter" is referring to some portion of 'stuff'<br>
primarily composed of (but not necessarily limited to) fallen, dead or<br>
dying plant material. As another example, when you use ENVO:water you<br>
roughly mean "a volume of material primarily composed of H2O, but which is<br>
likely to include stuff other than H2O found in some environment".<br>
<br>
I'm not sure that leaf litter works as a feature as it doesn't seem to have<br>
countable parts that would be called, e.g. "pieces of leaf litter" (does<br>
it?). One would rather say "dead leaf" or "dead twig". As an alternative<br>
example, "rock", as a mass noun, is a material, but a "piece of rock" can<br>
be a feature.<br>
<br>
>>> Joel sachs wrote:<br>
[...]<br>
<span class="">>>> I have some concerns with these terms. As far as I can tell, no one<br>
>>> knows how to use these them.<br>
</span>[...]<br>
<br>
I feel that creating interfaces for annotators to use ontologies without<br>
delving too deeply into (the individual) ontology are sorely needed. Some<br>
of us have discussed something like a GUI-based wizard to help people use<br>
ENVO (gamifying it to increase 'uptake' and annotation accuracy), but<br>
haven't had the time to put it together.<br>
In the meantime, I can certainly help write more sets of annotation<br>
guidelines for different communities (linking to them from the ENVO website<br>
to show that there are multiple ways to use the ontology).<br>
<span class=""><br>
>>> Creating tripartite (biome/feature/material) decompositions of habitats<br>
>>> sometimes makes sense. Certainly, it made sense for some of the early<br>
>>> metagenomic assays that gave rise to ENVO. But it doesn't always make<br>
>>> sense, and there are often better ways to characterize an environment.<br>
I<br>
>>> think it was a mistake for these terms to be made mandatory in<br>
>>> MIxS/MIMARKS.<br>
<br>
</span>The main arguments for using the tripartite annotation (and its mandatory<br>
status) were: 1) many of the better ways of describing environments (e.g.<br>
hard data) were non-recoverable and 2) adding more than one term for each<br>
of ENVO's main hierarchies would add too much to the already long<br>
checklist. Even when other data is missing, there is usually enough<br>
information around to compose a 'three-phase zoom in' (from biome to<br>
material) on an entity's environment. This way, at least rough comparative<br>
studies could be performed using an ontology (or, at the very least, a<br>
controlled vocabulary). It's clear, however, that many MIxS report<br>
submitters don't use ENVO very well, even after directed to the annotation<br>
guidelines. Again, some sort of nifty annotation interface would probably<br>
make this more successful.<br>
<br>
>>> ... I'd like to see our usage<br>
<span class="">>>> guides differ from current ENVO/MIxS guidelines which mandate one and<br>
>>> only one value for each of the terms. "Environmental feature",<br>
>>> in particular, often merits multiple uses within the same record,<br>
>>> and I think disallowing such usage would impede uptake of the term<br>
>>> set. (As far as I can see from browsing metagenomic sampling metadata,<br>
>>> it *has* impeded uptake of the term set.)<br>
</span>ENVO's guidelines suggest that there should be *at least* one class from<br>
each hierarchy used.<br>
Indeed, multiple feature and material classes can and should be used to<br>
fully characterise an entity's environment. There is certainly more than<br>
one feature that is likely to exert a strong<br>
causal influence on (i.e. determine) an entity's environment and all those<br>
that are deemed relevant should all be recorded. Ideally, they would be<br>
'ranked', but this requires some further thinking and implementation. For<br>
materials, entities can be partially surrounded by multiple materials<br>
(Chris' duck swimming in water example, for instance).<br>
<span class=""><br>
>>> So I'm not necessarily opposed to the addition of these terms, but I do<br>
>>> wonder why we need them.<br>
</span>I think there are some good reasons to use some form of ontology in<br>
annotations to enhance comparative power across granularities and shades of<br>
meaning. Naturally, ontologies like ENVO are constantly developing and if<br>
they don't meet a community's needs, there are usually ways to either<br>
report and discuss issues (e.g.<br>
<a href="https://github.com/EnvironmentOntology/envo/issues" target="_blank">https://github.com/EnvironmentOntology/envo/issues</a>) or become a<br>
co-developer.<br>
[...]<br>
<br>
I hope this has helped rather clarify our thinking. As always, we're very<br>
interested in insight (especially on our issue tracker) to help enhance the<br>
usefulness of the ontology.<br>
Best,<br>
Pier<br>
<br>
PS: For general interest, I'll be meeting some urban environment<br>
specialists next week and intend to add more city-based environment classes<br>
(e.g. "urban prairies" such as those proliferating in Detroit).<br>
</div><br></div></div></div>