[tdwg-content] Darwin Core Proposal - environment terms (biome)

Steve Baskauf steve.baskauf at vanderbilt.edu
Mon May 18 00:13:14 CEST 2015

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. 

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".

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].


[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. " 

[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."

[3] http://islandpress.org/terrestrial-ecoregions-north-america

Pier Luigi Buttigieg wrote:
>> The ENVO definition of biome is : "A biome is an environmental system to
>> which resident ecological communities have evolved adaptations." (http://purl.obolibrary.org/obo/ENVO_00000428)
> 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).
>> A resident ecological community from the perspective of a microbe likely
>> does not care about the large-scale plant and animal communities, so it
> is
>> 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.
> [...]
>>> 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". 
> [...]
>>> 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.
> 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
> (http://www.environmentontology.org/annotation-guidelines) 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.
>>> Ramona Walls wrote:
> [...]
>>>  -- 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
> same
>>> 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
> two
>>> 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.
> 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.
>>>> Joel sachs wrote:
> [...]
>>>> I have some concerns with these terms. As far as I can tell, no one
>>>> knows how to use these them. 
> [...]
> 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). 
>>>> 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.
> I
>>>> think it was a mistake for these terms to be made mandatory in
> 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.
>>>> ... 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.)
> 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).
>>>> So I'm not necessarily opposed to the addition of these terms, but I do
>>>> wonder why we need them.
> 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.
> https://github.com/EnvironmentOntology/envo/issues) 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).
> .

Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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