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

Daniel Janzen djanzen at sas.upenn.edu
Tue May 19 00:07:05 CEST 2015 

Pier, yes please you put this wherever it might be useful to anyone.  I am drowning.

Dan Janzen


On May 18, 2015, at 3:59 PM, Pier Luigi Buttigieg <pbuttigi at mpi-bremen.de> wrote:

> @Dan,
> Thanks for the feedback. Could you add this as an issue on our tracker?
> https://github.com/EnvironmentOntology/envo/issues
> Copy-pasting your text would be great (if you don't have and don't wish to
> create a github account, I could post it on your behalf).
> At the very least, we (the ENVO editors) should add a comment to this class
> reflecting these concerns. 
> 
> @Steve,
> Thanks for your thinking on this. I suppose there's an element of
> historical intertia here, and a relabelling is probably wise. Would it
> possible to post this to our issue tracker?
> 
> On Sun, 17 May 2015 16:46:00 -0600, Daniel Janzen <djanzen at sas.upenn.edu>
> wrote:
>> 17 May 2015
>> 
>> Folks, you are inserting "evolution" in a definition that has never had
>> one.  Worse, frankly, you have zero way of really knowing if a species in
>> hand evolved in or in response to the place where you are finding it. 
> And
>> evolved what?  MANY species arrive in this or that ecosystem under their
>> own steam, and simply "ecologically fit" into them according to their own
>> traits, with no evolution involved.   Introduce the agouti into Africa
>> without telling anyone and all future biologists will tell you that it is
>> highly evolved as a seed disperser for African rain forest trees (just as
>> people tell you today for the neotropics), which will be absolute
> nonsense.
>> It may of course evolve further once it has arrived somewhere, but it
>> certainly need not, and you (and I) have no way of knowing if it has. 
> And
>> furthermore, what particular trait are you thinking you can evaluate as
>> "evolved" at your site (and not elsewhere) and just how many of them need
>> there be, visible or invisible (to Homo sapiens) before it is "evolved"
> in
>> that ecosystem (or biome if you like)?  P.S.  Note that the "biome"
>> terminology is a peculiar mutant of extra-tropical northern biologists,
> and
>> "ecosystem" has vastly more geographic and social coverage around the
>> globe.
>> 
>> For whatever.  Not able or willing to enter into some massive discussion
> of
>> all this.  Just tossing this on the table in case it fits somewhere,
> since
>> it appears to me, as a lurker, that it has not been.
>> 
>> Dan Janzen
>> 
>> 
>> On May 17, 2015, at 4:13 PM, Steve Baskauf <steve.baskauf at vanderbilt.edu>
>> wrote:
>> 
>>> 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].
>>> 
>>> Steve
>>> 
>>> [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."
>>> 
> http://wwf.panda.org/about_our_earth/teacher_resources/webfieldtrips/major_biomes/
>>> 
>>> [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
>>>>>>> MIxS/MIMARKS.
>>>>>>> 
>>>> 
>>>> 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
>>> 
>>> 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.
>>> http://bioimages.vanderbilt.edu
>>> http://vanderbilt.edu/trees
>>> 
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> 
> -- 
> Dr. Pier Luigi Buttigieg
> HGF-MPG Group for Deep Sea Ecology and Technology
> Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung
> c/o Max Planck Institute for Marine Microbiology
> Celsiusstrasse 1, 28359 Bremen, Germany
> Tel: +49 421 2028 984
> Email: pbuttigi at mpi-bremen.de
>

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