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Re: [tdwg-content] Darwin Core Proposal - environment terms (biome)
by Daniel Janzen 18 May '15

18 May '15

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(a)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(a)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(a)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_… >>> >>> [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 >>> >>> _______________________________________________ >>> tdwg-content mailing list >>> tdwg-content(a)lists.tdwg.org >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > 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(a)mpi-bremen.de >

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Darwin Core Proposal - environment terms (joel sachs)
by Ramona Walls 18 May '15

18 May '15

This is my first chance to reply to this thread, but I think several of Joel's comments need to be addressed. 1. re.: ENVO terms: "As far as I can tell, no one knows how to use these them." -- I know how to use them, and I know a community of people who know how to use them. True, that just like Darwin Core, they are often used incorrectly, but further documentation and outreach can help with that. 2. "There was a lot of confusion over whether particular aspects of an environment constituted an environmental feature, an environmental material, or a biome. The correct answer was often dependent on context. For example if a small mammal were found in leaf litter, then "leaf litter" would be the environmental material, and the biome would be "forest". But if a microbe were sampled from the same leaf litter, then "leaf litter" would be the biome, and I'm not sure what the environmental material would be." -- 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. -- Joel and I seem to remember outcomes of that RCN meeting quite differently (probably we were in different break-out groups). As I recall, the major problem was that people couldn't use ENVO because the classes they needed were not in there, not because they didn't know how. This is a problem that would actually be helped by DwC adopting ENVO, because it would create more users, and therefore more contributors to the ontology. Another major problem was that people often want to describe environments in terms of parameters like light level, salinity, temperature, etc. ENVO does not currently include classes like this, but a movement is underfoot to perhaps add such a branch to ENVO. 3. "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." -- True, there are cases when you cannot specify a biome, feature, and material for an organism, but usually you can provide at least one of two of them, which goes a long way toward standardizing environmental records and making large-scale queries possible. I have not yet seen a better way to classify environment on this scale. As I mentioned above, when it comes to describing environments in terms of their physico-chemical paramaters, ENVO does not serve, but that does not negate the utility of ENVO-style descriptions. Furthermore, as with most DwC terms, these are optional, and people/institutions who don't have to provide them if they are not relevant. 4. "The terms "env_biome", "env_feature", and "env_material" already exist in the MIxS Sample extension to Darwin Core (along with "submitted to INSDC", etc.). Why do they need to be moved into the core?" -- The main reason I can see is that they have a lot of applicability outside of MIXS, that is, for occurrences that do not have any sequences associated with them, and should not be hidden away in a place that suggests they can only be applied to sequence data. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden On Fri, Apr 24, 2015 at 3:00 AM, <tdwg-content-request(a)lists.tdwg.org> wrote: > Send tdwg-content mailing list submissions to > tdwg-content(a)lists.tdwg.org > > > > Today's Topics: > > 1. Re: Darwin Core Proposal - environment terms (joel sachs) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 23 Apr 2015 13:29:47 -0400 (EDT) > From: joel sachs <jsachs(a)csee.umbc.edu> > Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms > To: John Wieczorek <tuco(a)berkeley.edu> > Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> > Message-ID: > <Pine.LNX.4.64.1504231321240.18117(a)linuxserver1.cs.umbc.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > John, > > I have some concerns with these terms. As far as I can tell, no one knows > how to use these them. I was at a phenotype RCN meeting last year where > the theme was environmental ontologies. The attendees were pretty savvy in > terms of both ontologies, and environmental terminology. We were given an > overview of ENVO, and then, as an experiment, we broke into groups, and > each group tried to use ENVO to describe particular environments. I don't > recall any group being successful. There was a lot of confusion over > whether particular aspects of an environment constituted an environmental > feature, an environmental material, or a biome. The correct answer was > often dependent on context. For example if a small mammal were found in > leaf litter, then "leaf litter" would be the environmental material, and > the biome would be "forest". But if a microbe were sampled from the same > leaf litter, then "leaf litter" would be the biome, and I'm not sure what > the environmental material would be. > > Due to the confusion, Pier Luigi gave us a more in-depth tutorial when we > re-convened. We didnt break back out into groups, but I wish we had, > because I wonder if we would have had much more success. > > 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. > > But the question isn't "What should MIxS do four years ago?", but "What > should TDWG do now?". One wrinkle is that dwc:Habitat already > exists. Will it stay in the core? Is the idea to create usage guides that > explain when to use dwc:Habitat and when and how to use biome, feature, > and material? Such an approach could work, but 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.) > > So I'm not necessarily opposed to the addition of these terms, but I do > wonder why we need them. > > You wrote that "there is currently no possibility of a Darwin Core > PreservedSpecimen or MaterialSample record to meet the minimum > requirements of a Mimarks Specimen record[6], as there is currently no way > to share required environment terms." But MIMARKS specimen records are > also required to have the fields "Submitted to INSDC", > "Investigation-type", "Project name", "Nucleic acid sequence source", > "Target gene or locus", and "Sequencing method". So won't it still be the > case that there will be no possibility of a Darwin Core record being > MIMARKS compliant, without appropriate > augmentation? > > The terms "env_biome", "env_feature", and "env_material" already exist in > the MIxS Sample extension to Darwin Core (along with "submitted to INSDC", > etc.). Why do they need to be moved into the core? > > Cheers, > Joel. > > > > On Thu, 26 Mar 2015, John Wieczorek wrote: > > > Dear all, > > > > This message pertains to a proposal[1] set forth in September 2013 > > concerning the environment terms biome, environmentalFeature, and > > environmentalMaterial. I'm renewing the proposal because so much time has > > passed and the original proposal was not carried through to completion. > > There were no objections to the addition of those terms during the > initial > > public commentary. Discussion revolved around how the recommendations for > > how to populate them. > > > > The recommendations for all three terms will suggest using a controlled > > vocabulary such as ENVO. The examples will be based on the set of > > subclasses of the corresponding ENVO terms for biome[2], > > environmentalFeature[3], and environmentalMaterial[4]. As with all Darwin > > Core terms, the constraints on content are not part of the definition - > > they are only illustrative recommendations. > > > > The importance of these terms was recognized anew at a Darwin Core and > MIxS > > Hackathon in Florence in Sep 2014[5]. One important outcome of that > > workshop was the the realization that there is currently no possibility > of > > a Darwin Core PreservedSpecimen or MaterialSample record to meet the > > minimum requirements of a Mimarks Specimen record[6], as there is > currently > > no way to share required environment terms. This creates a huge and easy > to > > solve barrier to integration of data across the collection, sample, and > > sequence realms. > > > > This proposal is not substantively different from the one discussed in > > 2013. It differs from the final amended previous proposal in two ways, 1) > > only the three terms biome, environmentalFeature, and > environmentalMaterial > > are proposed here (the proposal to change to the term 'habitat' has been > > dropped), and 2) the term definitions have been updated to agree with > those > > in ENVO. The terms will be in the Darwin Core namespace (following the > TDWG > > community consensus in the previous discussion as well the consensus to > > coin the MaterialSample class in the Darwin Core namespace rather than > use > > obi:specimen, with the equivalency being made on the ontology side in > > BCO[7]). > > > > The complete definitions of the three proposed terms is given below the > > following references. This reopens the 30-day public commentary period > for > > the addition of new terms as described in the Darwin Core Namespace > > Policy[8]. > > > > [1] Original tdwg-content proposal for environment terms. > > http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html > > [2] ENVO biome. http://purl.obolibrary.org/obo/ENVO_00000428 > > [3] ENVO environmentalFeature. > http://purl.obolibrary.org/obo/ENVO_00002297 > > [4] ENVO environmentalMaterial. > http://purl.obolibrary.org/obo/ENVO_00010483 > > [5] DwC MIxS Meeting Notes. > > > https://docs.google.com/document/d/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw… > > [6] Table of the core items of Mimarks checklists. > > http://www.nature.com/nbt/journal/v29/n5/fig_tab/nbt.1823_T1.html > > [7] Biological Collections Ontology. https://github.com/tucotuco/bco > > [8] Darwin Core Namespace Policy. > > http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges > > > > > > Term Name: biome > > Identifier: http://rs.tdwg.org/dwc/terms/biome > > Namespace: http://rs.tdwg.org/dwc/terms/ > > Label: Biome > > Definition: An environmental system to which resident ecological > > communities have evolved adaptations. > > Comment: Recommended best practice is to use a controlled vocabulary such > > as defined by the biome class of the Environment Ontology (ENVO). > Examples: > > "flooded grassland biome", > > "http://purl.obolibrary.org/obo/ENVO_01000195". > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > Refines: > > Status: proposed > > Date Issued: 2013-09-26 > > Date Modified: 2015-03-26 > > Has Domain: > > Has Range: > > Refines: > > Version: biome-2015-03-26 > > Replaces: > > IsReplaceBy: > > Class: http://rs.tdwg.org/dwc/terms/Event > > ABCD 2.0.6: not in ABCD > > > > Term Name: environmentalFeature > > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature > > Namespace: http://rs.tdwg.org/dwc/terms/ > > Label: Environmental Feature > > Definition: A material entity which determines an environmental system. > > Comment: Recommended best practice is to use a controlled vocabulary such > > as defined by the environmental feature class of the Environment Ontology > > (ENVO). Examples: "meadow", > > "http://purl.obolibrary.org/obo/ENVO_00000108". > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > Refines: > > Status: proposed > > Date Issued: 2013-09-26 > > Date Modified: 2015-03-26 > > Has Domain: > > Has Range: > > Refines: > > Version: environmentalFeature-2015-03-26 > > Replaces: > > IsReplaceBy: > > Class: http://rs.tdwg.org/dwc/terms/Event > > ABCD 2.0.6: not in ABCD > > > > Term Name: environmentalMaterial > > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial > > Namespace: http://rs.tdwg.org/dwc/terms/ > > Label: Environmental Material > > Definition: A portion of environmental material is a fiat object which > > forms the medium or part of the medium of an environmental system. > > Comment: Recommended best practice is to use a controlled vocabulary such > > as defined by the environmental feature class of the Environment Ontology > > (ENVO). Examples: "scum", > > "http://purl.obolibrary.org/obo/ENVO_00003930". > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > Refines: > > Status: proposed > > Date Issued: 2013-09-26 > > Date Modified: 2015-03-26 > > Has Domain: > > Has Range: > > Refines: > > Version: environmentalMaterial-2015-03-26 > > Replaces: > > IsReplaceBy: > > Class: http://rs.tdwg.org/dwc/terms/Event > > ABCD 2.0.6: not in ABCD > > >

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Re: [tdwg-content] Darwin Core Proposal - environment terms (biome)
by Steve Baskauf 17 May '15

17 May '15

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_… [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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Fwd: Darwin Core Proposal - environment terms (biome)
by Ramona Walls 16 May '15

16 May '15

Forwarding Pier's response, because he is not on the TDWG list. Thanks, Pier! ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden ---------- Forwarded message ---------- From: Pier Luigi Buttigieg <pbuttigi(a)mpi-bremen.de> Date: Fri, May 15, 2015 at 7:51 PM Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms (biome) To: John Deck <jdeck88(a)gmail.com> Cc: Steve Baskauf <steve.baskauf(a)vanderbilt.edu>, Ramona Walls < rlwalls2008(a)gmail.com>, TDWG Content Mailing List < tdwg-content(a)lists.tdwg.org>, Suzanna Lewis <suzi(a)berkeleybop.org>, Chris Mungall <cjmungall(a)lbl.gov> Hi all, I've restricted my responses (in line, below) to the usage of ENVO classes as I can't really comment on DwC strategy. > John Deck 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).

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[Fwd: Re: Darwin Core Proposal - environment terms]
by Steve Baskauf 12 May '15

12 May '15

I have lost track of where we were on the public comment period on this proposal. I don't think that there was ever a declared end to to comment period, so I'm going to go ahead and make another comment. On 2015-03-27 I objected to this proposal on the basis that it was not clear how the terms would be used with literal and IRI values. Although the ratification of the DwC RDF Guide has not yet been formally announced, since it has been approved by the Executive Committee, I withdraw my objections to the proposed addition of the environment terms. Under the system outlined in the RDF guide, a term such as dwc:biome would be used with a string literal value, while the analogous term dwciri:biome would be used with an IRI value. Steve -------- Original Message -------- Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms Date: Fri, 27 Mar 2015 09:37:25 -0500 From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Organization: Vanderbilt University Dept. of Biological Sciences To: <tuco(a)berkeley.edu> CC: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> References: <CAHwKGGdu=qaC0SBdGqF95VvBCxwmk2zrgWAmYmux9vrL2ut71g(a)mail.gmail.com> <55155B13.3080602(a)vanderbilt.edu> Actually, let me be more blunt. I object to the adoption of these terms as currently proposed because the recommendation in the comment is not clear. I think that these three term adoption issues are blocked by the adoption of the RDF guide. If the RDF guide is accepted by the Executive, then there is default mechanism for addressing my issue: there will be dwc:biome, which would have a literal value and dwciri:biome, which would have a value that is an IRI. If the RDF guide is not accepted by the executive, then there needs to be some other solution, such as the Audubon Core mechanism: dwc:biome and dwc:biomeLiteral. I don't know what the holdup is on the RDF guide. It had jumped through every hoop required for adoption and was submitted for approval by the Executive on 2014-12-29. There is no reason why it should take three months for a decision on this. Steve Steve Baskauf wrote: > For clarification, each example shows one string value that is free > text and another that is an ENVO IRI. Does this mean that if a user > wants to indicate the ENVO class for flooded grassland biome that they > can chose to provide either the text label for the class or the IRI? > Or is the example showing free text intended to show how a user might > provide a value if they aren't following the recommended best > practice (i.e. using some system other than ENVO that doesn't have > IRIs)? It seems to me counterproductive to provide two choices. I > would rather see the recommendation be to provide an IRI unless one > isn't available. Otherwise, consumers will be stuck with having to > try to interpret what free text means. > > Alternatively, provide two terms: one intended for use with literal > names (i.e. free text) and one intended for use with IRIs. That > precedent has been set in Audubon Core (e.g. ac:provider and > ac:providerLiteral). In DwC we have the dwc: and dwciri: solution in > the RDF guide (which appears once again to be stuck in Executive > Committee limbo). In the Audubon Core case, this isn't really an RDF > issue since AC doesn't assume any particular representation and I > think you could have a spreadsheet with an IRI value for ac:provider. > I suppose it would be kosher to have dwciri:biome expressed as an IRI > in string form in a spreadsheet for people who don't care about RDF. > I don't think this has actually been discussed. > > Steve > > John Wieczorek wrote: >> >> >> Term Name: biome >> Identifier: http://rs.tdwg.org/dwc/terms/biome >> Namespace: http://rs.tdwg.org/dwc/terms/ >> Label: Biome >> Definition: An environmental system to which resident ecological >> communities have evolved adaptations. >> Comment: Recommended best practice is to use a controlled vocabulary >> such as defined by the biome class of the Environment Ontology >> (ENVO). Examples: "flooded grassland biome", >> "http://purl.obolibrary.org/obo/ENVO_01000195". >> Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2013-09-26 >> Date Modified: 2015-03-26 >> Has Domain: >> Has Range: >> Refines: >> Version: biome-2015-03-26 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD >> >> Term Name: environmentalFeature >> Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature >> Namespace: http://rs.tdwg.org/dwc/terms/ >> Label: Environmental Feature >> Definition: A material entity which determines an environmental system. >> Comment: Recommended best practice is to use a controlled vocabulary >> such as defined by the environmental feature class of the Environment >> Ontology (ENVO). Examples: "meadow", >> "http://purl.obolibrary.org/obo/ENVO_00000108". >> Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2013-09-26 >> Date Modified: 2015-03-26 >> Has Domain: >> Has Range: >> Refines: >> Version: environmentalFeature-2015-03-26 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD >> >> Term Name: environmentalMaterial >> Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial >> Namespace: http://rs.tdwg.org/dwc/terms/ >> Label: Environmental Material >> Definition: A portion of environmental material is a fiat object >> which forms the medium or part of the medium of an environmental system. >> Comment: Recommended best practice is to use a controlled vocabulary >> such as defined by the environmental feature class of the Environment >> Ontology (ENVO). Examples: "scum", >> "http://purl.obolibrary.org/obo/ENVO_00003930". >> Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2013-09-26 >> Date Modified: 2015-03-26 >> Has Domain: >> Has Range: >> Refines: >> Version: environmentalMaterial-2015-03-26 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD > > -- > 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 > > -- 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 -- 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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Postdoctoral fellow in Computable Semantics for the Tree of Life
by Cellinese,Nico 04 May '15

04 May '15

A Postdoctoral position is available to work with Hilmar Lapp and Nico Cellinese on building phyloreferences for the Tree of Life. All details can be found here: http://www.flmnh.ufl.edu/museum-voices/cellinese-lab/2015/05/03/postdoctora… Spread the word so we can start having fun asap. Thanks! Nico <><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Associate Curator, Botany & Informatics Joint Associate Professor, Department of Biology University of Florida Florida Museum of Natural History 354 Dickinson Hall, 1659 Museum Rd. Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://www.flmnh.ufl.edu/museum-voices/nico-cellinese/ Twitter @ncellinese _______________________________________________ tdwg-phylo mailing list tdwg-phylo(a)lists.tdwg.org<mailto:tdwg-phylo@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

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Recap - Darwin Core Standard - proposed changes in governance
by John Wieczorek 23 Apr '15

23 Apr '15

Dear all, There has been consistent agreement (though I would hesitate to say consensus prematurely) about some aspects of the proposal to redefine which documents comprise the Darwin Core standard. The discussion has been fruitful and appreciated. Yet, I believe we are at an impasse in terms of implementing the proposed changes because a) I have not followed the correct process so far, and b) the interim TDWG Standards Process that are supposed to govern the process is not amenable to the changes that were proposed. I'll try to explain briefly. The proposal was to redefine which documents comprise the Darwin Core standard, not to make additions or changes to the Darwin Core terms, The latter would fall under Darwin Core's "internal" namespace policy[1]. Instead, this proposal is a change to the structure as well as documentary content of the standard as a whole, which falls under the interim TDWG Standards Documentation Specification[2], as Steve Baskauf pointed out[3]. To fulfill those requirements is an onerous task (my heartfelt pity for those who have had to go through it) - too onerous, I believe, for what we are trying to accomplish here, which is to change an existing standard (indeed, make it easier to manage) rather than create a new one. We are not allowed to do that according to the interim TDWG Standards Documentation Specification, which states, "Once a standard has been ratified it cannot be changed in any substantive way; it must be superseded by a standard with a different name." All question of versioning aside, we would have to follow the process of creating a new standard. Unless there is a way to get an Executive override of the interim process standard in order to allow us to make the proposed changes and liberate Darwin Core to evolve more effectively, I think we have to wait for the overhaul of the Standards Documentation Specification. The Task Group Charter to do that work has been submitted, but the results are not slated to be fully realized until 1 Jan 2016. This is unfortunate, as it leaves a huge body of work to refactor Darwin Core and its management [4] unrealizable in an official capacity. Ideas welcome. Cheers, John [1] Darwin Core Namespace Policy. http://rs.tdwg.org/dwc/terms/namespace/index.htm [2] TDWG Standards Documentation Specification. http://www.tdwg.org/standards/147/ [3] tdwg-content email from Steve Baskauf. http://lists.tdwg.org/pipermail/tdwg-content/2015-January/003429.html [4] Github branch of Darwin Core repository for streamlined management.

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Darwin Core Proposal - environment terms
by John Wieczorek 23 Apr '15

23 Apr '15

Dear all, This message pertains to a proposal[1] set forth in September 2013 concerning the environment terms biome, environmentalFeature, and environmentalMaterial. I'm renewing the proposal because so much time has passed and the original proposal was not carried through to completion. There were no objections to the addition of those terms during the initial public commentary. Discussion revolved around how the recommendations for how to populate them. The recommendations for all three terms will suggest using a controlled vocabulary such as ENVO. The examples will be based on the set of subclasses of the corresponding ENVO terms for biome[2], environmentalFeature[3], and environmentalMaterial[4]. As with all Darwin Core terms, the constraints on content are not part of the definition - they are only illustrative recommendations. The importance of these terms was recognized anew at a Darwin Core and MIxS Hackathon in Florence in Sep 2014[5]. One important outcome of that workshop was the the realization that there is currently no possibility of a Darwin Core PreservedSpecimen or MaterialSample record to meet the minimum requirements of a Mimarks Specimen record[6], as there is currently no way to share required environment terms. This creates a huge and easy to solve barrier to integration of data across the collection, sample, and sequence realms. This proposal is not substantively different from the one discussed in 2013. It differs from the final amended previous proposal in two ways, 1) only the three terms biome, environmentalFeature, and environmentalMaterial are proposed here (the proposal to change to the term 'habitat' has been dropped), and 2) the term definitions have been updated to agree with those in ENVO. The terms will be in the Darwin Core namespace (following the TDWG community consensus in the previous discussion as well the consensus to coin the MaterialSample class in the Darwin Core namespace rather than use obi:specimen, with the equivalency being made on the ontology side in BCO[7]). The complete definitions of the three proposed terms is given below the following references. This reopens the 30-day public commentary period for the addition of new terms as described in the Darwin Core Namespace Policy[8]. [1] Original tdwg-content proposal for environment terms. http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html [2] ENVO biome. http://purl.obolibrary.org/obo/ENVO_00000428 [3] ENVO environmentalFeature. http://purl.obolibrary.org/obo/ENVO_00002297 [4] ENVO environmentalMaterial. http://purl.obolibrary.org/obo/ENVO_00010483 [5] DwC MIxS Meeting Notes. https://docs.google.com/document/d/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw… [6] Table of the core items of Mimarks checklists. http://www.nature.com/nbt/journal/v29/n5/fig_tab/nbt.1823_T1.html [7] Biological Collections Ontology. https://github.com/tucotuco/bco [8] Darwin Core Namespace Policy. http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges Term Name: biome Identifier: http://rs.tdwg.org/dwc/terms/biome Namespace: http://rs.tdwg.org/dwc/terms/ Label: Biome Definition: An environmental system to which resident ecological communities have evolved adaptations. Comment: Recommended best practice is to use a controlled vocabulary such as defined by the biome class of the Environment Ontology (ENVO). Examples: "flooded grassland biome", "http://purl.obolibrary.org/obo/ENVO_01000195". Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2015-03-26 Has Domain: Has Range: Refines: Version: biome-2015-03-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD Term Name: environmentalFeature Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Feature Definition: A material entity which determines an environmental system. Comment: Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2015-03-26 Has Domain: Has Range: Refines: Version: environmentalFeature-2015-03-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD Term Name: environmentalMaterial Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Material Definition: A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. Comment: Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Examples: "scum", "http://purl.obolibrary.org/obo/ENVO_00003930". Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2015-03-26 Has Domain: Has Range: Refines: Version: environmentalMaterial-2015-03-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD

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Darwin Core and phylogenies
by Roderic Page 16 Apr '15

16 Apr '15

My apologies in advance if this has come up before. Historically it seems that phylogenetics and classical biodiversity informatics live in separate worlds, for a bunch of reasons. One area they clearly intersect though is “phylogeography” or “geophylogenies”. I’ve been playing simple ways to create and visualise geophylogenies (e.g., http://iphylo.blogspot.co.uk/2015/01/geojson-and-geophylogenies.html ) and it occurs to me that it might be useful to have a Darwin Core-style way of encoding these. Phylogenetic data is typically stored very differently from the simple row-based approach adopted by Darwin Core (e.g., NEXUS format, XML [yuck], or JSON [sometimes yucky if it’s full of XML-style baggage, but I digress]). This makes it a challenge to integrate phylogenetic data with projects such as GBIF. This lack of integration is regrettable, anyone looking at the rise of phylogeography and DNA barcoding will recognise that many classically-defined species are poor representations of actual biodiversity, even in taxa that we think we know quite well (e.g., vertebrates). Given that we can encode a phylogenetic tree as a set of rows, each one representing an edge in the tree (what those of a certain age would call and "ancestor function”), it would be easy to have a Darwin Core extension that had one row per node in the tree, optionally with branch lengths, and leaf nodes also labelled by occurrence id (the same id used in the standard occurrence table, where ideally most if not all would be georeferenced). In this way we could add geophylogenies to Darwin Core archives, and existing tools for importing these (e.g., GBIF) could simply ignore the phylogeny until such times as they can handle them, but other tools could read the trees and display them. Is anyone doing something along these lines? Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: Roderic.Page(a)glasgow.ac.uk<mailto:Roderic.Page@glasgow.ac.uk> Tel: +44 141 330 4778 Skype: rdmpage Facebook: http://www.facebook.com/rdmpage LinkedIn: http://uk.linkedin.com/in/rdmpage Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com ORCID: http://orcid.org/0000-0002-7101-9767 Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ ResearchGate https://www.researchgate.net/profile/Roderic_Page

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Re: [tdwg-content] Problem when validating Simple Darwin Core Recordset file
by Mergen Patricia 15 Apr '15

15 Apr '15

Dear Martin Thanks for your mail. I forward your mail to the experts list who may advice further. With my best wishes Pat Le 5 Avr. 2015 08:20, "Seifert-Martin" <Seifert-Martin(a)t-online.de> a écrit : > Dear Madam or Sir, > > when validating a Simple Darwin Core Recordset file I get the following > error messages: > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd, line 100, column 71: > Cannot resolve the name 'dwc:sampleSizeValue' to a(n) 'element > declaration' component. > <xs:element ref="dwc:sampleSizeValue" minOccurs="0"/> > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd, line 101, column > 70: > Cannot resolve the name 'dwc:sampleSizeUnit' to a(n) 'element declaration' > component. > <xs:element ref="dwc:sampleSizeUnit" minOccurs="0"/> > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwcterms.xsd, line 206, column 67: > Cannot resolve the name 'dwc:sampleSizeValue' to a(n) 'element > declaration' component. > <xs:element ref="dwc:sampleSizeValue" minOccurs="0"/> > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwcterms.xsd, line 207, column 66: > Cannot resolve the name 'dwc:sampleSizeUnit' to a(n) 'element declaration' > component. > <xs:element ref="dwc:sampleSizeUnit" minOccurs="0"/> > > Please, would you forward this e-mail to one of your technicians. > > Kind regards, > Martin Seifert > >

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