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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.<br>
<br>
Ramona Walls wrote:
<blockquote
cite="mid:CAJYF1k5KuUwe1xQPiadTtVn-T6LJJ1F3_aY6Uu8HGQzqU+H10g@mail.gmail.com"
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<div dir="ltr">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<br>
the biome would be "forest". But if a microbe were sampled from the same<br>
leaf litter, then "leaf litter" would be the biome, and I'm not sure
what the environmental material would be." <br>
-- 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.
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<div class="gmail_extra">
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<div dir="ltr">------------------------------------------------------<br>
Ramona L. Walls, Ph.D.<br>
Scientific Analyst, The iPlant Collaborative, University of Arizona<br>
Research Associate, Bio5 Institute, University of Arizona<br>
Laboratory Research Associate, New York Botanical Garden</div>
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<div class="gmail_quote">On Fri, Apr 24, 2015 at 3:00 AM, <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:tdwg-content-request@lists.tdwg.org" target="_blank">tdwg-content-request@lists.tdwg.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
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tdwg-content mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Darwin Core Proposal - environment terms (joel sachs)<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 23 Apr 2015 13:29:47 -0400 (EDT)<br>
From: joel sachs <<a moz-do-not-send="true"
href="mailto:jsachs@csee.umbc.edu">jsachs@csee.umbc.edu</a>><br>
Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms<br>
To: John Wieczorek <<a moz-do-not-send="true"
href="mailto:tuco@berkeley.edu">tuco@berkeley.edu</a>><br>
Cc: TDWG Content Mailing List <<a moz-do-not-send="true"
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Message-ID:<br>
<<a moz-do-not-send="true"
href="mailto:Pine.LNX.4.64.1504231321240.18117@linuxserver1.cs.umbc.edu">Pine.LNX.4.64.1504231321240.18117@linuxserver1.cs.umbc.edu</a>><br>
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<br>
John,<br>
<br>
I have some concerns with these terms. As far as I can tell, no one
knows<br>
how to use these them. I was at a phenotype RCN meeting last year where<br>
the theme was environmental ontologies. The attendees were pretty savvy
in<br>
terms of both ontologies, and environmental terminology. We were given
an<br>
overview of ENVO, and then, as an experiment, we broke into groups, and<br>
each group tried to use ENVO to describe particular environments. I
don't<br>
recall any group being successful. There was a lot of confusion over<br>
whether particular aspects of an environment constituted an
environmental<br>
feature, an environmental material, or a biome. The correct answer was<br>
often dependent on context. For example if a small mammal were found in<br>
leaf litter, then "leaf litter" would be the environmental material, and<br>
the biome would be "forest". But if a microbe were sampled from the same<br>
leaf litter, then "leaf litter" would be the biome, and I'm not sure
what<br>
the environmental material would be.<br>
<br>
Due to the confusion, Pier Luigi gave us a more in-depth tutorial when
we<br>
re-convened. We didnt break back out into groups, but I wish we had,<br>
because I wonder if we would have had much more success.<br>
<br>
Creating tripartite (biome/feature/material) decompositions of habitats<br>
sometimes makes sense. Certainly, it made sense for some of the early<br>
metagenomic assays that gave rise to ENVO. But it doesn't always make<br>
sense, and there are often better ways to characterize an environment. I<br>
think it was a mistake for these terms to be made mandatory in<br>
MIxS/MIMARKS.<br>
<br>
But the question isn't "What should MIxS do four years ago?", but "What<br>
should TDWG do now?". One wrinkle is that dwc:Habitat already<br>
exists. Will it stay in the core? Is the idea to create usage guides
that<br>
explain when to use dwc:Habitat and when and how to use biome, feature,<br>
and material? Such an approach could work, but I'd like to see our usage<br>
guides differ from current ENVO/MIxS guidelines which mandate one and
only<br>
one value for each of the terms. "Environmental feature", in particular,<br>
often merits multiple uses within the same record, and I think
disallowing<br>
such usage would impede uptake of the term set. (As far as I can see<br>
from browsing metagenomic sampling metadata, it *has* impeded uptake of
the term set.)<br>
<br>
So I'm not necessarily opposed to the addition of these terms, but I do<br>
wonder why we need them.<br>
<br>
You wrote that "there is currently no possibility of a Darwin Core<br>
PreservedSpecimen or MaterialSample record to meet the minimum<br>
requirements of a Mimarks Specimen record[6], as there is currently no
way<br>
to share required environment terms." But MIMARKS specimen records are<br>
also required to have the fields "Submitted to INSDC",<br>
"Investigation-type", "Project name", "Nucleic acid sequence source",<br>
"Target gene or locus", and "Sequencing method". So won't it still be
the<br>
case that there will be no possibility of a Darwin Core record being
MIMARKS compliant, without appropriate<br>
augmentation?<br>
<br>
The terms "env_biome", "env_feature", and "env_material" already exist
in<br>
the MIxS Sample extension to Darwin Core (along with "submitted to
INSDC",<br>
etc.). Why do they need to be moved into the core?<br>
<br>
Cheers,<br>
Joel.<br>
<br>
<br>
<br>
On Thu, 26 Mar 2015, John Wieczorek wrote:<br>
<br>
> Dear all,<br>
><br>
> This message pertains to a proposal[1] set forth in September 2013<br>
> concerning the environment terms biome, environmentalFeature, and<br>
> environmentalMaterial. I'm renewing the proposal because so much
time has<br>
> passed and the original proposal was not carried through to
completion.<br>
> There were no objections to the addition of those terms during the
initial<br>
> public commentary. Discussion revolved around how the
recommendations for<br>
> how to populate them.<br>
><br>
> The recommendations for all three terms will suggest using a
controlled<br>
> vocabulary such as ENVO. The examples will be based on the set of<br>
> subclasses of the corresponding ENVO terms for biome[2],<br>
> environmentalFeature[3], and environmentalMaterial[4]. As with all
Darwin<br>
> Core terms, the constraints on content are not part of the
definition -<br>
> they are only illustrative recommendations.<br>
><br>
> The importance of these terms was recognized anew at a Darwin Core
and MIxS<br>
> Hackathon in Florence in Sep 2014[5]. One important outcome of that<br>
> workshop was the the realization that there is currently no
possibility of<br>
> a Darwin Core PreservedSpecimen or MaterialSample record to meet
the<br>
> minimum requirements of a Mimarks Specimen record[6], as there is
currently<br>
> no way to share required environment terms. This creates a huge
and easy to<br>
> solve barrier to integration of data across the collection,
sample, and<br>
> sequence realms.<br>
><br>
> This proposal is not substantively different from the one
discussed in<br>
> 2013. It differs from the final amended previous proposal in two
ways, 1)<br>
> only the three terms biome, environmentalFeature, and
environmentalMaterial<br>
> are proposed here (the proposal to change to the term 'habitat'
has been<br>
> dropped), and 2) the term definitions have been updated to agree
with those<br>
> in ENVO. The terms will be in the Darwin Core namespace (following
the TDWG<br>
> community consensus in the previous discussion as well the
consensus to<br>
> coin the MaterialSample class in the Darwin Core namespace rather
than use<br>
> obi:specimen, with the equivalency being made on the ontology side
in<br>
> BCO[7]).<br>
><br>
> The complete definitions of the three proposed terms is given
below the<br>
> following references. This reopens the 30-day public commentary
period for<br>
> the addition of new terms as described in the Darwin Core Namespace<br>
> Policy[8].<br>
><br>
> [1] Original tdwg-content proposal for environment terms.<br>
> <a moz-do-not-send="true"
href="http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html"
target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html</a><br>
> [2] ENVO biome. <a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/ENVO_00000428" target="_blank">http://purl.obolibrary.org/obo/ENVO_00000428</a><br>
> [3] ENVO environmentalFeature. <a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/ENVO_00002297" target="_blank">http://purl.obolibrary.org/obo/ENVO_00002297</a><br>
> [4] ENVO environmentalMaterial. <a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/ENVO_00010483" target="_blank">http://purl.obolibrary.org/obo/ENVO_00010483</a><br>
> [5] DwC MIxS Meeting Notes.<br>
> <a moz-do-not-send="true"
href="https://docs.google.com/document/d/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw5w6c/edit?usp=sharing"
target="_blank">https://docs.google.com/document/d/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw5w6c/edit?usp=sharing</a><br>
> [6] Table of the core items of Mimarks checklists.<br>
> <a moz-do-not-send="true"
href="http://www.nature.com/nbt/journal/v29/n5/fig_tab/nbt.1823_T1.html"
target="_blank">http://www.nature.com/nbt/journal/v29/n5/fig_tab/nbt.1823_T1.html</a><br>
> [7] Biological Collections Ontology. <a moz-do-not-send="true"
href="https://github.com/tucotuco/bco" target="_blank">https://github.com/tucotuco/bco</a><br>
> [8] Darwin Core Namespace Policy.<br>
> <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges"
target="_blank">http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges</a><br>
><br>
><br>
> Term Name: biome<br>
> Identifier: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/biome" target="_blank">http://rs.tdwg.org/dwc/terms/biome</a><br>
> Namespace: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
> Label: Biome<br>
> Definition: An environmental system to which resident ecological<br>
> communities have evolved adaptations.<br>
> Comment: Recommended best practice is to use a controlled
vocabulary such<br>
> as defined by the biome class of the Environment Ontology (ENVO).
Examples:<br>
> "flooded grassland biome",<br>
> "<a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/ENVO_01000195" target="_blank">http://purl.obolibrary.org/obo/ENVO_01000195</a>".<br>
> Type of Term: <a moz-do-not-send="true"
href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"
target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
> Refines:<br>
> Status: proposed<br>
> Date Issued: 2013-09-26<br>
> Date Modified: 2015-03-26<br>
> Has Domain:<br>
> Has Range:<br>
> Refines:<br>
> Version: biome-2015-03-26<br>
> Replaces:<br>
> IsReplaceBy:<br>
> Class: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/Event" target="_blank">http://rs.tdwg.org/dwc/terms/Event</a><br>
> ABCD 2.0.6: not in ABCD<br>
><br>
> Term Name: environmentalFeature<br>
> Identifier: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/environmentalFeature"
target="_blank">http://rs.tdwg.org/dwc/terms/environmentalFeature</a><br>
> Namespace: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
> Label: Environmental Feature<br>
> Definition: A material entity which determines an environmental
system.<br>
> Comment: Recommended best practice is to use a controlled
vocabulary such<br>
> as defined by the environmental feature class of the Environment
Ontology<br>
> (ENVO). Examples: "meadow",<br>
> "<a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/ENVO_00000108" target="_blank">http://purl.obolibrary.org/obo/ENVO_00000108</a>".<br>
> Type of Term: <a moz-do-not-send="true"
href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"
target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
> Refines:<br>
> Status: proposed<br>
> Date Issued: 2013-09-26<br>
> Date Modified: 2015-03-26<br>
> Has Domain:<br>
> Has Range:<br>
> Refines:<br>
> Version: environmentalFeature-2015-03-26<br>
> Replaces:<br>
> IsReplaceBy:<br>
> Class: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/Event" target="_blank">http://rs.tdwg.org/dwc/terms/Event</a><br>
> ABCD 2.0.6: not in ABCD<br>
><br>
> Term Name: environmentalMaterial<br>
> Identifier: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/environmentalMaterial"
target="_blank">http://rs.tdwg.org/dwc/terms/environmentalMaterial</a><br>
> Namespace: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a><br>
> Label: Environmental Material<br>
> Definition: A portion of environmental material is a fiat object
which<br>
> forms the medium or part of the medium of an environmental system.<br>
> Comment: Recommended best practice is to use a controlled
vocabulary such<br>
> as defined by the environmental feature class of the Environment
Ontology<br>
> (ENVO). Examples: "scum",<br>
> "<a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/ENVO_00003930" target="_blank">http://purl.obolibrary.org/obo/ENVO_00003930</a>".<br>
> Type of Term: <a moz-do-not-send="true"
href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"
target="_blank">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
> Refines:<br>
> Status: proposed<br>
> Date Issued: 2013-09-26<br>
> Date Modified: 2015-03-26<br>
> Has Domain:<br>
> Has Range:<br>
> Refines:<br>
> Version: environmentalMaterial-2015-03-26<br>
> Replaces:<br>
> IsReplaceBy:<br>
> Class: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/Event" target="_blank">http://rs.tdwg.org/dwc/terms/Event</a><br>
> ABCD 2.0.6: not in ABCD<br>
><br>
</blockquote>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
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