Ramona,
Thanks for engaging. My thinking is this:
Our goal is to address the mess that is “habitat”. So much - environmental conditions, associated taxa, geography, geology - gets crammed into that one poor term.
We want to either replace or augment or subclass “habitat” with some new terms, with each new term capturing some key dimension of information that “people” are interested in. Before talking specifically about the terms under consideration, let me disclose some of my biases:
<statement of biases>
i. I’d like to see terms that will help organize the thousands of habitat terms used by the authors of taxonomic treatments in the Flora of North America. You can see some of these terms here - http://bit.ly/1Fnow3E
We’re currently categorizing these terms to enable semantic search over habitat; as we do so, we are also thinking about the user interface of treatment templates for future contributors. Our opinion is that we should look at existing habitat terms, answer the question “what have authors been trying to tell us?”, and then design interfaces that make it easier for them to tell us those things. (This isn’t to say that we shouldn’t also coax new types of information out of treatment authors, based on our understanding of what data consumers want to know.)
The habitat dimensions that, for plants, keep coming up are: wet vs dry; open canopy vs closed canopy; soil type; sloped vs. flat; and associated taxa. We also see a range of geography/geology related dimensions.
ii. I think the semantics of Darwin Core terms should be clear from their natural language definitions. Ontologies that can be used to provide values for the terms should not be relied upon as documentation for the terms themselves.
iii. I’ve long argued that Darwin Core should not make commitments to any particular upper ontologies. I explained some of my reasons in my 2013 TDWG talk (http://bit.ly/1FjCimJ). I recall that you spoke with me about this last year, and expressed support for the idea of creating ontological layers on top of Darwin Core. I’ve since tried to do this for BCO, but struggled. I’ve been meaning to ask for your help with this.
</statement of biases>
Back to the proposed terms:
Biome. As has been noted by others, the currently proposed definition is at odds with common understanding of the term, and is somewhat confusing due to its dependance on evolution. I think I understand what the definition is getting at - namely, expanding the traditional notion of biome to include microbiomes.
Environmental feature. We often see habitat terms such as “rocky outcrops”; “arroyos”; “bogs”; etc. So I can see a lot of utility in a “feature” term. My preference would be to call it “geographic feature” or “geologic feature”, since I think that’s how most people think of such features (see, e.g. geonames). The currently proposed definition is “A material entity which determines an environmental system.” This requirement that the feature “determine” the environmental system strikes me as too strong.
Environmental material. The currently proposed definition is “A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.” A much clearer definition is one that I’ve heard Pierre give, which was along the lines of “The substance that was displaced by the sample prior to its being removed from its environment”. In addition to being clearer, this second definition has the advantage of not relying on the BFO notion of “fiat object”.
Happy Victoria Day to all my fellow British subjects!
Joel.
On Wed, 13 May 2015, Ramona Walls wrote:
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@lists.tdwg.org>
wrote:
Send tdwg-content mailing list submissions to
tdwg-content@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@csee.umbc.edu>
Subject: Re: [tdwg-content] Darwin Core Proposal - environment
terms
To: John Wieczorek <tuco@berkeley.edu>
Cc: TDWG Content Mailing List <tdwg-content@lists.tdwg.org>
Message-ID:
<Pine.LNX.4.64.1504231321240.18117@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
5w6c/edit?usp=sharing
> [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
>