New subject: Darwin Core Proposal - environment terms (joel sachs)

29 May 2015

      Hi Pier,
I'll be happy to put my comments in the issue tracker. I also wanted to 
follow up on your comment that
"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 characterize an entity's environment."
I remember now that the ENVO paper mentions this, and gives, as an 
example, a duck in the water. Such a duck would have properties like
<dorsally_surrounded_by> <water>
<ventrally_surrounded_by> <air>
However, the sample data records provided as supplemental material to the 
MIXS paper all have one and only one value for each of "environmental 
feature", "environmental material", and "biome". The MIXS paper itself 
appears to be silent on the question of whether multiple values are 
allowed. The prototype annotation interface that my colleagues at AAFC are developing 
currently allows only a single value for each field. Do you know if this 
is right? wrong? unspecified? Maybe the real question is not what the 
standard permits/requires, but what will the repositories allow? Do you 
know what the repositories are thinking on this?
As an aside, I notice that MIXS uses the terms "biome", 
"environmental_material", and "environmental_feature" as properties, while 
ENVO uses them as classes. I like that, because I believe that we should 
allow semantics to be derived from syntax, and other forms of context.
I attended the Open Data conference here in Ottawa this week, and was 
a bit pressed for time, but would be happy to join a call about habitats.
Best,
Joel.
On Thu, 21 May 2015, Pier Luigi Buttigieg wrote:
...
Hi Joel,
These are valuable thoughts.
Could you post them to the ENVO issue tracker? It can be found here:
https://github.com/EnvironmentOntology/envo/issues
We can develop from there more effectively.
The habitat issue is one I plan to work on with Grant Godden next week in
Claremont.
I'm in Berkeley/Oakland right now working with a group interesting in urban
environments.
Shall we perhaps arrange a call?
Best,
Pier
On Wed, 20 May 2015 14:28:40 -0700, Ramona Walls rlwalls2008@gmail.com
wrote:
...
Hi Joel,
I completely agree about the need to unpack the multiple dimensions of
"habitat" in DWC, while not making DWC into an ontology. I suggest the
discussion of ENVO terms should probably move to the ENVO list (then come
back here, if/when we are ready to deal with adding them to DWC.
I'd be very happy to work with you on BCO/DWC stuff and here your needs.
Please feel free to just email me off list or email
bco-discuss@googlegroups.com. We have bi-weekly calls that are open to
anyone who wants to participate.
Ramona
[...]
...
On Mon, May 18, 2015 at 5:50 AM, joel sachs jsachs@csee.umbc.edu wrote:
...
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.

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.

"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.

"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.

"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
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  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
 >

Re: [tdwg-content] Darwin Core Proposal - environment terms (joel sachs)

joel sachs

Ramona Walls

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