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

Wed May 13 20:16:56 CEST 2015

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 at lists.tdwg.org>
wrote:

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> Today's Topics:
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>    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 at csee.umbc.edu>
> Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms
> To: John Wieczorek <tuco at berkeley.edu>
> Cc: TDWG Content Mailing List <tdwg-content at lists.tdwg.org>
> Message-ID:
>         <Pine.LNX.4.64.1504231321240.18117 at 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/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw5w6c/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
> >
>
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