[tdwg-content] Darwin Core Proposal - environment terms (biome)
Steve Baskauf
steve.baskauf at vanderbilt.edu
Fri May 15 14:07:03 CEST 2015
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.
Ramona Walls wrote:
> 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.
>
> ------------------------------------------------------
> 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
> <mailto:tdwg-content-request at lists.tdwg.org>> wrote:
>
> Send tdwg-content mailing list submissions to
> tdwg-content at lists.tdwg.org
> <mailto:tdwg-content at 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 at csee.umbc.edu <mailto:jsachs at csee.umbc.edu>>
> Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms
> To: John Wieczorek <tuco at berkeley.edu <mailto:tuco at berkeley.edu>>
> Cc: TDWG Content Mailing List <tdwg-content at lists.tdwg.org
> <mailto:tdwg-content at lists.tdwg.org>>
> Message-ID:
>
> <Pine.LNX.4.64.1504231321240.18117 at linuxserver1.cs.umbc.edu
> <mailto: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
> >
>
--
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20150515/3ec66edb/attachment.html
More information about the tdwg-content
mailing list