[tdwg-content] Darwin Core Proposal - environment terms

[joel sachs]

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
>