[tdwg-content] Darwin Core Proposal - environment terms

[John Wieczorek]

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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