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/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw5... [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