Darwin Core Proposal - environment terms
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
For clarification, each example shows one string value that is free text and another that is an ENVO IRI. Does this mean that if a user wants to indicate the ENVO class for flooded grassland biome that they can chose to provide either the text label for the class or the IRI? Or is the example showing free text intended to show how a user might provide a value if they aren't following the recommended best practice (i.e. using some system other than ENVO that doesn't have IRIs)? It seems to me counterproductive to provide two choices. I would rather see the recommendation be to provide an IRI unless one isn't available. Otherwise, consumers will be stuck with having to try to interpret what free text means.
Alternatively, provide two terms: one intended for use with literal names (i.e. free text) and one intended for use with IRIs. That precedent has been set in Audubon Core (e.g. ac:provider and ac:providerLiteral). In DwC we have the dwc: and dwciri: solution in the RDF guide (which appears once again to be stuck in Executive Committee limbo). In the Audubon Core case, this isn't really an RDF issue since AC doesn't assume any particular representation and I think you could have a spreadsheet with an IRI value for ac:provider. I suppose it would be kosher to have dwciri:biome expressed as an IRI in string form in a spreadsheet for people who don't care about RDF. I don't think this has actually been discussed.
Steve
John Wieczorek wrote:
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
Actually, let me be more blunt. I object to the adoption of these terms as currently proposed because the recommendation in the comment is not clear. I think that these three term adoption issues are blocked by the adoption of the RDF guide. If the RDF guide is accepted by the Executive, then there is default mechanism for addressing my issue: there will be dwc:biome, which would have a literal value and dwciri:biome, which would have a value that is an IRI. If the RDF guide is not accepted by the executive, then there needs to be some other solution, such as the Audubon Core mechanism: dwc:biome and dwc:biomeLiteral.
I don't know what the holdup is on the RDF guide. It had jumped through every hoop required for adoption and was submitted for approval by the Executive on 2014-12-29. There is no reason why it should take three months for a decision on this.
Steve
Steve Baskauf wrote:
For clarification, each example shows one string value that is free text and another that is an ENVO IRI. Does this mean that if a user wants to indicate the ENVO class for flooded grassland biome that they can chose to provide either the text label for the class or the IRI? Or is the example showing free text intended to show how a user might provide a value if they aren't following the recommended best practice (i.e. using some system other than ENVO that doesn't have IRIs)? It seems to me counterproductive to provide two choices. I would rather see the recommendation be to provide an IRI unless one isn't available. Otherwise, consumers will be stuck with having to try to interpret what free text means.
Alternatively, provide two terms: one intended for use with literal names (i.e. free text) and one intended for use with IRIs. That precedent has been set in Audubon Core (e.g. ac:provider and ac:providerLiteral). In DwC we have the dwc: and dwciri: solution in the RDF guide (which appears once again to be stuck in Executive Committee limbo). In the Audubon Core case, this isn't really an RDF issue since AC doesn't assume any particular representation and I think you could have a spreadsheet with an IRI value for ac:provider. I suppose it would be kosher to have dwciri:biome expressed as an IRI in string form in a spreadsheet for people who don't care about RDF. I don't think this has actually been discussed.
Steve
John Wieczorek wrote:
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
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On Fri, 27 Mar 2015 09:37:25 -0500 Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
Actually, let me be more blunt. I object to the adoption of these terms as currently proposed because the recommendation in the comment is not clear. I think that these three term adoption issues are blocked by the adoption of the RDF guide.
I concur. The dwc and dwcIRI namespaces provide a clear mechanism for separating the handling literals or IRIs. We shouldn't be providing contradictory guidance for using IRIs as values in the dwc namespace.
-Paul
I concur with Paul's concurrence.
On Fri, Mar 27, 2015 at 10:48 AM, Paul J. Morris mole@morris.net wrote:
On Fri, 27 Mar 2015 09:37:25 -0500 Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
Actually, let me be more blunt. I object to the adoption of these terms as currently proposed because the recommendation in the comment is not clear. I think that these three term adoption issues are blocked by the adoption of the RDF guide.
I concur. The dwc and dwcIRI namespaces provide a clear mechanism for separating the handling literals or IRIs. We shouldn't be providing contradictory guidance for using IRIs as values in the dwc namespace.
-Paul
Paul J. Morris Biodiversity Informatics Manager Harvard University Herbaria/Museum of Comparative Zoölogy mole@morris.net AA3SD PGP public key available _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
OK, those are easy fixes. Remove the IRI examples, maybe add another string literal example in place of each IRI removed.
On Fri, Mar 27, 2015 at 1:51 PM, Bob Morris morris.bob@gmail.com wrote:
I concur with Paul's concurrence.
On Fri, Mar 27, 2015 at 10:48 AM, Paul J. Morris mole@morris.net wrote:
On Fri, 27 Mar 2015 09:37:25 -0500 Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
Actually, let me be more blunt. I object to the adoption of these terms as currently proposed because the recommendation in the comment is not clear. I think that these three term adoption issues are blocked by the adoption of the RDF guide.
I concur. The dwc and dwcIRI namespaces provide a clear mechanism for separating the handling literals or IRIs. We shouldn't be providing contradictory guidance for using IRIs as values in the dwc namespace.
-Paul
Paul J. Morris Biodiversity Informatics Manager Harvard University Herbaria/Museum of Comparative Zoölogy mole@morris.net AA3SD PGP public key available _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- Robert A. Morris
Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390
Filtered Push Project Harvard University Herbaria Harvard University
email: morris.bob@gmail.com web: http://efg.cs.umb.edu/ web: http://wiki.filteredpush.org http://wiki.datakurator.net http://taxonconceptexplorer.org/ http://www.cs.umb.edu/~ram _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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/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
participants (5)
-
Bob Morris -
joel sachs -
John Wieczorek -
Paul J. Morris -
Steve Baskauf