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Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO
by Ramona Walls 03 Oct '13

03 Oct '13

Steve and others: The better solution (from an informatics point of view) would be to use the ENVO URI in the field, even if that means changing the DwC guidelines. If it is left as a string, then there would have to be another field that specifies where the term came from, then there would have to be some mechanism to convert the string to a URI. I realize that entering URIs requires some effort, but if someone is looking up the exact label for a term, it is not much harder to find the URI. Re. adding a term to DwC for ecoregion, I suggest you take that up on the ENVO list first. I don't know if they have considered adding a class for ecoregion. To me it makes sense to first work out the utility,definition, and classes in ENVO before adoption in DwC. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden On Thu, Oct 3, 2013 at 3:00 AM, <tdwg-content-request(a)lists.tdwg.org> wrote: > Send tdwg-content mailing list submissions to > tdwg-content(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-content > or, via email, send a message with subject or body 'help' to > tdwg-content-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-content-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > > Today's Topics: > > 1. Re: Proposed new Darwin Core environmental terms from ENVO > (Steve Baskauf) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Oct 2013 09:12:54 -0500 > From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> > Subject: Re: [tdwg-content] Proposed new Darwin Core environmental > terms from ENVO > To: <tuco(a)berkeley.edu> > Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> > Message-ID: <524C29E6.8030908(a)vanderbilt.edu> > Content-Type: text/plain; charset="iso-8859-1" > > John, > > Thank you for your response. I agree that anything that may change over > time should probably be grouped under Event. I guess in the case of > biomes I am thinking about this in a practical sense, i.e. realistically > how is somebody going to assign a particular event to a biome? A likely > scenario would be that they would take the location of an event, use its > latitude and longitude to find where it falls on a map such as > http://en.wikipedia.org/wiki/Biome#Map_of_biomes and then assign it to > whatever biome region it falls within on the map. That is a different > approach from assessing the biological and climatological > characteristics occurring at an event, comparing it with an ontology > that defines biomes, and then making the assignment based on how the > event lines up with the ontology. I suppose that in theory people might > do that, but realistically, it seems more likely that they would look it > up on a map. Under the scenario that they look it up on a map, it is > logical to consider biome to be a property of a location. Yes, biomes > might change over time, but then so do the names and boundaries of > countries, but we don't consider them to be properties of Event, we > consider them as properties of Location. We periodically update the > maps of countries, just as we might update the maps of biomes once a > century or so. But if there is a consensus that dwc:biome belongs under > Event, I can live with it. > > The other thing I'm wondering about the values of dwc:biome would be how > a user would indicate the controlled vocabulary one is using. The ENVO > ontology is mentioned. Under the scenario of the draft RDF guide, the > term dwcuri:biome would have a URI value of > <http://purl.obolibrary.org/obo/ENVO_01000195>. That would be > unambiguous. However, if dwc:biome is reserved for literal values (as > the RDF guide suggests it should be) then how does a machine know that > "flooded grassland biome" is a label from ENVO and not a literal > description of a biome from the Whittaker, Walter, Bailey, etc. systems > which are probably currently in much wider use than ENVO and therefore > likely controlled vocabularies of choice for many users? > > As far as dwc:ecoregion as a term is concerned, I was mostly just > testing the waters. I could submit it as a term addition in the DwC > issue tracker, but I'm not going to do that if I'm the only person who > cares about it. If anybody besides me cares, they can say so on the list. > > Thanks for clarifying, > Steve > > John Wieczorek wrote: > > It is true that the organizedInClass attribute of any given Darwin > > Core term does nothing more than associate properties with classes as > > an organizational aid. It says nothing about the class being the > > domain of the property, and with good reason. Darwin Core in its > > current manifestation is just not semantically detailed enough to make > > domain declarations. Most of our classes combine multiple concepts and > > get used in multiple ways. Occurrence is the best worst example of this. > > > > The environment properties are organized under Event because of their > > time-dependent nature - habitats and biomes definitely can change over > > museum time scales. Location alone does not have a time component - > > the definition of Location is "A spatial region or named place. For > > Darwin Core, a set of terms describing a place, whether named or > > not." Darwin Core has no other spatiotemporal concept except the > > Event, which combines everything in Location with time properties and > > sampling properties - the definition of an Event is: "The category of > > information pertaining to an event (an action that occurs at a place > > and during a period of time)." > > > > If we had a purely spatiotemporal class, then I would organize the > > environmental properties there. Without one, I would organize the > > properties in the class that does have time properties, namely Event. > > > > Until your message, no one has discussed the addition of an ecoregion > > term on tdwg-content. > > > > As to the question of country, I see > > On Tue, Oct 1, 2013 at 5:24 PM, Steve Baskauf > > <steve.baskauf(a)vanderbilt.edu> wrote: > > > I've had some time to read through the proposed changes more closely > > and had > > > a question. > > > > > > I realize that when a property is listed under a class in the dwc: > > > namespace, that is kind of a suggestion about the type of resource > > for which > > > that term would be an appropriate property (vs. a formal domain > > declaration > > > which would force the subject resource to BE an instance of that > > class). So > > > one doesn't really "break the rules" if one uses a DwC term as a > > property of > > > a resource that isn't a member of the class that the term is listed > > under. > > > Nevertheless, for the sake of consistency and to make it possible for > > > consuming applications to know what to "expect" as properties for > > particular > > > types of things, it would be good to place DwC properties under the > > "right" > > > class headings. > > > > > > So my question is, why are the terms dwc:habitat and dwc:biome being > > placed > > > under the dwc:Event class? I'll start with dwc:biome because that's > the > > > most straightforward one. It seems to me that dwc:biome should be > > organized > > > under the class dcterms:Location rather than dwc:Event. For example, I > > > would say > > > > > > <http://bioimages.vanderbilt.edu/baskauf/d0127#loc> dwc:biome > "temperate > > > broadleaf forest" > > > > > > (where http://bioimages.vanderbilt.edu/baskauf/d0127#loc is a > > > dcterms:Location) or something like that. Although I suppose over time > > > climate change could cause that location to be part of a different > > biome, > > > that probably wouldn't happen on a timescale the would be relevant. > One > > > could probably also make the case that dwc:habitat is a property of a > > > location, although I suppose that the habitat type of a location could > > > change, for example if it were a forest, but then somebody chopped > > down all > > > of the trees and converted it to agricultural use. In that case, it > > might > > > be desirable to record what the state of that location was at a > > particular > > > time (which is the way I think about dwc:Event - something that > > happens at a > > > particular place and time). Then it would make sense to group it under > > > dwc:Event. But we have other properties of location that could > > change over > > > time, such as dwc:country for which we have several examples in Europe > > > within the past few decades. > > > > > > I suppose the thinking is that the proposed terms (habitat, biome, > > > environmentalFeature, environmentalMaterial) would comprise a set of > > > properties that would be associated with a collecting or sampling > event. > > > But it doesn't really make sense to me to call dwc:biome a property > > of an > > > event. > > > > > > I'm also wondering if there was any consideration about creating a > > > dwc:ecoregion property, which I would consider to be something > > intermediate > > > in scale between a biome and a habitat. I would actually use that > > term a > > > lot, but I may be the only one (and I would use it as a property of a > > > location). If one were to create such a term, it would probably be > > good to > > > have some other term that specified the system used to define the > > controlled > > > vocabulary (e.g. Bailey vs. WWF ecoregions). Or use URIs but that's a > > > different issue and the DwC RDF guide would have a solution for that > > > (dwcuri:biome, dwcuri:ecoregion, etc.). > > > > > > Steve > > > > > > John Wieczorek wrote: > > > > > > Dear all, > > > > > > The spirit of the proposal is to satisfy use cases defined in the > > > document "Meeting Report: GBIF hackathon-workshop on > > > Darwin Core and sample data (22-24 May 2013)" found at > > > http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO > > > ontology. Steve is correct. All of the ENVO terms are classes in > > > keeping with the OBO Foundry way of doing things. As such, they don't > > > work in the intended Darwin Core context as they currently stand, > > > where what we want are properties whose values can come from ENVO as a > > > controlled vocabulary in the way Hilmar described. > > > > > > To satisfy the spirit of the proposal, I suggest that instead of > > > replacing the dwc:habitat property with the envo:habitat class and > > > adding the other three ENVO classes, we modify the existing > > > dwc:habitat property and introduce new properties whose ranges are > > > recommended to be the appropriate ENVO classes, as follows: > > > > > > Retain the property term dwc:habitat, but amend the definition to be: > > > > > > Term Name: habitat > > > Identifier: http://rs.tdwg.org/dwc/terms/habitat > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Habitat > > > Definition: A spatial region having environmental qualities which may > > > sustain an organism or a community of organisms. Recommended best > > > practice is to use a controlled vocabulary such as defined by the > > > habitat class of the Environment Ontology (ENVO). > > > Comment: Examples: "freshwater habitat", > > > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2008-11-19 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: habitat-2013-09-26 > > > Replaces: habitat-2009-04-24 > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Add the following new property terms for biome, > > > environmental feature, and environmental material: > > > > > > Term Name: biome > > > Identifier: http://rs.tdwg.org/dwc/terms/biome > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Biome > > > Definition: A major class of ecologically similar communities of > > > plants, animals, and other organisms. Biomes are defined based on > > > factors such as plant structures (such as trees, shrubs, and grasses), > > > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > > > woodland, savanna), and other factors like climate. Unlike ecozones, > > > biomes are not defined by genetic, taxonomic, or historical > > > similarities. Biomes are often identified with particular patterns of > > > ecological succession and climax vegetation. Recommended best practice > > > is to use a controlled vocabulary such as defined by the biome class > > > of the Environment Ontology (ENVO). > > > Comment: Examples: "flooded grassland biome", > > > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-26 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: biome-2013-09-26 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmentalFeature > > > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Environmental Feature > > > Definition: A prominent or distinctive aspect, quality, or > > > characteristic of a biome. Recommended best practice is to use a > > > controlled vocabulary such as defined by the environmental feature > > > class of the Environment Ontology (ENVO). > > > Comment: Examples: "meadow", > > > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-26 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: environmentalFeature-2013-09-26 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmentalMaterial > > > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Environmental Material > > > Definition: Material in or on which organisms may live. Recommended > > > best practice is to use a controlled vocabulary such as defined by the > > > environmental feature class of the Environment Ontology (ENVO). > > > Comment: Examples: "scum", > > > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-26 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: environmentalMaterial-2013-09-26 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > I hope this makes better sense. > > > > > > Cheers, > > > > > > John > > > > > > On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf > > > <steve.baskauf(a)vanderbilt.edu> wrote: > > > > > > > > > Well, the proposal says "The Darwin Core term habitat would be > > redefined..." > > > . I take that to mean that the term dwc:habitat is being replaced with > > > envo:00002036 . If that's not what it means, then it would be good to > > > clarify. If the intention is to provide values for other terms, > > that should > > > be stated. > > > > > > Steve > > > > > > > > > Hilmar Lapp wrote: > > > > > > I was assuming that the proposal was that subclasses of envo:habitat > > would > > > take the place of values for the dwc:habitat property. But perhaps I > was > > > naive or misunderstanding? > > > > > > -hilmar > > > > > > Sent from away > > > > > > On Sep 25, 2013, at 8:23 PM, Steve Baskauf > > <steve.baskauf(a)vanderbilt.edu> > > > wrote: > > > > > > OK, now that I've had a chance to look at the RDF, it is as I > > suspected. If > > > I am understanding the proposal correctly, the proposal is to > > replace the > > > term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with > > the term > > > <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call > > > envo:00002036 for brevity) However, the definition of dwc:habitat > > which you > > > can view at > > > > http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf > > > says > > > > > > dwc:habitat rdf:type rdfs:Property > > > > > > whereas the document I received at the end of those four redirects > > tells me > > > that > > > > > > envo:00002036 rdf:type owl:Class > > > > > > Since > > > > > > owl:Class rdfs:subclassOf rdfs:Class > > > > > > then we are effectively changing the current DwC "habitat" term from a > > > property into a class similar to dwc:Occurrence, dwc:Identification, > > > dwc:Taxon, etc. which are all of type rdfs:Class. > > > > > > So I'm left wondering what I can do with the new term. With the old > > term I > > > could make a statement like > > > > > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat > > "deciduous > > > forest" > > > > > > or something like that if I take the hint from the DwC class > > groupings that > > > dwc:habitat might be a property of dwc:Event instances. But I can't > > > meaningfully say > > > > > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 > > > "deciduous forest" > > > > > > That doesn't make any sense because the way I understand RDF, > predicates > > > should be properties, not classes. Even if we weren't talking about > > RDF, > > > I'd still have the same problem (we are changing a property into a > > class) - > > > it's just easier for me to make plain what the issue is by giving RDF > > > examples. So just exactly what can I "do" with envo:00002036 ????? > > > > > > I haven't looked up the RDF for the other proposed terms (too much > > work with > > > the four redirects), but I suspect if I did, I'd find that they are > also > > > classes and not properties. This particular issue is a case of a > > broader > > > issue that I have about OBO-style ontologies. They are great for > > defining > > > how many, many kinds of classes are related to each other. But they > > provide > > > very few properties that could be used as predicates to serve as > > properties > > > of instance data. > > > > > > Steve > > > > > > John Wieczorek wrote: > > > > > > Dear all, > > > > > > GBIF has just published "Meeting Report: GBIF hackathon-workshop on > > > Darwin Core and sample data (22-24 May 2013)" at > > > http://www.gbif.org/orc/?doc_id=5424. Now that this document is > > > available for public reference, I would like to formally open the > > > minimum 30-day comment period on the new environmental terms proposed > > > during the workshop and defined in the referenced document. > > > > > > The formal proposal would change the term habitat to align it with the > > > ENVO habitat term. The related issues in the Darwin Core issue tracker > > > is https://code.google.com/p/darwincore/issues/detail?id=178. The > > > Darwin Core term habitat would be redefined as follows: > > > > > > Term Name: habitat > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Habitat > > > Definition: A spatial region having environmental qualities which may > > > sustain an organism or a community of organisms. > > > Comment: Examples: "freshwater habitat", > > > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2008-11-19 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00002036 > > > Replaces: habitat-2009-04-24 > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > The formal proposal would add the following new terms for biome, > > > environmental feature, and environmental material: > > > > > > Term Name: biome > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Biome > > > Definition: A major class of ecologically similar communities of > > > plants, animals, and other organisms. Biomes are defined based on > > > factors such as plant structures (such as trees, shrubs, and grasses), > > > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > > > woodland, savanna), and other factors like climate. Unlike ecozones, > > > biomes are not defined by genetic, taxonomic, or historical > > > similarities. Biomes are often identified with particular patterns of > > > ecological succession and climax vegetation. > > > Comment: Examples: "flooded grassland biome", > > > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-25 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00000428 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmental feature > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Environmental Feature > > > Definition: A prominent or distinctive aspect, quality, or > > > characteristic of a biome. > > > Comment: Examples: "meadow", > > > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-25 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00002297 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmental material > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Environmental Material > > > Definition: Material in or on which organisms may live. > > > Comment: Examples: "scum", > > > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-25 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00010483 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > The related issues in the Darwin Core issue tracker are > > > https://code.google.com/p/darwincore/issues/detail?id=189 > > > https://code.google.com/p/darwincore/issues/detail?id=190 > > > and > > > https://code.google.com/p/darwincore/issues/detail?id=191 > > > > > > If there are any objections to the changes proposed for these terms, > > > or comments about their definitions, please respond to this message. > > > If there are no objections or if consensus can be reached on any > > > amendments put forward, the proposal will go before the Executive > > > Committee for authorization to put these additions into effect after > > > the public commentary period. > > > > > > Cheers, > > > > > > John > > > _______________________________________________ > > > tdwg-content mailing list > > > tdwg-content(a)lists.tdwg.org > > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > . > > > > > > > > > > > > > > > -- > > > 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 <tel:%28615%29%20343-4582>, fax: (615) > > 322-4942 <tel:%28615%29%20322-4942> > > > If you fax, please phone or email so that I will know to look for it. > > > http://bioimages.vanderbilt.edu > > > > > > > > > _______________________________________________ > > > tdwg-content mailing list > > > tdwg-content(a)lists.tdwg.org > > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > > > -- > > > 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 <tel:%28615%29%20343-4582>, fax: (615) > > 322-4942 <tel:%28615%29%20322-4942> > > > If you fax, please phone or email so that I will know to look for it. > > > http://bioimages.vanderbilt.edu > > > > > > > > > . > > > > > > > > > > > > > > > -- > > > 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 <tel:%28615%29%20343-4582>, fax: (615) > > 322-4942 <tel:%28615%29%20322-4942> > > > If you fax, please phone or email so that I will know to look for it. > > > http://bioimages.vanderbilt.edu > > > > -- > 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 > >

1 0

Proposed new Darwin Core environmental terms from ENVO
by John Wieczorek 03 Oct '13

03 Oct '13

Dear all, GBIF has just published "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at http://www.gbif.org/orc/?doc_id=5424. Now that this document is available for public reference, I would like to formally open the minimum 30-day comment period on the new environmental terms proposed during the workshop and defined in the referenced document. The formal proposal would change the term habitat to align it with the ENVO habitat term. The related issues in the Darwin Core issue tracker is https://code.google.com/p/darwincore/issues/detail?id=178. The Darwin Core term habitat would be redefined as follows: Term Name: habitat Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 Namespace: http://purl.obolibrary.org/obo/ Label: Habitat Definition: A spatial region having environmental qualities which may sustain an organism or a community of organisms. Comment: Examples: "freshwater habitat", "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: proposed Date Issued: 2008-11-19 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: http://purl.obolibrary.org/obo/ENVO_00002036 Replaces: habitat-2009-04-24 IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) The formal proposal would add the following new terms for biome, environmental feature, and environmental material: Term Name: biome Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 Namespace: http://purl.obolibrary.org/obo/ Label: Biome Definition: A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation. Comment: Examples: "flooded grassland biome", "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: proposed Date Issued: 2013-09-25 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: http://purl.obolibrary.org/obo/ENVO_00000428 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmental feature Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 Namespace: http://purl.obolibrary.org/obo/ Label: Environmental Feature Definition: A prominent or distinctive aspect, quality, or characteristic of a biome. Comment: Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: proposed Date Issued: 2013-09-25 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: http://purl.obolibrary.org/obo/ENVO_00002297 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmental material Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 Namespace: http://purl.obolibrary.org/obo/ Label: Environmental Material Definition: Material in or on which organisms may live. Comment: Examples: "scum", "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: proposed Date Issued: 2013-09-25 Date Modified: 2013-09-25 Has Domain: Has Range: Refines: Version: http://purl.obolibrary.org/obo/ENVO_00010483 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) The related issues in the Darwin Core issue tracker are https://code.google.com/p/darwincore/issues/detail?id=189 https://code.google.com/p/darwincore/issues/detail?id=190 and https://code.google.com/p/darwincore/issues/detail?id=191 If there are any objections to the changes proposed for these terms, or comments about their definitions, please respond to this message. If there are no objections or if consensus can be reached on any amendments put forward, the proposal will go before the Executive Committee for authorization to put these additions into effect after the public commentary period. Cheers, John

5 19

Proposed changes to Darwin Core Type term NomenclaturalChecklist
by John Wieczorek 01 Oct '13

01 Oct '13

Dear all, There is a proposal to change the Darwin Core Type vocabulary term dwctype:NomenclaturalChecklist (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm#NomenclaturalCheckli…) The basic issue this proposal attempts to solve is that a NomenclaturalChecklist is a data set, not a data record and Darwin Core Type vocabulary is meant to designate the type of a record. The types of records in a nomenclatural checklist data set would be taxonomic names, hence "dwctype:Nomen". As this is a substantive semantic change, we must follow the Darwin Core Namespace Policy's Term Change Policy, section 3.3, Semantic changes in Darwin Core terms, which includes a minimum 30-day public comment period beginning today. The issue is further described on the Darwin Core Project issue tracker at https://code.google.com/p/darwincore/issues/detail?id=177. The proposal would deprecate the current version of dwctype:NomenclaturalChecklist in favor of a new version with the following definition: Term Name: Nomen Identifier: http://rs.tdwg.org/dwc/dwctype/Nomen Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: Nomen Definition: A resource describing a scientific name. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Status: proposed Date Issued: 2009-01-23 Date Modified: 2013-09-30 Has Domain: Has Range: Refines: Version: Nomen-2013-09-30 Replaces: NomenclaturalChecklist-2009-01-23 IsReplaceBy: Class: ABCD 2.0.6: not in ABCD (someone please confirm or deny this) If there are any objections to the changes proposed for this existing term, or comments about its definition, please respond to this message. If there are no objections or if consensus can be reached on any amendments put forward, the proposal will go before the Executive Committee for authorization to put these additions into effect after the public commentary period. Cheers, John

3 2

Proposed changes to Darwin Core Type term Location
by John Wieczorek 30 Sep '13

30 Sep '13

Dear all, There is a proposal to deprecate the Darwin Core Type vocabulary term dwctype:Location (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm#Location) and instead recommend the Dublic Core equivalent http://purl.org/dc/terms/Location. Dublin Core has a broader scope than Darwin Core, and the Darwin Core term was created for reasons that no longer apply. Specifically, the Darwin Core Location term was created because the Dublin Core Location term was not a Dublin Core type vocabulary term. At the time, Darwin Core tried to use a combination of Dublin Core and Darwin Core types as values for the basisOfRecord field, and wanted them all to be in type vocabularies. This isn't necessary. As this is a substantive semantic change (a term deprecation and new recommendation to take its place), we must follow the Darwin Core Namespace Policy's Term Change Policy, section 3.3, Semantic changes in Darwin Core terms, which includes a minimum 30-day public comment period beginning today. The issue is further described on the Darwin Core Project issue tracker at https://code.google.com/p/darwincore/issues/detail?id=173. The proposal would deprecate the dwctype:Location in favor of a dcterms:Location with the following definition: Term Name: Location Identifier: http://purl.org/dc/terms/Location Namespace: http://purl.org/dc/terms/ Label: Location Definition: A spatial region or named place. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Status: proposed Date Issued: 2009-01-23 Date Modified: 2013-09-30 Has Domain: Has Range: Refines: Version: http://dublincore.org/usage/terms/history/#Location-001 Replaces: Location-2009-01-23 IsReplaceBy: Class: ABCD 2.0.6: not in ABCD (someone please confirm or deny this) If there are any objections this proposed change, please respond to this message. If there are no objections or if consensus can be reached on any amendments put forward, the proposal will go before the Executive Committee for authorization to put these additions into effect after the public commentary period. Cheers, John

1 0

Abundance
by Robert Stevenson 30 Sep '13

30 Sep '13

Some thoughts about usage of some of the terms under discussion and the ultimate goals I often use the term "abundance" as a refinement of the term "occurrence". I say "Species X occurs or does not occur at Location L. This kind of statement is refined with a statement such as "Females are rare in March" or "Juveniles are common or very abundant in July". The details of the life stage, timing and numbers of individuals or groups are more specific but still categorical. I think of such statements as being derived from "expert opinion" or being summary statements based on enumerations from a series of samples taken during several field trips. I think these kinds of generalities are useful for policy making. In terms of data, the simplest category is "presence only" data. Some times this is referred to as occurrence data - some number of individuals are seen at a particular time and location. Many museum records fall into this category as there is no other information associated with the specimen. Such records are equivalent to an incidental sighting by a field ecologist. Today many biodiversity data are collect following a particular protocol. Here sampling effort is known. A specific number of individuals seen in a "given area" and during a known time interval. From this information one can compute population densities. As several others have commented, the results are dependent on the particular protocols and it can be difficult to reconcile data from two different protocols. How are data from pitfall traps equivalent to data from baits.....? This is an important challenge because we know that usually one and often two protocols are insufficient to characterize the presence of all members of a taxon If I am not mistaken, the goal is to establish terms that will let humans efficiently prepare data and write programs so that machines can reason with the data. If so, the key challenges seem to be 1) Distinguishing presence-only data from data collected using known protocols 2) Finding ways to reconcile data from different protocols Rob Stevenson Rob Stevenson Biology Department UMass Boston

5 4

Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
by Ramona Walls 29 Sep '13

29 Sep '13

I would not recommend making abundance a property of material sample, because there are many cases where abundance would be used for observations (such as in Hannu's most recent example) and not for material samples. Many surveys are also observations, and not sampling events. While I sympathize with Rob's point (somewhere down on this list) that scrunching too much meaning into occurence is a problem, this is already the state of affairs. I would contend that a survey is "evidence of an occurence in nature" so abundance (when it is a property of a survey) is still a property of an occurence. In general, the notion of abundance is complex and context dependent, and capturing that complexity is probably beyond the scope of a flat vocabulary like Darwin Core. I am not opposed to adding abundance terms to Darwin Core, and I think the proposals are getting close to a good way for doing so. However, I think it is important to complement the DwC terms with a more semantically rich vocabulary like Biological Collections Ontology (BCO) or Population and Community Ontology. I would not call modeling abundance a "trivial" use case for the Biological Collections Ontology (BCO), but I would call it a central one. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden On Sat, Sep 28, 2013 at 3:00 AM, <tdwg-content-request(a)lists.tdwg.org>wrote: > Send tdwg-content mailing list submissions to > tdwg-content(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-content > or, via email, send a message with subject or body 'help' to > tdwg-content-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-content-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > > Today's Topics: > > 1. Re: Proposed new Darwin Core terms - abundance, > abundanceAsPercent (Hannu Saarenmaa) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 28 Sep 2013 08:25:55 +0300 > From: Hannu Saarenmaa <hannu(a)bioshare.com> > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > abundance, abundanceAsPercent > To: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org> > Message-ID: <52466863.8050703(a)bioshare.com> > Content-Type: text/plain; charset="iso-8859-1" > > Basically I support the views of Aaike and Donald. Keep the quantity > and unit separate. No need for special term for AbundanceAsPercentage, > then. > > However, I am a bit uncertain whether "Abundance" is the right term. > How about "Quantity"? It is more generic, and can be applied for > example, to a catch of 1000 kg of fish and a harvest of 200 cubic meters > of timber. "Abundance" is semantically not right for those measures. > > I also think that a range for the quantity is needed, to express > uncertainty about the quantity. I saw about 1000 geese this morning, > certainly more than 500 but less than 2000. Uncertainty is so common in > sightings. > > Are we also going to deprecate "IndividualCount"? I hope so. > > Hannu > > -- > > Hannu Saarenmaa, Research Director > hannu.saarenmaa(a)helsinki.fi > Mobile +358-50-4479668 > > University of Eastern Finland > School of Computing, SIB Labs, Joensuu Science Park > L?nsikatu 15 (P.O. Box 111) > FIN-80101 Joensuu > > www.digitarium.fi - Digitisation Centre of the Finnish Museum of Natural > History and the University of Eastern Finland > www.biovel.eu - Workflows for Scientific Research > www.eubon.eu - EU BON - GEO BON - Data Integration and Interoperability > > > > On 2013-09-26 18:07, Donald Hobern [GBIF] wrote: > > > > Hi Rob. > > > > I understand your concern, but my concern is with the opportunities we > > are currently missing to enable our occurrence mobilisation processes > > to offer significantly more value in many contexts. > > > > Some of the problem may be in the use of the word "abundance". If we > > understand "abundance" to refer to the size and density of a > > population or species, then a survey may give us a workable measure we > > can use to represent this. I am thinking of mobilisation of less > > ambitious measurements of relative abundance of a taxon in any > > sampling event or set of associated observations. I visit a reservoir > > and follow some standard protocol and count 30 mallards and a single > > gadwall. Today that might be exposed in simple Darwin Core as two > > occurrence records, each of which might somehow include an > > individualCount. In the absence of any other information, this count > > information cannot be seen as much more than an anecdotal annotation. > > If we understood that these two observations were part of a single > > survey event associated with a protocol also used for some number of > > other survey events for which we have observations, we could (in > > principle) find more ways to explore the significance of the count and > > use it to help to fine-tune distribution models and to enhance them to > > indicate patterns of abundance. If we can find a way to do this > > consistently for all types of biodiversity observation (malaise traps, > > transects, expression of ITS or CO1 from environmental samples), a > > large number of databases already contributing to GBIF and other > > networks could immediately offer a richer view to users and analysts. > > > > I believe we could readily handle this with three properties that are > > available for use with any occurrence -- a sampling event id, a > > sampling protocol identifier (ideally a URL leading to information on > > the protocol) and a relative abundance value within that sample. Any > > occurrence record could include these fields if appropriate. Of > > course more normalisation is possible, but DwC has never been about > > full normalisation. > > > > We can debate which DwC classes ought to include support for such > > elements. I personally think we've tied ourselves in unnecessary > > knots with our use of Occurrences, Events, Material Samples, etc. I > > wish we just had an agreed meta-model/ontology which provides a graph > > of classes of interest to our domain (specimen, collection, taxon > > concept, taxon name, locality, collector, etc.) and a set of uniquely > > named properties each of which is associated with one of these classes > > or links instances of these classes. Darwin Core should then allow > > for the denormalised representation of any view corresponding to a > > subgraph of that model. Occurrence, Event, etc. should then be names > > for popularly-used subgraphs and should represent the logic for > > unpacking those denormalised DwC records back into a graph of > > meta-model objects (in other words they should express something like > > what SPARQL query might be able to extract this kind of record from > > data organised using the meta-model/ontology). > > > > Best wishes, > > > > > > Donald > > > > ---------------------------------------------------------------------- > > > > Donald Hobern - GBIF Director - dhobern(a)gbif.org > > <mailto:dhobern@gbif.org> > > > > Global Biodiversity Information Facility http://www.gbif.org/ > > > > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > > > > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > > > > ---------------------------------------------------------------------- > > > > *From:*robgur@gmail.com [mailto:robgur@gmail.com] *On Behalf Of > > *Robert Guralnick > > *Sent:* Thursday, September 26, 2013 4:37 PM > > *To:* Donald Hobern [GBIF] > > *Cc:* John Wieczorek; TDWG Content Mailing List > > *Subject:* Re: [tdwg-content] Proposed new Darwin Core terms - > > abundance, abundanceAsPercent > > > > I agree with Donald here regarding the need for Abundance, but am, > > to be honest, not quite I understand (or agree) with the logic of the > > proposal. Abundance is listed as a property of an occurrence, and I > > wonder if that make sense given the class definition "The category of > > information pertaining to evidence of an occurrence in nature, in a > > collection, or in a dataset (specimen, observation, etc.)" Is > > abundance "evidence of an occurrence in nature". To me, abundance is > > a property of a survey and its associated methodology and is based on > > multiple occurrences that come from a sample and a definition of extent. > > > > It seems to me to be a bad fit to scrunch abundance into the > > occurrence class. I recognize that it might not quite fit anywhere in > > DwC yet. Wouldn't it be better to wait to see if materialSample is > > ratified as a class within the Darwin Core? > > > > Best, Rob > > > > On Thu, Sep 26, 2013 at 8:01 AM, Donald Hobern [GBIF] > > <dhobern(a)gbif.org <mailto:dhobern@gbif.org>> wrote: > > > > Thanks, John. > > > > You are correct. I think though that abundance is such a commonly needed > > property that it would be a mistake not to make it work easily even in > > Simple Darwin Core. > > > > > > Donald > > > > ---------------------------------------------------------------------- > > Donald Hobern - GBIF Director - dhobern(a)gbif.org <mailto: > dhobern(a)gbif.org> > > Global Biodiversity Information Facility http://www.gbif.org/ > > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > > Tel: +45 3532 1471 <tel:%2B45%203532%201471> Mob: +45 2875 1471 > > <tel:%2B45%202875%201471> Fax: +45 2875 1480 <tel:%2B45%202875%201480> > > ---------------------------------------------------------------------- > > > > > > -----Original Message----- > > > > From: gtuco.btuco(a)gmail.com <mailto:gtuco.btuco@gmail.com> > > [mailto:gtuco.btuco@gmail.com <mailto:gtuco.btuco@gmail.com>] On > > Behalf Of John > > Wieczorek > > Sent: Thursday, September 26, 2013 3:48 PM > > To: Donald Hobern [GBIF] > > Cc: aaike.dewever(a)naturalsciences.be > > <mailto:aaike.dewever@naturalsciences.be>; TDWG Content Mailing List > > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, > > abundanceAsPercent > > > > Could every concept of abundance be captured in a combination of > > abundance, > > abundanceUnit, abundanceMethod? > > > > If so, is there justification for creating new terms at all if the > > concepts > > can be captured in MeasurentsOrFacts > > (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the > > following properties? > > > > measurementType > > measurementValue > > measurementAccuracy > > measurementUnit > > measurementDeterminedDate > > measurementDeterminedBy > > measurementMethod > > measurementRemarks > > > > The only drawback I can see is that with MeasurementOrFacts you could not > > share the abunance information in Simple Darwin Core. To understand > > why, see > > http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. > > > > > > On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] > > <dhobern(a)gbif.org <mailto:dhobern@gbif.org>> > > wrote: > > > Thanks - I think I too have missed something. If we want to make > > > these terms usable, there needs to be a simple way to get numbers out > > > of records that can be compared with one another where sampling > > > methods allow such comparisons. The suggested plain text examples for > > > Abundance don't make this possible. Forcing normalisation into > > > percentages seems an unnecessary hurdle and risks encouraging the > > > impression that number of ducks on a reservoir is somehow comparable > > > with percentage dry mass, proportional expression of CO1 for a > > > particular species in an ecogenomics sample, or whatever. > > > > > > I would much rather we ensured we had a standard, preferred field > > > which the data publisher can populate directly with whatever number is > > > the most appropriate expression of the relative abundance in the > > > sample. That gives consumers a clear expectation of how to > > interpret and > > handle it. > > > > > > Donald > > > > > > ---------------------------------------------------------------------- > > > Donald Hobern - GBIF Director - dhobern(a)gbif.org > > <mailto:dhobern@gbif.org> Global Biodiversity > > > Information Facility http://www.gbif.org/ GBIF Secretariat, > > > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > > > Tel: +45 3532 1471 <tel:%2B45%203532%201471> Mob: +45 2875 1471 > > <tel:%2B45%202875%201471> Fax: +45 2875 1480 <tel:%2B45%202875%201480> > > > ---------------------------------------------------------------------- > > > > > > > > > -----Original Message----- > > > From: tdwg-content-bounces(a)lists.tdwg.org > > <mailto:tdwg-content-bounces@lists.tdwg.org> > > > [mailto:tdwg-content-bounces@lists.tdwg.org > > <mailto:tdwg-content-bounces@lists.tdwg.org>] On Behalf Of Aaike De > > > Wever > > > Sent: Thursday, September 26, 2013 8:44 AM > > > To: tuco(a)berkeley.edu <mailto:tuco@berkeley.edu>; TDWG Content > > Mailing List > > > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > > > abundance, abundanceAsPercent > > > > > > Dear all, > > > > > > As somewhat of an outsider I have another question with regards to the > > > proposed terms abundance and abundanceAsPercent. > > > > > > Is there a specific reason for not adopting: > > > * the abundance field as a field to store only the value and > > > * a field abundanceUnit/abundanceType to specify whether the value is > > > in % of species, % of biovolume, % of biomass, individuals/l, > > > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field > > specific for %)? > > > > > > Maybe this has been discussed during the hackathon and I missed it in > > > the report? > > > > > > Thanks for considering this question. > > > > > > With best regards, > > > Aaike > > > > > > John Wieczorek wrote: > > >> Dear all, > > >> > > >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on > > >> Darwin Core and sample data (22-24 May 2013)" at > > >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is > > >> available for public reference, I would like to formally open the > > >> minimum 30-day comment period on two related new terms proposed > > >> during the workshop and defined in the referenced document. > > >> > > >> The formal proposal would add the following new terms: > > >> > > >> Term Name: abundance > > >> Identifier: http://rs.tdwg.org/dwc/terms/abundance > > >> Namespace: http:/rs.tdwg.org/dwc/terms/ < > http://rs.tdwg.org/dwc/terms/> > > >> Label: Abundance > > >> Definition: The number of individuals of a taxon found in a sample. > > >> This is typically expressed as number per unit of area or volume. In > > >> the case of vegetation and colonial/encrusting species, percent cover > > >> can be used. > > >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", > > >> "24%". For discussion see > > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > > >> further documentation here until the term is ratified) Type of Term: > > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > >> Refines: > > >> Status: proposed > > >> Date Issued: 2012-03-01 > > >> Date Modified: 2013-09-25 > > >> Has Domain: > > >> Has Range: > > >> Refines: > > >> Version: abundance-2013-09-25 > > >> Replaces: > > >> IsReplaceBy: > > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > >> > > >> Term Name: abundanceAsPercent > > >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent > > >> Namespace: http:/rs.tdwg.org/dwc/terms/ < > http://rs.tdwg.org/dwc/terms/> > > >> Label: Abundance as Percent > > >> Definition: 100 times the number of individuals of a taxon found in a > > >> sample divided by the total number of individuals of all taxa in the > > >> sample. > > >> Comment: Examples: "2.4%". For discussion see > > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > > >> further documentation here until the term is ratified) Type of Term: > > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > >> Refines: > > >> Status: proposed > > >> Date Issued: 2012-08-01 > > >> Date Modified: 2013-09-25 > > >> Has Domain: > > >> Has Range: > > >> Refines: > > >> Version: abundanceAsPercent-2013-09-25 > > >> Replaces: > > >> IsReplaceBy: > > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > >> > > >> The related issues in the Darwin Core issue tracker are > > >> https://code.google.com/p/darwincore/issues/detail?id=142 > > >> and > > >> https://code.google.com/p/darwincore/issues/detail?id=187 > > >> > > >> If there are any objections to the changes proposed for these new > > >> terms, or comments about their definitions, please respond to this > > >> message. If there are no objections or if consensus can be reached on > > >> any amendments put forward, the proposal will go before the Executive > > >> Committee for authorization to put these additions into effect after > > >> the public commentary period. > > >> > > >> Cheers, > > >> > > >> John > > >> _______________________________________________ > > >> tdwg-content mailing list > > >> tdwg-content(a)lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org> > > >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > -- > > > Aaike De Wever > > > BioFresh Science Officer > > > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > > > Vautierstraat 29, 1000 Brussels Belgium > > > tel.: +32(0)2 627 43 90 <tel:%2B32%280%292%20627%2043%2090> > > > mobile.: +32(0)486 28 05 93 <tel:%2B32%280%29486%2028%2005%2093> > > > email: <aaike.dewever(a)naturalsciences.be > > <mailto:aaike.dewever@naturalsciences.be>> > > > skype: aaikew > > > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > > > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > > > <http://data.freshwaterbiodiversity.eu/> > > > Belgian Biodiversity Platform: <http://www.biodiversity.be> > > > _______________________________________________ > > > tdwg-content mailing list > > > tdwg-content(a)lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org> > > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > > > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org> > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

4 4

Proposed new Darwin Core terms - abundance, abundanceAsPercent
by John Wieczorek 28 Sep '13

28 Sep '13

8 18

Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
by Éamonn Ó Tuama [GBIF] 27 Sep '13

27 Sep '13

Aaike's suggestion of using the abundance field to store just the numeric value and then provide another field called abundanceUnit/abundanceType to specify what the value is does look like it might be a more workable, machine processable solution. It would, of course, require that the value be selected from a controlled list. At a guess, I do not think that list would be very long but we would need to define it in association with the property abundanceUnit/abundanceType. Eamonn > in % of species, % of biovolume, % of biomass, individuals/l, > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field specific for %)? -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of tdwg-content-request(a)lists.tdwg.org Sent: 26 September 2013 17:23 To: tdwg-content(a)lists.tdwg.org Subject: tdwg-content Digest, Vol 53, Issue 2 Send tdwg-content mailing list submissions to tdwg-content(a)lists.tdwg.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.tdwg.org/mailman/listinfo/tdwg-content or, via email, send a message with subject or body 'help' to tdwg-content-request(a)lists.tdwg.org You can reach the person managing the list at tdwg-content-owner(a)lists.tdwg.org When replying, please edit your Subject line so it is more specific than "Re: Contents of tdwg-content digest..." Today's Topics: 1. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 2. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 3. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 4. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 5. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick) 6. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Chuck Miller) 7. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 8. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 9. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 10. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick) ---------------------------------------------------------------------- Message: 1 Date: Thu, 26 Sep 2013 14:44:34 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdOf7rMwQ3UCGGw1T53c4J7X=amJ_ibSkSX_WSb5EoqcA(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear all, The spirit of the proposal is to satisfy use cases defined in the document "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" found at http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO ontology. Steve is correct. All of the ENVO terms are classes in keeping with the OBO Foundry way of doing things. As such, they don't work in the intended Darwin Core context as they currently stand, where what we want are properties whose values can come from ENVO as a controlled vocabulary in the way Hilmar described. To satisfy the spirit of the proposal, I suggest that instead of replacing the dwc:habitat property with the envo:habitat class and adding the other three ENVO classes, we modify the existing dwc:habitat property and introduce new properties whose ranges are recommended to be the appropriate ENVO classes, as follows: Retain the property term dwc:habitat, but amend the definition to be: Term Name: habitat Identifier: http://rs.tdwg.org/dwc/terms/habitat Namespace: http://rs.tdwg.org/dwc/terms/ Label: Habitat Definition: A spatial region having environmental qualities which may sustain an organism or a community of organisms. Recommended best practice is to use a controlled vocabulary such as defined by the habitat class of the Environment Ontology (ENVO). Comment: Examples: "freshwater habitat", "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2008-11-19 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: habitat-2013-09-26 Replaces: habitat-2009-04-24 IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Add the following new property terms for biome, environmental feature, and environmental material: Term Name: biome Identifier: http://rs.tdwg.org/dwc/terms/biome Namespace: http://rs.tdwg.org/dwc/terms/ Label: Biome Definition: A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation. Recommended best practice is to use a controlled vocabulary such as defined by the biome class of the Environment Ontology (ENVO). Comment: Examples: "flooded grassland biome", "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: biome-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmentalFeature Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Feature Definition: A prominent or distinctive aspect, quality, or characteristic of a biome. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Comment: Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: environmentalFeature-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmentalMaterial Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Material Definition: Material in or on which organisms may live. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Comment: Examples: "scum", "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: environmentalMaterial-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) I hope this makes better sense. Cheers, John On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > Well, the proposal says "The Darwin Core term habitat would be redefined..." > . I take that to mean that the term dwc:habitat is being replaced with > envo:00002036 . If that's not what it means, then it would be good to > clarify. If the intention is to provide values for other terms, that should > be stated. > > Steve > > > Hilmar Lapp wrote: > > I was assuming that the proposal was that subclasses of envo:habitat would > take the place of values for the dwc:habitat property. But perhaps I was > naive or misunderstanding? > > -hilmar > > Sent from away > > On Sep 25, 2013, at 8:23 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> > wrote: > > OK, now that I've had a chance to look at the RDF, it is as I suspected. If > I am understanding the proposal correctly, the proposal is to replace the > term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with the term > <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call > envo:00002036 for brevity) However, the definition of dwc:habitat which you > can view at > http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf > says > > dwc:habitat rdf:type rdfs:Property > > whereas the document I received at the end of those four redirects tells me > that > > envo:00002036 rdf:type owl:Class > > Since > > owl:Class rdfs:subclassOf rdfs:Class > > then we are effectively changing the current DwC "habitat" term from a > property into a class similar to dwc:Occurrence, dwc:Identification, > dwc:Taxon, etc. which are all of type rdfs:Class. > > So I'm left wondering what I can do with the new term. With the old term I > could make a statement like > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat "deciduous > forest" > > or something like that if I take the hint from the DwC class groupings that > dwc:habitat might be a property of dwc:Event instances. But I can't > meaningfully say > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 > "deciduous forest" > > That doesn't make any sense because the way I understand RDF, predicates > should be properties, not classes. Even if we weren't talking about RDF, > I'd still have the same problem (we are changing a property into a class) - > it's just easier for me to make plain what the issue is by giving RDF > examples. So just exactly what can I "do" with envo:00002036 ????? > > I haven't looked up the RDF for the other proposed terms (too much work with > the four redirects), but I suspect if I did, I'd find that they are also > classes and not properties. This particular issue is a case of a broader > issue that I have about OBO-style ontologies. They are great for defining > how many, many kinds of classes are related to each other. But they provide > very few properties that could be used as predicates to serve as properties > of instance data. > > Steve > > John Wieczorek wrote: > > Dear all, > > GBIF has just published "Meeting Report: GBIF hackathon-workshop on > Darwin Core and sample data (22-24 May 2013)" at > http://www.gbif.org/orc/?doc_id=5424. Now that this document is > available for public reference, I would like to formally open the > minimum 30-day comment period on the new environmental terms proposed > during the workshop and defined in the referenced document. > > The formal proposal would change the term habitat to align it with the > ENVO habitat term. The related issues in the Darwin Core issue tracker > is https://code.google.com/p/darwincore/issues/detail?id=178. The > Darwin Core term habitat would be redefined as follows: > > Term Name: habitat > Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 > Namespace: http://purl.obolibrary.org/obo/ > Label: Habitat > Definition: A spatial region having environmental qualities which may > sustain an organism or a community of organisms. > Comment: Examples: "freshwater habitat", > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2008-11-19 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00002036 > Replaces: habitat-2009-04-24 > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > The formal proposal would add the following new terms for biome, > environmental feature, and environmental material: > > Term Name: biome > Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 > Namespace: http://purl.obolibrary.org/obo/ > Label: Biome > Definition: A major class of ecologically similar communities of > plants, animals, and other organisms. Biomes are defined based on > factors such as plant structures (such as trees, shrubs, and grasses), > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > woodland, savanna), and other factors like climate. Unlike ecozones, > biomes are not defined by genetic, taxonomic, or historical > similarities. Biomes are often identified with particular patterns of > ecological succession and climax vegetation. > Comment: Examples: "flooded grassland biome", > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00000428 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmental feature > Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 > Namespace: http://purl.obolibrary.org/obo/ > Label: Environmental Feature > Definition: A prominent or distinctive aspect, quality, or > characteristic of a biome. > Comment: Examples: "meadow", > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00002297 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmental material > Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 > Namespace: http://purl.obolibrary.org/obo/ > Label: Environmental Material > Definition: Material in or on which organisms may live. > Comment: Examples: "scum", > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00010483 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > The related issues in the Darwin Core issue tracker are > https://code.google.com/p/darwincore/issues/detail?id=189 > https://code.google.com/p/darwincore/issues/detail?id=190 > and > https://code.google.com/p/darwincore/issues/detail?id=191 > > If there are any objections to the changes proposed for these terms, > or comments about their definitions, please respond to this message. > If there are no objections or if consensus can be reached on any > amendments put forward, the proposal will go before the Executive > Committee for authorization to put these additions into effect after > the public commentary period. > > Cheers, > > John > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > . > > > > > -- > 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 > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > -- > 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 ------------------------------ Message: 2 Date: Thu, 26 Sep 2013 14:51:13 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdARDj32v9EPaofwHrzwonQ3czgwMaiyDmnj3c7L0tMnA(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I've been in communication with the OBO-ENVO group (obo-envo(a)lists.sourceforge.net) about the proposed re-use of the ENVO terms. The ENVO ontology remains in active development, with a proposed forthcoming guide on how to use ENVO. I have agreed to forward an invitation extended by Pier Buttigieg to the TDWG community to actively contribute. "To be clear, the habitat class itself isn't queued for obsoletion, but its current subclasses are. Once habitat is better-defined, new subclasses will be created. If anyone in TDWG wishes to help shape the definition of this concept or share any observations to promote its usefulness to the biodiversity community we're certainly open to input." On Thu, Sep 26, 2013 at 2:44 PM, John Wieczorek <tuco(a)berkeley.edu> wrote: > Dear all, > > The spirit of the proposal is to satisfy use cases defined in the > document "Meeting Report: GBIF hackathon-workshop on > Darwin Core and sample data (22-24 May 2013)" found at > http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO > ontology. Steve is correct. All of the ENVO terms are classes in > keeping with the OBO Foundry way of doing things. As such, they don't > work in the intended Darwin Core context as they currently stand, > where what we want are properties whose values can come from ENVO as a > controlled vocabulary in the way Hilmar described. > > To satisfy the spirit of the proposal, I suggest that instead of > replacing the dwc:habitat property with the envo:habitat class and > adding the other three ENVO classes, we modify the existing > dwc:habitat property and introduce new properties whose ranges are > recommended to be the appropriate ENVO classes, as follows: > > Retain the property term dwc:habitat, but amend the definition to be: > > Term Name: habitat > Identifier: http://rs.tdwg.org/dwc/terms/habitat > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Habitat > Definition: A spatial region having environmental qualities which may > sustain an organism or a community of organisms. Recommended best > practice is to use a controlled vocabulary such as defined by the > habitat class of the Environment Ontology (ENVO). > Comment: Examples: "freshwater habitat", > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2008-11-19 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: habitat-2013-09-26 > Replaces: habitat-2009-04-24 > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Add the following new property terms for biome, > environmental feature, and environmental material: > > Term Name: biome > Identifier: http://rs.tdwg.org/dwc/terms/biome > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Biome > Definition: A major class of ecologically similar communities of > plants, animals, and other organisms. Biomes are defined based on > factors such as plant structures (such as trees, shrubs, and grasses), > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > woodland, savanna), and other factors like climate. Unlike ecozones, > biomes are not defined by genetic, taxonomic, or historical > similarities. Biomes are often identified with particular patterns of > ecological succession and climax vegetation. Recommended best practice > is to use a controlled vocabulary such as defined by the biome class > of the Environment Ontology (ENVO). > Comment: Examples: "flooded grassland biome", > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: biome-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmentalFeature > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Environmental Feature > Definition: A prominent or distinctive aspect, quality, or > characteristic of a biome. Recommended best practice is to use a > controlled vocabulary such as defined by the environmental feature > class of the Environment Ontology (ENVO). > Comment: Examples: "meadow", > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: environmentalFeature-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmentalMaterial > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Environmental Material > Definition: Material in or on which organisms may live. Recommended > best practice is to use a controlled vocabulary such as defined by the > environmental feature class of the Environment Ontology (ENVO). > Comment: Examples: "scum", > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: environmentalMaterial-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > I hope this makes better sense. > > Cheers, > > John > > On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf > <steve.baskauf(a)vanderbilt.edu> wrote: >> Well, the proposal says "The Darwin Core term habitat would be redefined..." >> . I take that to mean that the term dwc:habitat is being replaced with >> envo:00002036 . If that's not what it means, then it would be good to >> clarify. If the intention is to provide values for other terms, that should >> be stated. >> >> Steve >> >> >> Hilmar Lapp wrote: >> >> I was assuming that the proposal was that subclasses of envo:habitat would >> take the place of values for the dwc:habitat property. But perhaps I was >> naive or misunderstanding? >> >> -hilmar >> >> Sent from away >> >> On Sep 25, 2013, at 8:23 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> >> wrote: >> >> OK, now that I've had a chance to look at the RDF, it is as I suspected. If >> I am understanding the proposal correctly, the proposal is to replace the >> term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with the term >> <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call >> envo:00002036 for brevity) However, the definition of dwc:habitat which you >> can view at >> http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf >> says >> >> dwc:habitat rdf:type rdfs:Property >> >> whereas the document I received at the end of those four redirects tells me >> that >> >> envo:00002036 rdf:type owl:Class >> >> Since >> >> owl:Class rdfs:subclassOf rdfs:Class >> >> then we are effectively changing the current DwC "habitat" term from a >> property into a class similar to dwc:Occurrence, dwc:Identification, >> dwc:Taxon, etc. which are all of type rdfs:Class. >> >> So I'm left wondering what I can do with the new term. With the old term I >> could make a statement like >> >> <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat "deciduous >> forest" >> >> or something like that if I take the hint from the DwC class groupings that >> dwc:habitat might be a property of dwc:Event instances. But I can't >> meaningfully say >> >> <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 >> "deciduous forest" >> >> That doesn't make any sense because the way I understand RDF, predicates >> should be properties, not classes. Even if we weren't talking about RDF, >> I'd still have the same problem (we are changing a property into a class) - >> it's just easier for me to make plain what the issue is by giving RDF >> examples. So just exactly what can I "do" with envo:00002036 ????? >> >> I haven't looked up the RDF for the other proposed terms (too much work with >> the four redirects), but I suspect if I did, I'd find that they are also >> classes and not properties. This particular issue is a case of a broader >> issue that I have about OBO-style ontologies. They are great for defining >> how many, many kinds of classes are related to each other. But they provide >> very few properties that could be used as predicates to serve as properties >> of instance data. >> >> Steve >> >> John Wieczorek wrote: >> >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on the new environmental terms proposed >> during the workshop and defined in the referenced document. >> >> The formal proposal would change the term habitat to align it with the >> ENVO habitat term. The related issues in the Darwin Core issue tracker >> is https://code.google.com/p/darwincore/issues/detail?id=178. The >> Darwin Core term habitat would be redefined as follows: >> >> Term Name: habitat >> Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Habitat >> Definition: A spatial region having environmental qualities which may >> sustain an organism or a community of organisms. >> Comment: Examples: "freshwater habitat", >> "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2008-11-19 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00002036 >> Replaces: habitat-2009-04-24 >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The formal proposal would add the following new terms for biome, >> environmental feature, and environmental material: >> >> Term Name: biome >> Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Biome >> Definition: A major class of ecologically similar communities of >> plants, animals, and other organisms. Biomes are defined based on >> factors such as plant structures (such as trees, shrubs, and grasses), >> leaf types (such as broadleaf and needleleaf), plant spacing (forest, >> woodland, savanna), and other factors like climate. Unlike ecozones, >> biomes are not defined by genetic, taxonomic, or historical >> similarities. Biomes are often identified with particular patterns of >> ecological succession and climax vegetation. >> Comment: Examples: "flooded grassland biome", >> "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00000428 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: environmental feature >> Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Environmental Feature >> Definition: A prominent or distinctive aspect, quality, or >> characteristic of a biome. >> Comment: Examples: "meadow", >> "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00002297 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: environmental material >> Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Environmental Material >> Definition: Material in or on which organisms may live. >> Comment: Examples: "scum", >> "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00010483 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=189 >> https://code.google.com/p/darwincore/issues/detail?id=190 >> and >> https://code.google.com/p/darwincore/issues/detail?id=191 >> >> If there are any objections to the changes proposed for these terms, >> or comments about their definitions, please respond to this message. >> If there are no objections or if consensus can be reached on any >> amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> . >> >> >> >> >> -- >> 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 >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> -- >> 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 ------------------------------ Message: 3 Date: Thu, 26 Sep 2013 15:48:16 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdrmyEAwZ-TcTxUqcdGemwc330_H51XUTo9abb0Mez8-g(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod? If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the following properties? measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> wrote: > Thanks - I think I too have missed something. If we want to make these > terms usable, there needs to be a simple way to get numbers out of records > that can be compared with one another where sampling methods allow such > comparisons. The suggested plain text examples for Abundance don't make > this possible. Forcing normalisation into percentages seems an unnecessary > hurdle and risks encouraging the impression that number of ducks on a > reservoir is somehow comparable with percentage dry mass, proportional > expression of CO1 for a particular species in an ecogenomics sample, or > whatever. > > I would much rather we ensured we had a standard, preferred field which the > data publisher can populate directly with whatever number is the most > appropriate expression of the relative abundance in the sample. That gives > consumers a clear expectation of how to interpret and handle it. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org > Global Biodiversity Information Facility http://www.gbif.org/ > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De Wever > Sent: Thursday, September 26, 2013 8:44 AM > To: tuco(a)berkeley.edu; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, > abundanceAsPercent > > Dear all, > > As somewhat of an outsider I have another question with regards to the > proposed terms abundance and abundanceAsPercent. > > Is there a specific reason for not adopting: > * the abundance field as a field to store only the value and > * a field abundanceUnit/abundanceType to specify whether the value is in % > of species, % of biovolume, % of biomass, individuals/l, ind./m^2, ind/m^3, > ind./sampling effort,...(instead of having a field specific for %)? > > Maybe this has been discussed during the hackathon and I missed it in the > report? > > Thanks for considering this question. > > With best regards, > Aaike > > John Wieczorek wrote: >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on two related new terms proposed during >> the workshop and defined in the referenced document. >> >> The formal proposal would add the following new terms: >> >> Term Name: abundance >> Identifier: http://rs.tdwg.org/dwc/terms/abundance >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance >> Definition: The number of individuals of a taxon found in a sample. >> This is typically expressed as number per unit of area or volume. In >> the case of vegetation and colonial/encrusting species, percent cover >> can be used. >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", >> "24%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-03-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundance-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: abundanceAsPercent >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance as Percent >> Definition: 100 times the number of individuals of a taxon found in a >> sample divided by the total number of individuals of all taxa in the >> sample. >> Comment: Examples: "2.4%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-08-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundanceAsPercent-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=142 >> and >> https://code.google.com/p/darwincore/issues/detail?id=187 >> >> If there are any objections to the changes proposed for these new >> terms, or comments about their definitions, please respond to this >> message. If there are no objections or if consensus can be reached on >> any amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > Aaike De Wever > BioFresh Science Officer > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > Vautierstraat 29, 1000 Brussels Belgium > tel.: +32(0)2 627 43 90 > mobile.: +32(0)486 28 05 93 > email: <aaike.dewever(a)naturalsciences.be> > skype: aaikew > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > <http://data.freshwaterbiodiversity.eu/> > Belgian Biodiversity Platform: <http://www.biodiversity.be> > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > ------------------------------ Message: 4 Date: Thu, 26 Sep 2013 16:01:10 +0200 From: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: <tuco(a)berkeley.edu> Cc: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org> Message-ID: <01fd01cebac0$da9a8550$8fcf8ff0$(a)gbif.org> Content-Type: text/plain; charset="iso-8859-1" Thanks, John. You are correct. I think though that abundance is such a commonly needed property that it would be a mistake not to make it work easily even in Simple Darwin Core. Donald ---------------------------------------------------------------------- Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 ---------------------------------------------------------------------- -----Original Message----- From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Thursday, September 26, 2013 3:48 PM To: Donald Hobern [GBIF] Cc: aaike.dewever(a)naturalsciences.be; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod? If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the following properties? measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> wrote: > Thanks - I think I too have missed something. If we want to make > these terms usable, there needs to be a simple way to get numbers out > of records that can be compared with one another where sampling > methods allow such comparisons. The suggested plain text examples for > Abundance don't make this possible. Forcing normalisation into > percentages seems an unnecessary hurdle and risks encouraging the > impression that number of ducks on a reservoir is somehow comparable > with percentage dry mass, proportional expression of CO1 for a > particular species in an ecogenomics sample, or whatever. > > I would much rather we ensured we had a standard, preferred field > which the data publisher can populate directly with whatever number is > the most appropriate expression of the relative abundance in the > sample. That gives consumers a clear expectation of how to interpret and handle it. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity > Information Facility http://www.gbif.org/ GBIF Secretariat, > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De > Wever > Sent: Thursday, September 26, 2013 8:44 AM > To: tuco(a)berkeley.edu; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > abundance, abundanceAsPercent > > Dear all, > > As somewhat of an outsider I have another question with regards to the > proposed terms abundance and abundanceAsPercent. > > Is there a specific reason for not adopting: > * the abundance field as a field to store only the value and > * a field abundanceUnit/abundanceType to specify whether the value is > in % of species, % of biovolume, % of biomass, individuals/l, > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field specific for %)? > > Maybe this has been discussed during the hackathon and I missed it in > the report? > > Thanks for considering this question. > > With best regards, > Aaike > > John Wieczorek wrote: >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on two related new terms proposed >> during the workshop and defined in the referenced document. >> >> The formal proposal would add the following new terms: >> >> Term Name: abundance >> Identifier: http://rs.tdwg.org/dwc/terms/abundance >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance >> Definition: The number of individuals of a taxon found in a sample. >> This is typically expressed as number per unit of area or volume. In >> the case of vegetation and colonial/encrusting species, percent cover >> can be used. >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", >> "24%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-03-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundance-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: abundanceAsPercent >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance as Percent >> Definition: 100 times the number of individuals of a taxon found in a >> sample divided by the total number of individuals of all taxa in the >> sample. >> Comment: Examples: "2.4%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-08-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundanceAsPercent-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=142 >> and >> https://code.google.com/p/darwincore/issues/detail?id=187 >> >> If there are any objections to the changes proposed for these new >> terms, or comments about their definitions, please respond to this >> message. If there are no objections or if consensus can be reached on >> any amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > Aaike De Wever > BioFresh Science Officer > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > Vautierstraat 29, 1000 Brussels Belgium > tel.: +32(0)2 627 43 90 > mobile.: +32(0)486 28 05 93 > email: <aaike.dewever(a)naturalsciences.be> > skype: aaikew > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > <http://data.freshwaterbiodiversity.eu/> > Belgian Biodiversity Platform: <http://www.biodiversity.be> > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > ------------------------------ Message: 5 Date: Thu, 26 Sep 2013 08:37:15 -0600 From: Robert Guralnick <Robert.Guralnick(a)colorado.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CADAgxGX=ZRknz2T-kd0e9wwwP72pSrtoeRVb175fm1EQQ7iovQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" I agree with Donald here regarding the need for Abundance, but am, to be honest, not quite I understand (or agree) with the logic of the proposal. Abundance is listed as a property of an occurrence, and I wonder if that make sense given the class definition "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)" Is abundance "evidence of an occurrence in nature". To me, abundance is a property of a survey and its associated methodology and is based on multiple occurrences that come from a sample and a definition of extent. It seems to me to be a bad fit to scrunch abundance into the occurrence class. I recognize that it might not quite fit anywhere in DwC yet. Wouldn't it be better to wait to see if materialSample is ratified as a class within the Darwin Core? Best, Rob On Thu, Sep 26, 2013 at 8:01 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org>wrote: > Thanks, John. > > You are correct. I think though that abundance is such a commonly needed > property that it would be a mistake not to make it work easily even in > Simple Darwin Core. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org > Global Biodiversity Information Facility http://www.gbif.org/ > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of > John > Wieczorek > Sent: Thursday, September 26, 2013 3:48 PM > To: Donald Hobern [GBIF] > Cc: aaike.dewever(a)naturalsciences.be; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, > abundanceAsPercent > > Could every concept of abundance be captured in a combination of abundance, > abundanceUnit, abundanceMethod? > > If so, is there justification for creating new terms at all if the concepts > can be captured in MeasurentsOrFacts > (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the > following properties? > > measurementType > measurementValue > measurementAccuracy > measurementUnit > measurementDeterminedDate > measurementDeterminedBy > measurementMethod > measurementRemarks > > The only drawback I can see is that with MeasurementOrFacts you could not > share the abunance information in Simple Darwin Core. To understand why, > see > http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. > > > On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> > wrote: > > Thanks - I think I too have missed something. If we want to make > > these terms usable, there needs to be a simple way to get numbers out > > of records that can be compared with one another where sampling > > methods allow such comparisons. The suggested plain text examples for > > Abundance don't make this possible. Forcing normalisation into > > percentages seems an unnecessary hurdle and risks encouraging the > > impression that number of ducks on a reservoir is somehow comparable > > with percentage dry mass, proportional expression of CO1 for a > > particular species in an ecogenomics sample, or whatever. > > > > I would much rather we ensured we had a standard, preferred field > > which the data publisher can populate directly with whatever number is > > the most appropriate expression of the relative abundance in the > > sample. That gives consumers a clear expectation of how to interpret and > handle it. > > > > Donald > > > > ---------------------------------------------------------------------- > > Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity > > Information Facility http://www.gbif.org/ GBIF Secretariat, > > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > > ---------------------------------------------------------------------- > > > > > > -----Original Message----- > > From: tdwg-content-bounces(a)lists.tdwg.org > > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De > > Wever > > Sent: Thursday, September 26, 2013 8:44 AM > > To: tuco(a)berkeley.edu; TDWG Content Mailing List > > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > > abundance, abundanceAsPercent > > > > Dear all, > > > > As somewhat of an outsider I have another question with regards to the > > proposed terms abundance and abundanceAsPercent. > > > > Is there a specific reason for not adopting: > > * the abundance field as a field to store only the value and > > * a field abundanceUnit/abundanceType to specify whether the value is > > in % of species, % of biovolume, % of biomass, individuals/l, > > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field > specific for %)? > > > > Maybe this has been discussed during the hackathon and I missed it in > > the report? > > > > Thanks for considering this question. > > > > With best regards, > > Aaike > > > > John Wieczorek wrote: > >> Dear all, > >> > >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on > >> Darwin Core and sample data (22-24 May 2013)" at > >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is > >> available for public reference, I would like to formally open the > >> minimum 30-day comment period on two related new terms proposed > >> during the workshop and defined in the referenced document. > >> > >> The formal proposal would add the following new terms: > >> > >> Term Name: abundance > >> Identifier: http://rs.tdwg.org/dwc/terms/abundance > >> Namespace: http:/rs.tdwg.org/dwc/terms/ > >> Label: Abundance > >> Definition: The number of individuals of a taxon found in a sample. > >> This is typically expressed as number per unit of area or volume. In > >> the case of vegetation and colonial/encrusting species, percent cover > >> can be used. > >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", > >> "24%". For discussion see > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > >> further documentation here until the term is ratified) Type of Term: > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > >> Refines: > >> Status: proposed > >> Date Issued: 2012-03-01 > >> Date Modified: 2013-09-25 > >> Has Domain: > >> Has Range: > >> Refines: > >> Version: abundance-2013-09-25 > >> Replaces: > >> IsReplaceBy: > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > >> > >> Term Name: abundanceAsPercent > >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent > >> Namespace: http:/rs.tdwg.org/dwc/terms/ > >> Label: Abundance as Percent > >> Definition: 100 times the number of individuals of a taxon found in a > >> sample divided by the total number of individuals of all taxa in the > >> sample. > >> Comment: Examples: "2.4%". For discussion see > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > >> further documentation here until the term is ratified) Type of Term: > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > >> Refines: > >> Status: proposed > >> Date Issued: 2012-08-01 > >> Date Modified: 2013-09-25 > >> Has Domain: > >> Has Range: > >> Refines: > >> Version: abundanceAsPercent-2013-09-25 > >> Replaces: > >> IsReplaceBy: > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > >> > >> The related issues in the Darwin Core issue tracker are > >> https://code.google.com/p/darwincore/issues/detail?id=142 > >> and > >> https://code.google.com/p/darwincore/issues/detail?id=187 > >> > >> If there are any objections to the changes proposed for these new > >> terms, or comments about their definitions, please respond to this > >> message. If there are no objections or if consensus can be reached on > >> any amendments put forward, the proposal will go before the Executive > >> Committee for authorization to put these additions into effect after > >> the public commentary period. > >> > >> Cheers, > >> > >> John > >> _______________________________________________ > >> tdwg-content mailing list > >> tdwg-content(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > -- > > Aaike De Wever > > BioFresh Science Officer > > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > > Vautierstraat 29, 1000 Brussels Belgium > > tel.: +32(0)2 627 43 90 > > mobile.: +32(0)486 28 05 93 > > email: <aaike.dewever(a)naturalsciences.be> > > skype: aaikew > > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > > <http://data.freshwaterbiodiversity.eu/> > > Belgian Biodiversity Platform: <http://www.biodiversity.be> > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO
by Éamonn Ó Tuama [GBIF] 27 Sep '13

27 Sep '13

The DwC workshop report in which the use of ENVO terms was discussed clearly distinguished between properties and classes. The revised proposal by John in which dwc:habitat is retained and three new properties created (material, environmental feature, biome) whose ranges are drawn from the equivalent ENVO classes meets the proposal outlined in the report. ----from DwC workshop report (http://www.gbif.org/orc/?doc_id=5424 )---- Habitat and ENVO The Environment Ontology (ENVO) [10] provides a more granular way of referring to the environment in which an organism lives than is currently possible with the Darwin Core habitat term. In addition to habitat (http://purl.obolibrary.org/obo/ENVO_00002036) ENVO provides three broad classifications for environment - biome, feature, and material... The advantage of integrating Darwin Core with ENVO is that it provides a mechanism for integrating environmental descriptions for a broad range of species. Further, ENVO provides distinct URIs that can be used to denote the exact material, feature, or biome in question, making the content more semantically precise. Thus, it is recommended that the value of the Darwin Core habitat property be selected from the ENVO habitat class... It is also recommended that Darwin Core include three new properties (environmental material, environmental feature, and biome), the recommended vocabulary for which should be from the equivalent ENVO classes. Éamonn -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of tdwg-content-request(a)lists.tdwg.org Sent: 26 September 2013 17:23 To: tdwg-content(a)lists.tdwg.org Subject: tdwg-content Digest, Vol 53, Issue 2 Send tdwg-content mailing list submissions to tdwg-content(a)lists.tdwg.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.tdwg.org/mailman/listinfo/tdwg-content or, via email, send a message with subject or body 'help' to tdwg-content-request(a)lists.tdwg.org You can reach the person managing the list at tdwg-content-owner(a)lists.tdwg.org When replying, please edit your Subject line so it is more specific than "Re: Contents of tdwg-content digest..." Today's Topics: 1. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 2. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 3. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 4. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 5. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick) 6. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Chuck Miller) 7. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 8. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 9. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 10. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick) ---------------------------------------------------------------------- Message: 1 Date: Thu, 26 Sep 2013 14:44:34 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdOf7rMwQ3UCGGw1T53c4J7X=amJ_ibSkSX_WSb5EoqcA(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear all, The spirit of the proposal is to satisfy use cases defined in the document "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" found at http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO ontology. Steve is correct. All of the ENVO terms are classes in keeping with the OBO Foundry way of doing things. As such, they don't work in the intended Darwin Core context as they currently stand, where what we want are properties whose values can come from ENVO as a controlled vocabulary in the way Hilmar described. To satisfy the spirit of the proposal, I suggest that instead of replacing the dwc:habitat property with the envo:habitat class and adding the other three ENVO classes, we modify the existing dwc:habitat property and introduce new properties whose ranges are recommended to be the appropriate ENVO classes, as follows: Retain the property term dwc:habitat, but amend the definition to be: Term Name: habitat Identifier: http://rs.tdwg.org/dwc/terms/habitat Namespace: http://rs.tdwg.org/dwc/terms/ Label: Habitat Definition: A spatial region having environmental qualities which may sustain an organism or a community of organisms. Recommended best practice is to use a controlled vocabulary such as defined by the habitat class of the Environment Ontology (ENVO). Comment: Examples: "freshwater habitat", "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2008-11-19 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: habitat-2013-09-26 Replaces: habitat-2009-04-24 IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Add the following new property terms for biome, environmental feature, and environmental material: Term Name: biome Identifier: http://rs.tdwg.org/dwc/terms/biome Namespace: http://rs.tdwg.org/dwc/terms/ Label: Biome Definition: A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation. Recommended best practice is to use a controlled vocabulary such as defined by the biome class of the Environment Ontology (ENVO). Comment: Examples: "flooded grassland biome", "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: biome-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmentalFeature Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Feature Definition: A prominent or distinctive aspect, quality, or characteristic of a biome. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Comment: Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: environmentalFeature-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmentalMaterial Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Material Definition: Material in or on which organisms may live. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Comment: Examples: "scum", "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: environmentalMaterial-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) I hope this makes better sense. Cheers, John On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > Well, the proposal says "The Darwin Core term habitat would be redefined..." > . I take that to mean that the term dwc:habitat is being replaced with > envo:00002036 . If that's not what it means, then it would be good to > clarify. If the intention is to provide values for other terms, that should > be stated. > > Steve > > > Hilmar Lapp wrote: > > I was assuming that the proposal was that subclasses of envo:habitat would > take the place of values for the dwc:habitat property. But perhaps I was > naive or misunderstanding? > > -hilmar > > Sent from away > > On Sep 25, 2013, at 8:23 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> > wrote: > > OK, now that I've had a chance to look at the RDF, it is as I suspected. If > I am understanding the proposal correctly, the proposal is to replace the > term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with the term > <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call > envo:00002036 for brevity) However, the definition of dwc:habitat which you > can view at > http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf > says > > dwc:habitat rdf:type rdfs:Property > > whereas the document I received at the end of those four redirects tells me > that > > envo:00002036 rdf:type owl:Class > > Since > > owl:Class rdfs:subclassOf rdfs:Class > > then we are effectively changing the current DwC "habitat" term from a > property into a class similar to dwc:Occurrence, dwc:Identification, > dwc:Taxon, etc. which are all of type rdfs:Class. > > So I'm left wondering what I can do with the new term. With the old term I > could make a statement like > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat "deciduous > forest" > > or something like that if I take the hint from the DwC class groupings that > dwc:habitat might be a property of dwc:Event instances. But I can't > meaningfully say > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 > "deciduous forest" > > That doesn't make any sense because the way I understand RDF, predicates > should be properties, not classes. Even if we weren't talking about RDF, > I'd still have the same problem (we are changing a property into a class) - > it's just easier for me to make plain what the issue is by giving RDF > examples. So just exactly what can I "do" with envo:00002036 ????? > > I haven't looked up the RDF for the other proposed terms (too much work with > the four redirects), but I suspect if I did, I'd find that they are also > classes and not properties. This particular issue is a case of a broader > issue that I have about OBO-style ontologies. They are great for defining > how many, many kinds of classes are related to each other. But they provide > very few properties that could be used as predicates to serve as properties > of instance data. > > Steve > > John Wieczorek wrote: > > Dear all, > > GBIF has just published "Meeting Report: GBIF hackathon-workshop on > Darwin Core and sample data (22-24 May 2013)" at > http://www.gbif.org/orc/?doc_id=5424. Now that this document is > available for public reference, I would like to formally open the > minimum 30-day comment period on the new environmental terms proposed > during the workshop and defined in the referenced document. > > The formal proposal would change the term habitat to align it with the > ENVO habitat term. The related issues in the Darwin Core issue tracker > is https://code.google.com/p/darwincore/issues/detail?id=178. The > Darwin Core term habitat would be redefined as follows: > > Term Name: habitat > Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 > Namespace: http://purl.obolibrary.org/obo/ > Label: Habitat > Definition: A spatial region having environmental qualities which may > sustain an organism or a community of organisms. > Comment: Examples: "freshwater habitat", > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2008-11-19 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00002036 > Replaces: habitat-2009-04-24 > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > The formal proposal would add the following new terms for biome, > environmental feature, and environmental material: > > Term Name: biome > Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 > Namespace: http://purl.obolibrary.org/obo/ > Label: Biome > Definition: A major class of ecologically similar communities of > plants, animals, and other organisms. Biomes are defined based on > factors such as plant structures (such as trees, shrubs, and grasses), > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > woodland, savanna), and other factors like climate. Unlike ecozones, > biomes are not defined by genetic, taxonomic, or historical > similarities. Biomes are often identified with particular patterns of > ecological succession and climax vegetation. > Comment: Examples: "flooded grassland biome", > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00000428 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmental feature > Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 > Namespace: http://purl.obolibrary.org/obo/ > Label: Environmental Feature > Definition: A prominent or distinctive aspect, quality, or > characteristic of a biome. > Comment: Examples: "meadow", > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00002297 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmental material > Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 > Namespace: http://purl.obolibrary.org/obo/ > Label: Environmental Material > Definition: Material in or on which organisms may live. > Comment: Examples: "scum", > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00010483 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > The related issues in the Darwin Core issue tracker are > https://code.google.com/p/darwincore/issues/detail?id=189 > https://code.google.com/p/darwincore/issues/detail?id=190 > and > https://code.google.com/p/darwincore/issues/detail?id=191 > > If there are any objections to the changes proposed for these terms, > or comments about their definitions, please respond to this message. > If there are no objections or if consensus can be reached on any > amendments put forward, the proposal will go before the Executive > Committee for authorization to put these additions into effect after > the public commentary period. > > Cheers, > > John > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > . > > > > > -- > 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 > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > -- > 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 ------------------------------ Message: 2 Date: Thu, 26 Sep 2013 14:51:13 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdARDj32v9EPaofwHrzwonQ3czgwMaiyDmnj3c7L0tMnA(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I've been in communication with the OBO-ENVO group (obo-envo(a)lists.sourceforge.net) about the proposed re-use of the ENVO terms. The ENVO ontology remains in active development, with a proposed forthcoming guide on how to use ENVO. I have agreed to forward an invitation extended by Pier Buttigieg to the TDWG community to actively contribute. "To be clear, the habitat class itself isn't queued for obsoletion, but its current subclasses are. Once habitat is better-defined, new subclasses will be created. If anyone in TDWG wishes to help shape the definition of this concept or share any observations to promote its usefulness to the biodiversity community we're certainly open to input." On Thu, Sep 26, 2013 at 2:44 PM, John Wieczorek <tuco(a)berkeley.edu> wrote: > Dear all, > > The spirit of the proposal is to satisfy use cases defined in the > document "Meeting Report: GBIF hackathon-workshop on > Darwin Core and sample data (22-24 May 2013)" found at > http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO > ontology. Steve is correct. All of the ENVO terms are classes in > keeping with the OBO Foundry way of doing things. As such, they don't > work in the intended Darwin Core context as they currently stand, > where what we want are properties whose values can come from ENVO as a > controlled vocabulary in the way Hilmar described. > > To satisfy the spirit of the proposal, I suggest that instead of > replacing the dwc:habitat property with the envo:habitat class and > adding the other three ENVO classes, we modify the existing > dwc:habitat property and introduce new properties whose ranges are > recommended to be the appropriate ENVO classes, as follows: > > Retain the property term dwc:habitat, but amend the definition to be: > > Term Name: habitat > Identifier: http://rs.tdwg.org/dwc/terms/habitat > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Habitat > Definition: A spatial region having environmental qualities which may > sustain an organism or a community of organisms. Recommended best > practice is to use a controlled vocabulary such as defined by the > habitat class of the Environment Ontology (ENVO). > Comment: Examples: "freshwater habitat", > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2008-11-19 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: habitat-2013-09-26 > Replaces: habitat-2009-04-24 > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Add the following new property terms for biome, > environmental feature, and environmental material: > > Term Name: biome > Identifier: http://rs.tdwg.org/dwc/terms/biome > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Biome > Definition: A major class of ecologically similar communities of > plants, animals, and other organisms. Biomes are defined based on > factors such as plant structures (such as trees, shrubs, and grasses), > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > woodland, savanna), and other factors like climate. Unlike ecozones, > biomes are not defined by genetic, taxonomic, or historical > similarities. Biomes are often identified with particular patterns of > ecological succession and climax vegetation. Recommended best practice > is to use a controlled vocabulary such as defined by the biome class > of the Environment Ontology (ENVO). > Comment: Examples: "flooded grassland biome", > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: biome-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmentalFeature > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Environmental Feature > Definition: A prominent or distinctive aspect, quality, or > characteristic of a biome. Recommended best practice is to use a > controlled vocabulary such as defined by the environmental feature > class of the Environment Ontology (ENVO). > Comment: Examples: "meadow", > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: environmentalFeature-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmentalMaterial > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Environmental Material > Definition: Material in or on which organisms may live. Recommended > best practice is to use a controlled vocabulary such as defined by the > environmental feature class of the Environment Ontology (ENVO). > Comment: Examples: "scum", > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: environmentalMaterial-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > I hope this makes better sense. > > Cheers, > > John > > On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf > <steve.baskauf(a)vanderbilt.edu> wrote: >> Well, the proposal says "The Darwin Core term habitat would be redefined..." >> . I take that to mean that the term dwc:habitat is being replaced with >> envo:00002036 . If that's not what it means, then it would be good to >> clarify. If the intention is to provide values for other terms, that should >> be stated. >> >> Steve >> >> >> Hilmar Lapp wrote: >> >> I was assuming that the proposal was that subclasses of envo:habitat would >> take the place of values for the dwc:habitat property. But perhaps I was >> naive or misunderstanding? >> >> -hilmar >> >> Sent from away >> >> On Sep 25, 2013, at 8:23 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> >> wrote: >> >> OK, now that I've had a chance to look at the RDF, it is as I suspected. If >> I am understanding the proposal correctly, the proposal is to replace the >> term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with the term >> <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call >> envo:00002036 for brevity) However, the definition of dwc:habitat which you >> can view at >> http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf >> says >> >> dwc:habitat rdf:type rdfs:Property >> >> whereas the document I received at the end of those four redirects tells me >> that >> >> envo:00002036 rdf:type owl:Class >> >> Since >> >> owl:Class rdfs:subclassOf rdfs:Class >> >> then we are effectively changing the current DwC "habitat" term from a >> property into a class similar to dwc:Occurrence, dwc:Identification, >> dwc:Taxon, etc. which are all of type rdfs:Class. >> >> So I'm left wondering what I can do with the new term. With the old term I >> could make a statement like >> >> <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat "deciduous >> forest" >> >> or something like that if I take the hint from the DwC class groupings that >> dwc:habitat might be a property of dwc:Event instances. But I can't >> meaningfully say >> >> <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 >> "deciduous forest" >> >> That doesn't make any sense because the way I understand RDF, predicates >> should be properties, not classes. Even if we weren't talking about RDF, >> I'd still have the same problem (we are changing a property into a class) - >> it's just easier for me to make plain what the issue is by giving RDF >> examples. So just exactly what can I "do" with envo:00002036 ????? >> >> I haven't looked up the RDF for the other proposed terms (too much work with >> the four redirects), but I suspect if I did, I'd find that they are also >> classes and not properties. This particular issue is a case of a broader >> issue that I have about OBO-style ontologies. They are great for defining >> how many, many kinds of classes are related to each other. But they provide >> very few properties that could be used as predicates to serve as properties >> of instance data. >> >> Steve >> >> John Wieczorek wrote: >> >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on the new environmental terms proposed >> during the workshop and defined in the referenced document. >> >> The formal proposal would change the term habitat to align it with the >> ENVO habitat term. The related issues in the Darwin Core issue tracker >> is https://code.google.com/p/darwincore/issues/detail?id=178. The >> Darwin Core term habitat would be redefined as follows: >> >> Term Name: habitat >> Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Habitat >> Definition: A spatial region having environmental qualities which may >> sustain an organism or a community of organisms. >> Comment: Examples: "freshwater habitat", >> "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2008-11-19 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00002036 >> Replaces: habitat-2009-04-24 >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The formal proposal would add the following new terms for biome, >> environmental feature, and environmental material: >> >> Term Name: biome >> Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Biome >> Definition: A major class of ecologically similar communities of >> plants, animals, and other organisms. Biomes are defined based on >> factors such as plant structures (such as trees, shrubs, and grasses), >> leaf types (such as broadleaf and needleleaf), plant spacing (forest, >> woodland, savanna), and other factors like climate. Unlike ecozones, >> biomes are not defined by genetic, taxonomic, or historical >> similarities. Biomes are often identified with particular patterns of >> ecological succession and climax vegetation. >> Comment: Examples: "flooded grassland biome", >> "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00000428 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: environmental feature >> Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Environmental Feature >> Definition: A prominent or distinctive aspect, quality, or >> characteristic of a biome. >> Comment: Examples: "meadow", >> "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00002297 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: environmental material >> Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Environmental Material >> Definition: Material in or on which organisms may live. >> Comment: Examples: "scum", >> "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00010483 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=189 >> https://code.google.com/p/darwincore/issues/detail?id=190 >> and >> https://code.google.com/p/darwincore/issues/detail?id=191 >> >> If there are any objections to the changes proposed for these terms, >> or comments about their definitions, please respond to this message. >> If there are no objections or if consensus can be reached on any >> amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> . >> >> >> >> >> -- >> 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 >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> -- >> 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 ------------------------------ Message: 3 Date: Thu, 26 Sep 2013 15:48:16 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdrmyEAwZ-TcTxUqcdGemwc330_H51XUTo9abb0Mez8-g(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod? If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the following properties? measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> wrote: > Thanks - I think I too have missed something. If we want to make these > terms usable, there needs to be a simple way to get numbers out of records > that can be compared with one another where sampling methods allow such > comparisons. The suggested plain text examples for Abundance don't make > this possible. Forcing normalisation into percentages seems an unnecessary > hurdle and risks encouraging the impression that number of ducks on a > reservoir is somehow comparable with percentage dry mass, proportional > expression of CO1 for a particular species in an ecogenomics sample, or > whatever. > > I would much rather we ensured we had a standard, preferred field which the > data publisher can populate directly with whatever number is the most > appropriate expression of the relative abundance in the sample. That gives > consumers a clear expectation of how to interpret and handle it. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org > Global Biodiversity Information Facility http://www.gbif.org/ > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De Wever > Sent: Thursday, September 26, 2013 8:44 AM > To: tuco(a)berkeley.edu; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, > abundanceAsPercent > > Dear all, > > As somewhat of an outsider I have another question with regards to the > proposed terms abundance and abundanceAsPercent. > > Is there a specific reason for not adopting: > * the abundance field as a field to store only the value and > * a field abundanceUnit/abundanceType to specify whether the value is in % > of species, % of biovolume, % of biomass, individuals/l, ind./m^2, ind/m^3, > ind./sampling effort,...(instead of having a field specific for %)? > > Maybe this has been discussed during the hackathon and I missed it in the > report? > > Thanks for considering this question. > > With best regards, > Aaike > > John Wieczorek wrote: >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on two related new terms proposed during >> the workshop and defined in the referenced document. >> >> The formal proposal would add the following new terms: >> >> Term Name: abundance >> Identifier: http://rs.tdwg.org/dwc/terms/abundance >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance >> Definition: The number of individuals of a taxon found in a sample. >> This is typically expressed as number per unit of area or volume. In >> the case of vegetation and colonial/encrusting species, percent cover >> can be used. >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", >> "24%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-03-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundance-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: abundanceAsPercent >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance as Percent >> Definition: 100 times the number of individuals of a taxon found in a >> sample divided by the total number of individuals of all taxa in the >> sample. >> Comment: Examples: "2.4%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-08-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundanceAsPercent-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=142 >> and >> https://code.google.com/p/darwincore/issues/detail?id=187 >> >> If there are any objections to the changes proposed for these new >> terms, or comments about their definitions, please respond to this >> message. If there are no objections or if consensus can be reached on >> any amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > Aaike De Wever > BioFresh Science Officer > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > Vautierstraat 29, 1000 Brussels Belgium > tel.: +32(0)2 627 43 90 > mobile.: +32(0)486 28 05 93 > email: <aaike.dewever(a)naturalsciences.be> > skype: aaikew > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > <http://data.freshwaterbiodiversity.eu/> > Belgian Biodiversity Platform: <http://www.biodiversity.be> > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > ------------------------------ Message: 4 Date: Thu, 26 Sep 2013 16:01:10 +0200 From: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: <tuco(a)berkeley.edu> Cc: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org> Message-ID: <01fd01cebac0$da9a8550$8fcf8ff0$(a)gbif.org> Content-Type: text/plain; charset="iso-8859-1" Thanks, John. You are correct. I think though that abundance is such a commonly needed property that it would be a mistake not to make it work easily even in Simple Darwin Core. Donald ---------------------------------------------------------------------- Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 ---------------------------------------------------------------------- -----Original Message----- From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Thursday, September 26, 2013 3:48 PM To: Donald Hobern [GBIF] Cc: aaike.dewever(a)naturalsciences.be; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod? If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the following properties? measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> wrote: > Thanks - I think I too have missed something. If we want to make > these terms usable, there needs to be a simple way to get numbers out > of records that can be compared with one another where sampling > methods allow such comparisons. The suggested plain text examples for > Abundance don't make this possible. Forcing normalisation into > percentages seems an unnecessary hurdle and risks encouraging the > impression that number of ducks on a reservoir is somehow comparable > with percentage dry mass, proportional expression of CO1 for a > particular species in an ecogenomics sample, or whatever. > > I would much rather we ensured we had a standard, preferred field > which the data publisher can populate directly with whatever number is > the most appropriate expression of the relative abundance in the > sample. That gives consumers a clear expectation of how to interpret and handle it. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity > Information Facility http://www.gbif.org/ GBIF Secretariat, > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De > Wever > Sent: Thursday, September 26, 2013 8:44 AM > To: tuco(a)berkeley.edu; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > abundance, abundanceAsPercent > > Dear all, > > As somewhat of an outsider I have another question with regards to the > proposed terms abundance and abundanceAsPercent. > > Is there a specific reason for not adopting: > * the abundance field as a field to store only the value and > * a field abundanceUnit/abundanceType to specify whether the value is > in % of species, % of biovolume, % of biomass, individuals/l, > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field specific for %)? > > Maybe this has been discussed during the hackathon and I missed it in > the report? > > Thanks for considering this question. > > With best regards, > Aaike > > John Wieczorek wrote: >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on two related new terms proposed >> during the workshop and defined in the referenced document. >> >> The formal proposal would add the following new terms: >> >> Term Name: abundance >> Identifier: http://rs.tdwg.org/dwc/terms/abundance >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance >> Definition: The number of individuals of a taxon found in a sample. >> This is typically expressed as number per unit of area or volume. In >> the case of vegetation and colonial/encrusting species, percent cover >> can be used. >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", >> "24%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-03-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundance-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: abundanceAsPercent >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance as Percent >> Definition: 100 times the number of individuals of a taxon found in a >> sample divided by the total number of individuals of all taxa in the >> sample. >> Comment: Examples: "2.4%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-08-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundanceAsPercent-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=142 >> and >> https://code.google.com/p/darwincore/issues/detail?id=187 >> >> If there are any objections to the changes proposed for these new >> terms, or comments about their definitions, please respond to this >> message. If there are no objections or if consensus can be reached on >> any amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > Aaike De Wever > BioFresh Science Officer > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > Vautierstraat 29, 1000 Brussels Belgium > tel.: +32(0)2 627 43 90 > mobile.: +32(0)486 28 05 93 > email: <aaike.dewever(a)naturalsciences.be> > skype: aaikew > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > <http://data.freshwaterbiodiversity.eu/> > Belgian Biodiversity Platform: <http://www.biodiversity.be> > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > ------------------------------ Message: 5 Date: Thu, 26 Sep 2013 08:37:15 -0600 From: Robert Guralnick <Robert.Guralnick(a)colorado.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CADAgxGX=ZRknz2T-kd0e9wwwP72pSrtoeRVb175fm1EQQ7iovQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" I agree with Donald here regarding the need for Abundance, but am, to be honest, not quite I understand (or agree) with the logic of the proposal. Abundance is listed as a property of an occurrence, and I wonder if that make sense given the class definition "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)" Is abundance "evidence of an occurrence in nature". To me, abundance is a property of a survey and its associated methodology and is based on multiple occurrences that come from a sample and a definition of extent. It seems to me to be a bad fit to scrunch abundance into the occurrence class. I recognize that it might not quite fit anywhere in DwC yet. Wouldn't it be better to wait to see if materialSample is ratified as a class within the Darwin Core? Best, Rob On Thu, Sep 26, 2013 at 8:01 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org>wrote: > Thanks, John. > > You are correct. I think though that abundance is such a commonly needed > property that it would be a mistake not to make it work easily even in > Simple Darwin Core. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org > Global Biodiversity Information Facility http://www.gbif.org/ > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of > John > Wieczorek > Sent: Thursday, September 26, 2013 3:48 PM > To: Donald Hobern [GBIF] > Cc: aaike.dewever(a)naturalsciences.be; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, > abundanceAsPercent > > Could every concept of abundance be captured in a combination of abundance, > abundanceUnit, abundanceMethod? > > If so, is there justification for creating new terms at all if the concepts > can be captured in MeasurentsOrFacts > (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the > following properties? > > measurementType > measurementValue > measurementAccuracy > measurementUnit > measurementDeterminedDate > measurementDeterminedBy > measurementMethod > measurementRemarks > > The only drawback I can see is that with MeasurementOrFacts you could not > share the abunance information in Simple Darwin Core. To understand why, > see > http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. > > > On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> > wrote: > > Thanks - I think I too have missed something. If we want to make > > these terms usable, there needs to be a simple way to get numbers out > > of records that can be compared with one another where sampling > > methods allow such comparisons. The suggested plain text examples for > > Abundance don't make this possible. Forcing normalisation into > > percentages seems an unnecessary hurdle and risks encouraging the > > impression that number of ducks on a reservoir is somehow comparable > > with percentage dry mass, proportional expression of CO1 for a > > particular species in an ecogenomics sample, or whatever. > > > > I would much rather we ensured we had a standard, preferred field > > which the data publisher can populate directly with whatever number is > > the most appropriate expression of the relative abundance in the > > sample. That gives consumers a clear expectation of how to interpret and > handle it. > > > > Donald > > > > ---------------------------------------------------------------------- > > Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity > > Information Facility http://www.gbif.org/ GBIF Secretariat, > > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > > ---------------------------------------------------------------------- > > > > > > -----Original Message----- > > From: tdwg-content-bounces(a)lists.tdwg.org > > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De > > Wever > > Sent: Thursday, September 26, 2013 8:44 AM > > To: tuco(a)berkeley.edu; TDWG Content Mailing List > > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > > abundance, abundanceAsPercent > > > > Dear all, > > > > As somewhat of an outsider I have another question with regards to the > > proposed terms abundance and abundanceAsPercent. > > > > Is there a specific reason for not adopting: > > * the abundance field as a field to store only the value and > > * a field abundanceUnit/abundanceType to specify whether the value is > > in % of species, % of biovolume, % of biomass, individuals/l, > > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field > specific for %)? > > > > Maybe this has been discussed during the hackathon and I missed it in > > the report? > > > > Thanks for considering this question. > > > > With best regards, > > Aaike > > > > John Wieczorek wrote: > >> Dear all, > >> > >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on > >> Darwin Core and sample data (22-24 May 2013)" at > >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is > >> available for public reference, I would like to formally open the > >> minimum 30-day comment period on two related new terms proposed > >> during the workshop and defined in the referenced document. > >> > >> The formal proposal would add the following new terms: > >> > >> Term Name: abundance > >> Identifier: http://rs.tdwg.org/dwc/terms/abundance > >> Namespace: http:/rs.tdwg.org/dwc/terms/ > >> Label: Abundance > >> Definition: The number of individuals of a taxon found in a sample. > >> This is typically expressed as number per unit of area or volume. In > >> the case of vegetation and colonial/encrusting species, percent cover > >> can be used. > >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", > >> "24%". For discussion see > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > >> further documentation here until the term is ratified) Type of Term: > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > >> Refines: > >> Status: proposed > >> Date Issued: 2012-03-01 > >> Date Modified: 2013-09-25 > >> Has Domain: > >> Has Range: > >> Refines: > >> Version: abundance-2013-09-25 > >> Replaces: > >> IsReplaceBy: > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > >> > >> Term Name: abundanceAsPercent > >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent > >> Namespace: http:/rs.tdwg.org/dwc/terms/ > >> Label: Abundance as Percent > >> Definition: 100 times the number of individuals of a taxon found in a > >> sample divided by the total number of individuals of all taxa in the > >> sample. > >> Comment: Examples: "2.4%". For discussion see > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > >> further documentation here until the term is ratified) Type of Term: > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > >> Refines: > >> Status: proposed > >> Date Issued: 2012-08-01 > >> Date Modified: 2013-09-25 > >> Has Domain: > >> Has Range: > >> Refines: > >> Version: abundanceAsPercent-2013-09-25 > >> Replaces: > >> IsReplaceBy: > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > >> > >> The related issues in the Darwin Core issue tracker are > >> https://code.google.com/p/darwincore/issues/detail?id=142 > >> and > >> https://code.google.com/p/darwincore/issues/detail?id=187 > >> > >> If there are any objections to the changes proposed for these new > >> terms, or comments about their definitions, please respond to this > >> message. If there are no objections or if consensus can be reached on > >> any amendments put forward, the proposal will go before the Executive > >> Committee for authorization to put these additions into effect after > >> the public commentary period. > >> > >> Cheers, > >> > >> John > >> _______________________________________________ > >> tdwg-content mailing list > >> tdwg-content(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > -- > > Aaike De Wever > > BioFresh Science Officer > > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > > Vautierstraat 29, 1000 Brussels Belgium > > tel.: +32(0)2 627 43 90 > > mobile.: +32(0)486 28 05 93 > > email: <aaike.dewever(a)naturalsciences.be> > > skype: aaikew > > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > > <http://data.freshwaterbiodiversity.eu/> > > Belgian Biodiversity Platform: <http://www.biodiversity.be> > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Semantics for Biodiversity Symposium -- Call for Abstracts
by Robert Guralnick 21 Aug '13

21 Aug '13

*Semantics for Biodiversity Symposium -- Call for Abstracts *http://semantics4biodiversity.nceas.ucsb.edu at TDWG Conference 2013 October 28 - November 1, 2013 - Florence, Italy. *Symposium Description and Scope * This Symposium includes a series of three, 90 minute sessions at TDWG that together constitute a "Semantics for Biodiversity" track, focused on -- Ontologies and formal models Technologies, Reasoning and Annotation methods Interoperability with genomic and ecological semantics These sessions are not parallel tracked and they are placed on separate days to avoid saturation on the topic. Additionally, there will be an initial "primer/tutorial" session of 60 minutes, to provide basic background for TDWG participants about semantic technologies, and how these can help inform biodiversity research. The conveners of this Symposium will be soliciting participation from diverse communities, including those from the biodiversity informatics and standards-development community per se, but also researchers interested in knowledge modeling and semantic application development in the biodiversity sciences, including relevant linkages to investigations in the ecological, genomic and phylogenetic sciences. *These thematic areas recommend a stronger-than-usual outreach to the computer science community, as researchers in that community will be particularly attracted by the prospects of reporting their work in a planned (and approved) special issue of the Semantic Web Journal on "Semantics for Biodiversity"*. Multiple groups of informaticians and technologists are currently developing semantic technologies to enhance discovery, interpretation, and interoperability of biodiversity data, so the upcoming meeting will provide a signal opportunity to present and discuss these activities in a coordinated fashion before perhaps the most relevant community who can inform, critique, and contribute to these efforts. Further, it's anticipated that these sessions will significantly raise awareness among computer scientists and engineers relative to the informatics challenges confronting the biodiversity community, particularly among those developing generalized knowledge representation and reasoning technologies, and machine-learning approaches. *Important Dates * Submission due: September 4, 2013 Acceptance Notification: September 11, 2013 Symposium dates: October 29 - November 1, 2013 *Symposium Format and Submissions* We invite abstract submissions (500 words maximum) for the three sessions, which will be dedicated to short presentations on the topics described in abstracts. We anticipate presentations will be for 20 minutes, with the possibility that these times will change depending on the number of quality submissions. Please visit http://semantics4biodiversity.nceas.ucsb.edu for additional information on each of the sessions. Questions for the organizers can be directed to semantics4biodiversity(a)nceas.ucsb.edu Submission site: https://www.easychair.org/conferences/?conf=s4bdtdwg2013 _______________________________________________ Semantics4biodiversity mailing list Semantics4biodiversity(a)nceas.ucsb.edu http://lists.nceas.ucsb.edu/mailman/listinfo/semantics4biodiversity

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